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Created: Sat, May 4, 08:48

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	diff --git a/DeconvolutionLab2/build.xml b/DeconvolutionLab2/build.xml
	index f2d1dd2..e0d0384 100644
	--- a/DeconvolutionLab2/build.xml
	+++ b/DeconvolutionLab2/build.xml
	@@ -1,26 +1,28 @@
	<?xml version="1.0" encoding="UTF-8"?>
	<project name="DeconvolutionLab2" default="build" basedir=".">

	<property name="imagej" location="../../ImageJ/plugins"/>
	<property name="fiji" location="../../Fiji-deconv.app/plugins"/>
	+ <property name="matlab" location="/Applications/MATLAB_R2014b.app/java/"/>

	<target name="build">
	<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>

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

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

	</target>
	</project>
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/DL2.java b/DeconvolutionLab2/src/DL2.java
	new file mode 100644
	index 0000000..8e0ee74
	--- /dev/null
	+++ b/DeconvolutionLab2/src/DL2.java
	@@ -0,0 +1,84 @@
	+import ij.ImagePlus;
	+import ij.WindowManager;
	+
	+import java.io.File;
	+
	+import matlab.Converter;
	+import deconvolution.Deconvolution;
	+import deconvolutionlab.Config;
	+import deconvolutionlab.Lab;
	+import deconvolutionlab.dialog.LabDialog;
	+
	+/*
	+ * 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/>.
	+ */
	+
	+/**
	+ * This class is dedicated to the Matlab interface for DeconvolutionLab2
	+ * @author sage
	+ *
	+ */
	+public class DL2 {
	+
	+ public static void lab() {
	+ String config = System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config";
	+ Config.getInstance(config);
	+ LabDialog dialog = new LabDialog();
	+ dialog.setVisible(true);
	+ }
	+
	+ public static void run(String command) {
	+ return;
	+ }
	+
	+ public static void launch(String command) {
	+ return;
	+ }
	+
	+ public static Object get(String image) {
	+ ImagePlus imp = WindowManager.getCurrentImage();
	+ if (imp != null)
	+ return Converter.get(imp);
	+ return null;
	+ }
	+
	+ public static void run(Object image, Object psf, String algo) {
	+ Converter.createImage("input", image, true);
	+ Converter.createImage("psf", psf, true);
	+ String cmd = " -image platform input -psf platform psf -algorithm " + algo;
	+ Deconvolution d = new Deconvolution(cmd);
	+ d.deconvolve(false);
	+ }
	+
	+ public static void help() {
	+ Lab.help();
	+ }
	+
	+}
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2.java b/DeconvolutionLab2/src/DeconvolutionLab2.java
	index 2efede5..e51c8f2 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2.java
	@@ -1,93 +1,127 @@
	+/*
	+ * 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 matlab.Converter;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	import deconvolutionlab.dialog.LabDialog;
	import deconvolutionlab.monitor.Monitors;

	public class DeconvolutionLab2 {

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

	public static void main(String arg[]) {

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

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

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

	if (flag.equalsIgnoreCase("lab")) {
	lab(arg);
	}

	if (flag.equalsIgnoreCase("fft")) {
	Lab.checkFFT(Monitors.createDefaultMonitor());
	}

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

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

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

	- private static void help() {
	+ 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.print("Keywords of {command}: ");
	for (String keyword : Command.keywords)
	System.out.print(keyword + " ");

	}

	public DeconvolutionLab2(String cmd) {
	System.out.println("cmd: " + cmd);
	deconvolutionlab.Lab.getInstance(Platform.STANDALONE);
	String config = System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config";
	Config.getInstance(config);
	new Deconvolution(cmd).deconvolve(false);
	}
	+
	+
	}
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2_FFT.java b/DeconvolutionLab2/src/DeconvolutionLab2_FFT.java
	index 1a86876..943f976 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2_FFT.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_FFT.java
	@@ -1,13 +1,44 @@
	+/*
	+ * 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.Lab;
	import deconvolutionlab.Platform;
	import deconvolutionlab.monitor.Monitors;
	import ij.plugin.PlugIn;

	public class DeconvolutionLab2_FFT implements PlugIn {

	@Override
	public void run(String arg) {
	Lab.getInstance(Platform.IMAGEJ);
	Lab.checkFFT(Monitors.createDefaultMonitor());
	}
	}
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2_Help.java b/DeconvolutionLab2/src/DeconvolutionLab2_Help.java
	index 33cfb52..1b08f49 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2_Help.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_Help.java
	@@ -1,12 +1,43 @@
	+/*
	+ * 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 ij.plugin.PlugIn;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;

	public class DeconvolutionLab2_Help implements PlugIn {

	@Override
	public void run(String arg) {
	Lab.getInstance(Platform.IMAGEJ);
	Lab.help();
	}
	}
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2_Lab.java b/DeconvolutionLab2/src/DeconvolutionLab2_Lab.java
	index e7ba40f..d99963b 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2_Lab.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_Lab.java
	@@ -1,19 +1,50 @@
	+/*
	+ * 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 deconvolutionlab.Config;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	import deconvolutionlab.dialog.LabDialog;
	import ij.IJ;
	import ij.plugin.PlugIn;

	public class DeconvolutionLab2_Lab implements PlugIn {

	@Override
	public void run(String arg) {
	Lab.getInstance(Platform.IMAGEJ);
	String config = IJ.getDirectory("plugins") + File.separator + "DeconvolutionLab2.config";
	Config.getInstance(config);
	new LabDialog().setVisible(true);
	}
	}
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2_Launch.java b/DeconvolutionLab2/src/DeconvolutionLab2_Launch.java
	index 33a8d1c..8a3d331 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2_Launch.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_Launch.java
	@@ -1,24 +1,55 @@
	+/*
	+ * 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.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	import deconvolutionlab.dialog.LabDialog;
	import ij.IJ;
	import ij.Macro;
	import ij.plugin.PlugIn;

	public class DeconvolutionLab2_Launch implements PlugIn {

	@Override
	public void run(String arg) {
	Lab.getInstance(Platform.IMAGEJ);
	String config = IJ.getDirectory("plugins") + File.separator + "DeconvolutionLab2.config";
	Config.getInstance(config);
	if (Macro.getOptions() == null)
	new LabDialog().setVisible(true);
	else
	new Deconvolution(Macro.getOptions()).launch("", false);
	}
	}
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2_Run.java b/DeconvolutionLab2/src/DeconvolutionLab2_Run.java
	index 0462b41..ce534b5 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2_Run.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_Run.java
	@@ -1,24 +1,55 @@
	+/*
	+ * 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.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	import deconvolutionlab.dialog.LabDialog;
	import ij.IJ;
	import ij.Macro;
	import ij.plugin.PlugIn;

	public class DeconvolutionLab2_Run implements PlugIn {

	@Override
	public void run(String arg) {
	Lab.getInstance(Platform.IMAGEJ);
	String config = IJ.getDirectory("plugins") + File.separator + "DeconvolutionLab2.config";
	Config.getInstance(config);
	if (Macro.getOptions() == null)
	new LabDialog().setVisible(true);
	else
	new Deconvolution(Macro.getOptions()).deconvolve(false);
	}
	}
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Celegans.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Celegans.java
	index 2f51a44..9343fed 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Celegans.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Celegans.java
	@@ -1,81 +1,91 @@
	package course;

	// Course Version 2

	import ij.ImagePlus;
	import ij.io.FileSaver;
	import ij.io.Opener;
	import ij.plugin.PlugIn;
	import ij.process.ColorProcessor;

	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

	import deconvolution.Deconvolution;

	public class DeconvolutionLab2_Course_Celegans implements PlugIn {

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

	public DeconvolutionLab2_Course_Celegans() {

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

	- run(" -algorithm I ", "IN_");
	- run(" -algorithm RIF 0.001 ", "RIF_");
	+ run(" -algorithm RIF 0.000001 ", "RIF6_");
	+ run(" -algorithm RIF 0.0000001 ", "RIF7_");
	+ //run(" -algorithm RL 100 ", "RL_");
	+ run(" -algorithm LW+ 200 1 ", "LW+_");
	+ //run(" -algorithm I ", "IN_");
	+ //run(" -algorithm RIF 0.001 ", "RIF3_");
	+ //run(" -algorithm RIF 0.0001 ", "RIF4_");
	+ //run(" -algorithm RIF 0.00001 ", "RIF5_");
	+ //run(" -algorithm VC 100 ", "VC");
	+ //run(" -algorithm RLTV 10 0.1 ", "RLTV");
	+ //run(" -algorithm FISTA 50 1 0.1 ", "FISTA");
	+ //run(" -algorithm ISTA 50 1 0.1 ", "ISTA");
	}

	private void run(String a, String name) {
	String channels[] = new String[] { "CY3", "FITC", "DAPI"};

	ImagePlus[] ort = new ImagePlus[3];
	ImagePlus[] fig = new ImagePlus[3];
	for (int i=0; i<3; i++) {
	String channel = channels[i];
	String psf = " -psf file " + data + "psf-CElegans-" + channel + ".tif";
	String img = " -image file " + data + "CElegans-" + channel +".tif";
	String param = " -fft JTransforms -disable display multithreading";
	String algo = a + out(name + channel);
	new Deconvolution(img + psf + algo + param).deconvolve(false);
	ort[i] = new Opener().openImage( res + name + channel + "_ortho_8.tif");
	fig[i] = new Opener().openImage( res + name + channel + "_figure_8.tif");
	}
	new FileSaver(color(ort)).saveAsTiff(res + name + "-ortho-rgb.tif");
	new FileSaver(color(fig)).saveAsTiff(res + name + "-figure-rgb.tif");
	}

	private static String out(String name) {
	return
	" -out ortho " + name + "_ortho_8 rescaled byte (160,180,50) noshow" +
	" -out mip " + name + "_mip_8 rescaled byte noshow" +
	" -out figure " + name + "_figure_8 rescaled byte (160,180,50) ";

	}

	private static ImagePlus color(ImagePlus imp[]) {
	int nx = imp[0].getWidth();
	int ny = imp[0].getHeight();
	ColorProcessor cp = new ColorProcessor(nx, ny);
	byte r[] = (byte[])imp[0].getProcessor().getPixels();
	byte g[] = (byte[])imp[1].getProcessor().getPixels();
	byte b[] = (byte[])imp[2].getProcessor().getPixels();
	cp.setRGB(r, g, b);
	ImagePlus out = new ImagePlus( "rgb", cp);
	out.show();
	return out;
	}
	public static void main(String arg[]) {
	new DeconvolutionLab2_Course_Celegans();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_Course_Celegans();
	}

	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/deconvolution/Deconvolution.java b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	index 16de499..ccbd1bf 100644
	--- a/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	+++ b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	@@ -1,663 +1,660 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution;

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

	import javax.swing.JFrame;

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

	public class Deconvolution implements Runnable {

	private AbstractAlgorithm algo = null;

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

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

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

	private ArrayList<String> report = new ArrayList<String>();

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

	private boolean watcherMonitor = true;
	private boolean watcherConsole = true;
	private boolean watcherDisplay = true;
	private boolean watcherMultithreading = true;

	private ArrayList<DeconvolutionListener> listeners = new ArrayList<DeconvolutionListener>();

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

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

	public String getCommand() {
	return command;
	}

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

	/**
	* This method runs the deconvolution without graphical user interface.
	*
	* @param exit
	* System.exit call is true
	*/
	public void deconvolve(boolean exit) {
	this.exit = exit;

	monitors = new Monitors();
	if (watcherConsole)
	monitors.add(new ConsoleMonitor());

	if (watcherMonitor) {
	TableMonitor m = new TableMonitor(440, 440);
	monitors.add(m);
	String t = algo == null ? "Monitor " + name : name + " " + algo.getName();
	JFrame frame = new JFrame(t);
	frame.add(m.getPanel());
	frame.pack();
	frame.setVisible(true);
	}

	if (fftlib == null) {
	run();
	return;
	}
	if (!fftlib.isMultithreadable()) {
	run();
	return;
	}

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

	}

	/**
	* This method runs the deconvolution with a graphical user interface.
	*
	* @param job
	* Name of the job of deconvolution
	* @param exit
	* System.exit call is true
	*/
	public void launch(String job, boolean exit) {
	this.name = job;
	this.exit = exit;
	DeconvolutionDialog d = new DeconvolutionDialog(this);
	monitors = new Monitors();
	monitors.add(new StatusMonitor(d.getProgressBar()));
	if (watcherConsole)
	monitors.add(new ConsoleMonitor());

	if (watcherMonitor) {
	TableMonitor m = new TableMonitor(440, 440);
	monitors.add(m);
	d.addTableMonitor("Monitor", m);
	}

	}

	public void decode() {

	algo = null;

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

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

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

	live = false;

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

	if (token.keyword.equalsIgnoreCase("-disable")) {
	watcherMonitor = Command.decodeDisable(token, "monitor");
	watcherConsole = Command.decodeDisable(token, "console");
	watcherDisplay = Command.decodeDisable(token, "display");
	watcherMultithreading = Command.decodeDisable(token, "multithreading");
	}

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

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

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

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

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

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

	}

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

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

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

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

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

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

	RealSignal psf = openPSF();
	if (psf == null) {
	monitors.error("PSF: not valid");
	report.add("PSF: Not valid");
	if (exit)
	System.exit(-102);
	return;
	}
	- report.add("PSF: " + psf.dimAsString());
	-
	- monitors.log("PSF: " + psf.nx + " x " + psf.ny + " x " + psf.nz);
	+ report.add( "PSF: " + psf.dimAsString());
	+ monitors.log("PSF: " + psf.dimAsString());
	+
	monitors.log("PSF: normalization " + (factorNormalization <= 0 ? "no" : factorNormalization));
	RealSignal h = psf.changeSizeAs(y).normalize(factorNormalization);

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

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

	AbstractFFT fft;
	if (fftlib != null)
	fft = FFT.createFFT(monitors, fftlib, image.nx, image.ny, image.nz);
	else
	fft = FFT.createDefaultFFT(monitors, image.nx, image.ny, image.nz);
	report.add("FFT: " + fft.getName());

	algo.setFFT(fft);
	controller.setFFT(fft);

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

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

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

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

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

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

	report.add("End " + algo.getName() + " in " + NumFormat.time(System.nanoTime()-chrono));

	if (watcherDisplay)
	Lab.show(monitors, result, "Result of " + algo.getShortname());

	if (exit) {
	System.out.println("End");
	System.exit(0);
	}
	-
	}

	/**
	* This methods make a recap of the deconvolution. Useful before starting the processing.
	*
	* @return list of messages to print
	*/
	public ArrayList<String> recap() {
	ArrayList<String> lines = new ArrayList<String>();
	Token image = Command.extract(command, "-image");
	if (image == null)
	lines.add("<b>Image</b>: <span color=\"red\">keyword -image not found</span>");
	else
	lines.add("<b>Image</b>: " + image.parameters);

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

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

	lines.add("<b>Verbose</b>: " + verbose.name().toLowerCase());
	lines.add("<b>Monitor</b>: " + (watcherMonitor ? "on" : "off"));
	lines.add("<b>Console</b>: " + (watcherConsole ? "on" : "off"));
	lines.add("<b>Final Display</b>: " + (watcherDisplay ? "on" : "off"));
	lines.add("<b>Multithreading</b>: " + (watcherMultithreading ? "on" : "off"));

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

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

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

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

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

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

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

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

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

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

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

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

	public ArrayList<String> getDeconvolutionReports() {
	return report;
	}

	public String getName() {
	return name;
	}

	public boolean isLive() {
	return live;
	}

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

	public Padding getPadding1() {
	return padding;
	}

	public Apodization getApodization() {
	return apodization;
	}

	public OutputCollection getOuts() {
	return outs;
	}

	public AbstractAlgorithm getAlgo() {
	return algo;
	}

	public String getPath() {
	return path;
	}

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

	public RealSignal openImage() {
	Token token = Command.extract(command, "-image");
	if (token == null)
	return null;
	if (token.parameters.startsWith(">>>"))
	return null;
	return getImage(monitors, token);
	}

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

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

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

	}

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

	return null;
	}

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

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

	}
	diff --git a/DeconvolutionLab2/src/matlab/Converter.java b/DeconvolutionLab2/src/matlab/Converter.java
	new file mode 100644
	index 0000000..86001e3
	--- /dev/null
	+++ b/DeconvolutionLab2/src/matlab/Converter.java
	@@ -0,0 +1,409 @@
	+package matlab;
	+
	+import ij.ImagePlus;
	+import ij.ImageStack;
	+import ij.process.ByteProcessor;
	+import ij.process.ColorProcessor;
	+import ij.process.FloatProcessor;
	+import ij.process.ShortProcessor;
	+
	+public class Converter {
	+
	+ public static boolean verbose;
	+
	+ /**
	+ * Get an image.
	+ *
	+ * @param imageplus image
	+ * @return an N x M array representing the input image
	+ */
	+ public static Object get(ImagePlus imageplus) {
	+ if (imageplus == null)
	+ return null;
	+ int width = imageplus.getWidth();
	+ int height = imageplus.getHeight();
	+ int stackSize = imageplus.getStackSize();
	+ int counter = 0;
	+ ImageStack imagestack = imageplus.getStack();
	+ switch (imageplus.getType()) {
	+
	+ case ImagePlus.COLOR_256: {
	+ ;
	+ }
	+ case ImagePlus.GRAY8: {
	+ short[][][] is = new short[height][width][stackSize];
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ ByteProcessor byteprocessor = (ByteProcessor) imagestack.getProcessor(sz + 1);
	+ byte[] pixels = (byte[]) byteprocessor.getPixels();
	+ counter = 0;
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ is[h][w][sz] = (short)(pixels[counter]&0xff);
	+ w++;
	+ counter++;
	+ }
	+ counter = ++h * width;
	+ }
	+ }
	+ return is;
	+ }
	+ case ImagePlus.GRAY16: {
	+ int[][][] is = new int[height][width][stackSize];
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ counter = 0;
	+ ShortProcessor shortprocessor = (ShortProcessor) imagestack.getProcessor(sz + 1);
	+ short[] spixels = (short[]) shortprocessor.getPixels();
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ is[h][w][sz] = (int)(spixels[counter]&0xffff);
	+ w++;
	+ counter++;
	+ }
	+ counter = ++h * width;
	+ }
	+ }
	+ return is;
	+ }
	+ case ImagePlus.GRAY32: {
	+ double[][][] fs = new double[height][width][stackSize];
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ FloatProcessor floatprocessor = (FloatProcessor) imagestack.getProcessor(sz + 1);
	+ float[] fpixels = (float[]) floatprocessor.getPixels();
	+ counter = 0;
	+ int i = 0;
	+ while (i < height) {
	+ int j = 0;
	+ while (j < width) {
	+ fs[i][j][sz] = (double) fpixels[counter];
	+ j++;
	+ counter++;
	+ }
	+ counter = ++i * width;
	+ }
	+ }
	+ return fs;
	+ }
	+ case ImagePlus.COLOR_RGB: {
	+ if (stackSize == 1) {
	+ short[][][] is = new short[height][width][3];
	+ ColorProcessor colorprocessor = (ColorProcessor) imagestack.getProcessor(1);
	+ byte[] red = new byte[width * height];
	+ byte[] green = new byte[width * height];
	+ byte[] blue = new byte[width * height];
	+ colorprocessor.getRGB(red, green, blue);
	+ counter = 0;
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ is[h][w][0] = (short)(red[counter]&0xff);
	+ is[h][w][1] = (short)(green[counter]&0xff);
	+ is[h][w][2] = (short)(blue[counter]&0xff);
	+ w++;
	+ counter++;
	+ }
	+ counter = ++h * width;
	+ }
	+ return is;
	+ }
	+ short[][][][] is = new short[height][width][stackSize][3];
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ ColorProcessor colorprocessor = (ColorProcessor) imagestack.getProcessor(sz + 1);
	+ byte[] red = new byte[width * height];
	+ byte[] green = new byte[width * height];
	+ byte[] blue = new byte[width * height];
	+ colorprocessor.getRGB(red, green, blue);
	+ counter = 0;
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ is[h][w][sz][0] = (short)red[counter];
	+ is[h][w][sz][1] = (short)green[counter];
	+ is[h][w][sz][2] = (short)blue[counter];
	+ w++;
	+ counter++;
	+ }
	+ counter = ++h * width;
	+ }
	+ }
	+ return is;
	+ }
	+ default:
	+ System.out.println("MIJ Error message: Unknow type of volumes.");
	+ return null;
	+ }
	+ }
	+ /**
	+ * Create a new image in ImageJ from a Matlab variable with a specified
	+ * title.
	+ *
	+ * This method try to create a image (ImagePlus of ImageJ) from a Matlab's
	+ * variable which should be an 2D or 3D array The recognize type are byte,
	+ * short, int, float and double. The dimensionality of the 2 (image) or 3
	+ * (stack of images)
	+ *
	+ * @param title
	+ * title of the new image
	+ * @param object
	+ * Matlab variable
	+ * @param showImage
	+ * Whether to display the newly created image or not
	+ * @return the resulting ImagePlus instance
	+ */
	+ public static ImagePlus createImage(String title, Object object, boolean showImage) {
	+ ImagePlus imp = null;
	+ int i = 0;
	+ if (object instanceof byte[][]) {
	+ byte[][] is = (byte[][]) object;
	+ int height = is.length;
	+ int width = is[0].length;
	+ ByteProcessor byteprocessor = new ByteProcessor(width, height);
	+ byte[] bp = (byte[]) byteprocessor.getPixels();
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ bp[i] = is[h][w];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ imp = new ImagePlus(title, byteprocessor);
	+
	+ }
	+ else if (object instanceof short[][]) {
	+ short[][] is = (short[][]) object;
	+ int height = is.length;
	+ int width = is[0].length;
	+ ShortProcessor shortprocessor = new ShortProcessor(width, height);
	+ short[] sp = (short[]) shortprocessor.getPixels();
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ sp[i] = is[h][w];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ imp = new ImagePlus(title, shortprocessor);
	+
	+ }
	+ else if (object instanceof int[][]) {
	+ if (verbose)
	+ System.out.println("MIJ warning message: Loss of precision: convert int 32-bit to short 16-bit");
	+ int[][] is = (int[][]) object;
	+ int height = is.length;
	+ int width = is[0].length;
	+ ShortProcessor shortprocessor = new ShortProcessor(width, height);
	+ short[] sp = (short[]) shortprocessor.getPixels();
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ sp[i] = (short) is[h][w];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ imp = new ImagePlus(title, shortprocessor);
	+ }
	+ else if (object instanceof float[][]) {
	+ float[][] fs = (float[][]) object;
	+ int height = fs.length;
	+ int width = fs[0].length;
	+ FloatProcessor floatprocessor = new FloatProcessor(width, height);
	+ float[] fp = (float[]) floatprocessor.getPixels();
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ fp[i] = fs[h][w];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ floatprocessor.resetMinAndMax();
	+ imp = new ImagePlus(title, floatprocessor);
	+
	+ }
	+ else if (object instanceof double[][]) {
	+ if (verbose)
	+ System.out.println("MIJ warning message: Loss of precision: convert double 32-bit to float 32-bit");
	+ double[][] ds = (double[][]) object;
	+ int height = ds.length;
	+ int width = ds[0].length;
	+ FloatProcessor floatprocessor = new FloatProcessor(width, height);
	+ float[] fp = (float[]) floatprocessor.getPixels();
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ fp[i] = (float) ds[h][w];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ floatprocessor.resetMinAndMax();
	+ imp = new ImagePlus(title, floatprocessor);
	+
	+ }
	+ else if (object instanceof byte[][][]) {
	+ byte[][][] is = (byte[][][]) object;
	+ int height = is.length;
	+ int width = is[0].length;
	+ int stackSize = is[0][0].length;
	+ ImageStack imagestack = new ImageStack(width, height);
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ ByteProcessor byteprocessor = new ByteProcessor(width, height);
	+ byte[] bp = (byte[]) byteprocessor.getPixels();
	+ i = 0;
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ bp[i] = is[h][w][sz];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ imagestack.addSlice("", byteprocessor);
	+ }
	+ imp = new ImagePlus(title, imagestack);
	+
	+ }
	+ else if (object instanceof short[][][]) {
	+ short[][][] is = (short[][][]) object;
	+ int height = is.length;
	+ int width = is[0].length;
	+ int stackSize = is[0][0].length;
	+ ImageStack imagestack = new ImageStack(width, height);
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ ShortProcessor shortprocessor = new ShortProcessor(width, height);
	+ short[] sp = (short[]) shortprocessor.getPixels();
	+ i = 0;
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ sp[i] = is[h][w][sz];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ imagestack.addSlice("", shortprocessor);
	+ }
	+ imp = new ImagePlus(title, imagestack);
	+
	+ }
	+ else if (object instanceof int[][][]) {
	+ if (verbose)
	+ System.out.println("MIJ warning message: Loss of precision: convert int 32 bits to short 16 bits");
	+ int[][][] is = (int[][][]) object;
	+ int height = is.length;
	+ int width = is[0].length;
	+ int stackSize = is[0][0].length;
	+ ImageStack imagestack = new ImageStack(width, height);
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ ShortProcessor shortprocessor = new ShortProcessor(width, height);
	+ short[] sp = (short[]) shortprocessor.getPixels();
	+ i = 0;
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ sp[i] = (short) is[h][w][sz];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ if (sz == 0)
	+ shortprocessor.resetMinAndMax();
	+ imagestack.addSlice("", shortprocessor);
	+
	+ }
	+ imp = new ImagePlus(title, imagestack);
	+
	+ }
	+ else if (object instanceof float[][][]) {
	+ float[][][] fs = (float[][][]) object;
	+ int height = fs.length;
	+ int width = fs[0].length;
	+ int stackSize = fs[0][0].length;
	+ ImageStack imagestack = new ImageStack(width, height);
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ FloatProcessor floatprocessor = new FloatProcessor(width, height);
	+ float[] fp = (float[]) floatprocessor.getPixels();
	+ i = 0;
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ fp[i] = fs[h][w][sz];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ if (sz == 0)
	+ floatprocessor.resetMinAndMax();
	+ imagestack.addSlice("", floatprocessor);
	+ }
	+ imp = new ImagePlus(title, imagestack);
	+
	+ }
	+ else if (object instanceof double[][][]) {
	+ if (verbose)
	+ System.out.println("MIJ warning message: Loss of precision: convert double 32-bit to float 32-bit");
	+ double[][][] ds = (double[][][]) object;
	+ int height = ds.length;
	+ int width = ds[0].length;
	+ int stackSize = ds[0][0].length;
	+ ImageStack imagestack = new ImageStack(width, height);
	+ for (int sz = 0; sz < stackSize; sz++) {
	+ FloatProcessor floatprocessor = new FloatProcessor(width, height);
	+ float[] fp = (float[]) floatprocessor.getPixels();
	+ i = 0;
	+ int h = 0;
	+ while (h < height) {
	+ int w = 0;
	+ while (w < width) {
	+ fp[i] = (float) ds[h][w][sz];
	+ w++;
	+ i++;
	+ }
	+ i = ++h * width;
	+ }
	+ if (sz == 0)
	+ floatprocessor.resetMinAndMax();
	+ imagestack.addSlice("", floatprocessor);
	+ }
	+ imp = new ImagePlus(title, imagestack);
	+
	+ }
	+ else {
	+ System.out.println("MIJ Error message: Unknow type of images or volumes.");
	+ return null;
	+ }
	+
	+ if (showImage) {
	+ imp.show();
	+ imp.updateAndDraw();
	+ }
	+ return imp;
	+ }
	+
	+}

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