No OneTemporary
Actions

Subscribers

None

File Metadata

Created: Mon, Nov 25, 07:03

View Options

	diff --git a/DeconvolutionLab2/DeconvolutionLab2.config b/DeconvolutionLab2/DeconvolutionLab2.config
	index 48b59a1..728fdc7 100644
	--- a/DeconvolutionLab2/DeconvolutionLab2.config
	+++ b/DeconvolutionLab2/DeconvolutionLab2.config
	@@ -1,82 +1,82 @@
	#DeconvolutionLab2 [Beta 1]
	#DeconvolutionLab2 [Beta 1]
	-#Fri Feb 03 08:33:07 CET 2017
	+#Fri Feb 03 09:17:03 CET 2017
	Algorithm.FISTA.iterations=10
	Algorithm.FISTA.reg=0.1
	Algorithm.FISTA.scale=3
	Algorithm.FISTA.step=1.0
	Algorithm.FISTA.wavelets=Haar
	Algorithm.ICTM.iterations=10
	Algorithm.ICTM.reg=0.1
	Algorithm.ICTM.step=1.0
	Algorithm.ISTA.iterations=10
	Algorithm.ISTA.reg=0.1
	Algorithm.ISTA.scale=3
	Algorithm.ISTA.step=1.0
	Algorithm.ISTA.wavelets=Haar
	Algorithm.LW+.iterations=10
	Algorithm.LW+.step=1.0
	Algorithm.LW.iterations=10
	Algorithm.LW.step=1.0
	Algorithm.RIF.reg=0.1
	Algorithm.RL.iterations=10
	Algorithm.RLTV.reg=0.1
	Algorithm.SIM.gaussian.mean=0.0
	Algorithm.SIM.gaussian.stdev=1.0
	Algorithm.SIM.poisson=0.0
	Algorithm.TM.iterations=10
	Algorithm.TM.reg=0.1
	Algorithm.TM.step=1.0
	Algorithm.TRIF.reg=0.1
	Algorithm.VC.iterations=10
	Algorithm.VC.step=1.0
	Algorithm.algorithm=Landweber
	Border.apoxy=Uniform
	Border.apoz=Uniform
	Border.extxy=0
	Border.extz=0
	Border.normalization=1
	Border.padxy=None
	Border.padz=None
	Controller.constraint.enable=false
	Controller.constraint.snapshot=1
	Controller.constraint.value=No
	Controller.reference.enable=false
	Controller.reference.snapshot=1
	Controller.reference.value=
	Controller.residu.enable=false
	Controller.residu.snapshot=1
	Controller.residu.value=0.01
	Controller.savestats.enable=false
	Controller.savestats.snapshot=1
	Controller.savestats.value=Stats
	Controller.showstats.enable=false
	Controller.showstats.snapshot=1
	Controller.showstats.value=Stats
	DeconvolutionLab.MainDialog.location.h=579
	DeconvolutionLab.MainDialog.location.w=573
	DeconvolutionLab.MainDialog.location.x=124
	DeconvolutionLab.MainDialog.location.y=52
	Fourier.dim=XYZ
	Fourier.epsilon=1E-6
	Fourier.fft=Academic
	Image.image.row0=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;null
	Image.image.row1=resolution;directory;/Users/dsage/Desktop/DeconvolutionLab2-Course/resolution;null
	Image.image.selected=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;null
	Language.headless=Run (Headless)
	Language.job=Job
	Language.language=ImageJ Macro
	Output.output.row0=mip @1;MI1;;;;\u2713;null;null
	Output.output.selected=mip @1;MI1;;;;\u2713;null;null
	-PSF.psf.row0=MotionBlur;synthetic;MotionBlur 100.0 0.0 3.0 30.0 3.0 size 128 128 32 ;
	+PSF.psf.row0=MotionBlur2D;synthetic;MotionBlur2D 100.0 0.0 3.0 3.0 3.0 size 128 128 32 ;
	PSF.psf.row1=Airy;synthetic;Airy 100.0 0.0 1.0 size 128 128 32 ;null
	PSF.psf.row2=Defocus;synthetic;Defocus 100.0 0.0 3.0 10.0 10.0 size 3 3 100 ;null
	-PSF.psf.selected=MotionBlur;synthetic;MotionBlur 100.0 0.0 3.0 30.0 3.0 size 128 128 32 ;
	+PSF.psf.selected=MotionBlur2D;synthetic;MotionBlur2D 100.0 0.0 3.0 3.0 3.0 size 128 128 32 ;
	Watcher.disable.console=false
	Watcher.disable.display=false
	Watcher.disable.multithreading=false
	Watcher.disable.table=false
	Watcher.path=/Users/dsage/git/deconvolution/DeconvolutionLab2
	Watcher.time.value=3600
	Watcher.time=No time limitation
	Watcher.verbose=Verbose\: log
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2_FFT.java b/DeconvolutionLab2/src/DeconvolutionLab2_FFT.java
	index ccf0775..1a86876 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2_FFT.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_FFT.java
	@@ -1,17 +1,13 @@
	-import java.io.File;
	-
	-import deconvolutionlab.Config;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	import deconvolutionlab.monitor.Monitors;
	-import ij.IJ;
	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_Lab.java b/DeconvolutionLab2/src/DeconvolutionLab2_Lab.java
	new file mode 100644
	index 0000000..e7ba40f
	--- /dev/null
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_Lab.java
	@@ -0,0 +1,19 @@
	+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/deconvolution/Deconvolution.java b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	index bf4cf98..7ebf639 100644
	--- a/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	+++ b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	@@ -1,667 +1,662 @@
	/*
	* 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.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();
	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);
	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);
	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);

	- String m = "";
	- if (monitors != null) {
	- for (AbstractMonitor monitor : monitors)
	- m += monitor.getName() + " ";
	- }
	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/deconvolutionlab/LabImager.java b/DeconvolutionLab2/src/deconvolutionlab/LabImager.java
	index 2667f60..4d6702a 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/LabImager.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/LabImager.java
	@@ -1,214 +1,218 @@
	/*
	* 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 ij.ImagePlus;
	import ij.ImageStack;
	import ij.WindowManager;
	import ij.io.FileSaver;
	import ij.io.Opener;
	import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;
	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class LabImager extends PlatformImager {

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

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

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

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

	@Override
	public void show(RealSignal signal, String title) {
	show(signal, title, PlatformImager.Type.FLOAT);
	}

	@Override
	public void show(RealSignal signal, String title, PlatformImager.Type type) {
	show(signal, title, type, signal.nz / 2);
	}

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

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

	@Override
	public void append(ContainerImage container, RealSignal signal, String title) {
	append(container, signal, title, PlatformImager.Type.FLOAT);
	}

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

	@Override
	public void save(RealSignal signal, String filename) {
	save(signal, filename, PlatformImager.Type.FLOAT);
	}

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

	@Override
	public void show(ComplexSignal signal, String title) {
	show(signal, title, ComplexComponent.MODULE);
	}

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

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

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

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

	@Override
	public String getName() {
	return "ImageJ";
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java
	index cc97a88..c8d4d57 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java
	@@ -1,199 +1,199 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

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

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

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

	public class FFTModule extends AbstractModule implements ActionListener, ChangeListener {

	private HTMLPane info;

	private JComboBox<String> cmbFFT;
	private JComboBox<String> cmbType;
	private JComboBox<String> cmbSep;
	private JComboBox<String> cmbEpsilon;

	private CustomizedTable table;

	public FFTModule(boolean expanded) {
	super("Fourier", "", "", "Default", expanded);
	}

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

	@Override
	public JPanel buildExpandedPanel() {

	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Name", String.class, 120, false));
	columns.add(new CustomizedColumn("Installed", String.class, 120, false));
	+ columns.add(new CustomizedColumn("Multithreadable", String.class, 120, false));
	columns.add(new CustomizedColumn("Location", String.class, Constants.widthGUI, false));
	table = new CustomizedTable(columns, true);
	table.setRowSelectionAllowed(false);

	info = new HTMLPane(100, 100);
	cmbFFT = new JComboBox<String>(FFT.getLibrariesAsArray());
	cmbType = new JComboBox<String>(new String[] { "float" });
	cmbSep = new JComboBox<String>(new String[] { "XYZ" });
	cmbEpsilon = new JComboBox<String>(new String[] { "1E-0", "1E-1", "1E-2", "1E-3", "1E-4", "1E-5", "1E-6", "1E-7", "1E-8", "1E-9", "1E-10", "1E-11", "1E-12" });
	cmbEpsilon.setSelectedItem("1E-6");

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

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

	JPanel control = new JPanel(new BorderLayout());
	Border b1 = BorderFactory.createEtchedBorder();
	Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);

	control.setBorder(BorderFactory.createCompoundBorder(b1, b2));
	control.add(scroll2, BorderLayout.NORTH);
	control.add(info.getPane(), BorderLayout.CENTER);
	control.add(table.getPane(80, 80), BorderLayout.SOUTH);

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

	Config.register(getName(), "epsilon", cmbEpsilon, "1E-6");
	Config.register(getName(), "fft", cmbFFT, Algorithm.getDefaultAlgorithm());
	Config.register(getName(), "dim", cmbSep, "XYZ");

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

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

	private void fillInstallation() {

	ArrayList<AbstractFFTLibrary> libs = FFT.getRegisteredLibraries();
	for (AbstractFFTLibrary lib : libs) {
	String name = lib.getLibraryName();
	String installed = lib.isInstalled() ? " Yes" : "No";
	+ String multit = lib.isMultithreadable() ? " Yes" : "No";
	String location = lib.getLocation();
	- table.append(new String[] { name, installed, location });
	+ table.append(new String[] { name, installed, multit, location });
	}
	AbstractFFTLibrary fftlib = FFT.getLibraryByName((String) cmbFFT.getSelectedItem());
	info.clear();
	info.append("p", fftlib.getLicence());
	}

	private void update() {
	setCommand(getCommand());
	Signal.epsilon = NumFormat.parseNumber((String) cmbEpsilon.getSelectedItem(), 1e-6);
	Command.command();
	}

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

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == cmbFFT \|\| e.getSource() == cmbSep) {
	AbstractFFTLibrary fftlib = FFT.getLibraryByName((String) cmbFFT.getSelectedItem());
	info.clear();
	info.append("p", fftlib.getLicence());
	}

	if (e.getSource() == getAction1Button()) {
	cmbFFT.removeActionListener(this);
	cmbType.removeActionListener(this);
	cmbEpsilon.removeActionListener(this);
	cmbFFT.setSelectedIndex(0);
	cmbType.setSelectedIndex(0);
	cmbEpsilon.setSelectedIndex(0);
	cmbFFT.addActionListener(this);
	cmbType.addActionListener(this);
	cmbEpsilon.addActionListener(this);
	}
	update();
	}

	@Override
	public void close() {
	getAction1Button().removeActionListener(this);
	getAction2Button().removeActionListener(this);
	cmbFFT.removeActionListener(this);
	cmbType.removeActionListener(this);
	cmbEpsilon.removeActionListener(this);
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
	index d65ba6c..705ea4c 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
	@@ -1,341 +1,352 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.GridLayout;
	import java.awt.datatransfer.DataFlavor;
	import java.awt.datatransfer.Transferable;
	import java.awt.datatransfer.UnsupportedFlavorException;
	import java.awt.dnd.DnDConstants;
	import java.awt.dnd.DropTarget;
	import java.awt.dnd.DropTargetDropEvent;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.MouseEvent;
	import java.awt.event.MouseListener;
	import java.io.File;
	import java.io.IOException;
	import java.util.ArrayList;
	import java.util.List;

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

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

	public class ImageModule extends AbstractModule implements ActionListener, MouseListener {

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

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

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

	@Override
	public JPanel buildExpandedPanel() {

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

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

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

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

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

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

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

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

	return panel;
	}

	public void update() {
	int row = table.getSelectedRow();
	if (row >= 0) {
	setCommand(getCommand());
	setSynopsis(table.getCell(row, 0));
	Command.command();
	}
	else {
	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) {
	Deconvolution deconvolution = new Deconvolution(Command.command());
	file(deconvolution.getPath());
	}
	else if (e.getSource() == bnDirectory) {
	Deconvolution deconvolution = new Deconvolution(Command.command());
	dir(deconvolution.getPath());
	}
	else if (e.getSource() == bnSynthetic)
	synthetic(false);
	else if (e.getSource() == bnPlatform)
	platform();
	- else if (e.getSource() == getAction1Button())
	- platform();
	+ else if (e.getSource() == 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", "" });
	+ else
	+ table.setRowSelectionInterval(row, row);
	+ }
	else if (e.getSource() == getAction2Button())
	display();
	update();
	}

	public void platform() {
	PlatformImageSelector selector = new ImageSelector(Lab.getPlatform()).getImageSelector();
	String name = selector.getSelectedImage();
	if (name != null)
	if (name != "")
	table.insert(new String[] { name, "platform", name, "" });
	}

	private void file(String path) {
	File file = Files.browseFile(path);
	if (file == null)
	return;
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	}

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

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

	private void edit() {
	int row = table.getSelectedRow();

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

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

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

	@Override
	public void mousePressed(MouseEvent e) {
	}

	@Override
	public void mouseReleased(MouseEvent e) {
	}

	@Override
	public void mouseEntered(MouseEvent e) {
	}

	@Override
	public void mouseExited(MouseEvent e) {
	}

	@Override
	public void close() {
	bnFile.removeActionListener(this);
	bnDirectory.removeActionListener(this);
	bnSynthetic.removeActionListener(this);
	bnPlatform.removeActionListener(this);
	}

	public class LocalDropTarget extends DropTarget {

	@Override
	public void drop(DropTargetDropEvent e) {
	e.acceptDrop(DnDConstants.ACTION_COPY);
	e.getTransferable().getTransferDataFlavors();
	Transferable transferable = e.getTransferable();
	DataFlavor[] flavors = transferable.getTransferDataFlavors();
	for (DataFlavor flavor : flavors) {
	if (flavor.isFlavorJavaFileListType()) {
	try {
	List<File> files = (List<File>) transferable.getTransferData(flavor);
	for (File file : files) {
	if (file.isDirectory()) {
	table.insert(new String[] { file.getName(), "directory", file.getAbsolutePath(), "" });
	table.setRowSelectionInterval(0, 0);
	update();
	}
	if (file.isFile()) {
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	update();
	}
	}
	}
	catch (UnsupportedFlavorException ex) {
	ex.printStackTrace();
	}
	catch (IOException ex) {
	ex.printStackTrace();
	}
	}
	}
	e.dropComplete(true);
	super.drop(e);
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
	index e79c845..2eeabc5 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
	@@ -1,343 +1,343 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.GridLayout;
	import java.awt.datatransfer.DataFlavor;
	import java.awt.datatransfer.Transferable;
	import java.awt.datatransfer.UnsupportedFlavorException;
	import java.awt.dnd.DnDConstants;
	import java.awt.dnd.DropTarget;
	import java.awt.dnd.DropTargetDropEvent;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.MouseEvent;
	import java.awt.event.MouseListener;
	import java.io.File;
	import java.io.IOException;
	import java.util.ArrayList;
	import java.util.List;

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

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

	public class PSFModule extends AbstractModule implements ActionListener, MouseListener {

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

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

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

	@Override
	public JPanel buildExpandedPanel() {

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

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

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

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

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

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

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

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

	return panel;
	}

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

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

	public void platform() {
	PlatformImageSelector selector = new ImageSelector(Lab.getPlatform()).getImageSelector();
	String name = selector.getSelectedImage();
	if (name != null)
	if (name != "")
	table.insert(new String[] {name, "platform", name, "" });
	}

	private void file(String path) {
	File file = Files.browseFile(path);
	if (file == null)
	return;
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	}

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

	private void synthetic(boolean edit) {
	ArrayList<SignalFactory> list = SignalFactory.getPSF();
	SyntheticDialog dlg = new SyntheticDialog(list);
	if (edit) {
	int row = table.getSelectedRow();
	if (row >= 0) {
	dlg.setParameters(table.getCell(row, 0), table.getCell(row, 1));
	}
	}
	dlg.setVisible(true);

	if (dlg.wasCancel())
	return;

	if (edit) {
	int row = table.getSelectedRow();
	if (row <= 0)
	table.removeRow(row);
	}
	table.insert(new String[] { dlg.getShapeName(), "synthetic", dlg.getCommand(), "" });
	}

	private void edit() {
	int row = table.getSelectedRow();

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

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

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

	@Override
	public void mousePressed(MouseEvent e) {
	}

	@Override
	public void mouseReleased(MouseEvent e) {
	}

	@Override
	public void mouseEntered(MouseEvent e) {
	}

	@Override
	public void mouseExited(MouseEvent e) {
	}

	@Override
	public void close() {
	bnFile.removeActionListener(this);
	bnDirectory.removeActionListener(this);
	bnSynthetic.removeActionListener(this);
	bnPlatform.removeActionListener(this);
	}

	public class LocalDropTarget extends DropTarget {

	@Override
	public void drop(DropTargetDropEvent e) {
	e.acceptDrop(DnDConstants.ACTION_COPY);
	e.getTransferable().getTransferDataFlavors();
	Transferable transferable = e.getTransferable();
	DataFlavor[] flavors = transferable.getTransferDataFlavors();
	for (DataFlavor flavor : flavors) {
	if (flavor.isFlavorJavaFileListType()) {
	try {
	List<File> files = (List<File>) transferable.getTransferData(flavor);
	for (File file : files) {
	if (file.isDirectory()) {
	table.insert(new String[] { file.getName(), "directory", file.getAbsolutePath(), "" });
	table.setRowSelectionInterval(0, 0);
	update();
	}
	if (file.isFile()) {
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	update();
	}
	}
	}
	catch (UnsupportedFlavorException ex) {
	ex.printStackTrace();
	}
	catch (IOException ex) {
	ex.printStackTrace();
	}
	}
	}
	e.dropComplete(true);
	super.drop(e);
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/imagej/IJImager.java b/DeconvolutionLab2/src/imagej/IJImager.java
	index f60c2eb..ac47161 100644
	--- a/DeconvolutionLab2/src/imagej/IJImager.java
	+++ b/DeconvolutionLab2/src/imagej/IJImager.java
	@@ -1,218 +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 imagej;

	import java.util.HashMap;

	import deconvolutionlab.PlatformImager;
	import deconvolutionlab.PlatformImager.ContainerImage;
	import ij.ImagePlus;
	import ij.ImageStack;
	import ij.WindowManager;
	import ij.io.FileSaver;
	import ij.io.Opener;
	import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;
	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class IJImager extends PlatformImager {

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

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

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

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

	@Override
	public void show(RealSignal signal, String title) {
	show(signal, title, PlatformImager.Type.FLOAT);
	}

	@Override
	public void show(RealSignal signal, String title, PlatformImager.Type type) {
	show(signal, title, type, signal.nz / 2);
	}

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

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

	@Override
	public void append(ContainerImage container, RealSignal signal, String title) {
	append(container, signal, title, PlatformImager.Type.FLOAT);
	}

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

	@Override
	public void save(RealSignal signal, String filename) {
	save(signal, filename, PlatformImager.Type.FLOAT);
	}

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

	@Override
	public void show(ComplexSignal signal, String title) {
	show(signal, title, ComplexComponent.MODULE);
	}

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

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

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

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

	@Override
	public String getName() {
	return "ImageJ";
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/MotionBlur.java b/DeconvolutionLab2/src/signal/factory/MotionBlur.java
	index 59a0bbf..0bb21bc 100644
	--- a/DeconvolutionLab2/src/signal/factory/MotionBlur.java
	+++ b/DeconvolutionLab2/src/signal/factory/MotionBlur.java
	@@ -1,89 +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 signal.RealSignal;
	+import signal.Signal;

	public class MotionBlur extends SignalFactory {

	- private double sigma = 3.0;
	- private double direction = 30.0;
	- private double elongation = 3.0;
	+ private double sigma = 3.0;
	+ private double direction = 30.0;
	+ private double elongation = 3.0;

	public MotionBlur(double sigma, double direction, double elongation) {
	- super(new double[] {sigma, direction, elongation});
	+ super(new double[] { sigma, direction, elongation });
	}

	@Override
	public String getName() {
	return "MotionBlur";
	}
	-
	+
	@Override
	public String[] getParametersName() {
	- return new String[] {"Sigma", "Direction", "Elongation"};
	- }
	+ return new String[] { "Sigma", "Direction", "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};
	+ return new double[] { sigma, direction, elongation };
	}

	@Override
	public void fill(RealSignal signal) {
	- double K1 = 0.5 / (sigma*sigma);
	- double K2 = 0.5 / (sigmasigmaelongation*elongation);
	+ 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 ps = (1.0 + (dxcosa + dysina)/(dxdx + dydy)) * 0.5;
	- double K = K1 + dx * K2 /(dxdx + dydy);
	- double r2 = (x-xc)(x-xc) + (y-yc)(y-yc);
	- for(int z=0; z<nz; z++) {
	- signal.data[z][x+nxy] = (float)((amplitude-background) Math.exp(-r2*K) + background);
	+ 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, Signal.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);
	+ }
	}
	- }
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/SignalFactory.java b/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	index b9aee46..32776a0 100644
	--- a/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	+++ b/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	@@ -1,213 +1,213 @@
	/*
	* 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 deconvolutionlab.monitor.Monitors;
	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 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 Airy(1));
	list.add(new Astigmatism(3, 0.2));
	list.add(new Constant());
	list.add(new Cross(1, 1, 30));
	list.add(new Cube(10 ,1));
	list.add(new Defocus(3, 10, 10));
	list.add(new DoG(3, 4));
	list.add(new DoubleHelix(3, 10, 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 MotionBlur(3, 30, 3));
	list.add(new Ramp(1, 0, 0));
	list.add(new RandomLines(3));
	list.add(new Sinc(3, 3, 3));
	list.add(new Sphere(10, 1));
	list.add(new Torus(10));
	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 Airy(1));
	list.add(new Astigmatism(3, 0.2));
	list.add(new Cross(3, 1, 10));
	list.add(new Cube(10, 1));
	list.add(new Defocus(3, 10, 10));
	list.add(new DoG(3, 4));
	list.add(new DoubleHelix(3, 10, 10));
	list.add(new Gaussian(3, 3, 3));
	- list.add(new MotionBlur(3, 30, 3));
	+ //list.add(new MotionBlur(3, 30, 3));
	list.add(new Impulse());
	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;
	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(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() {
	System.out.println("Done");
	done = true;
	}

	}
	}

No OneTemporaryActions

File Metadata

View Options

Event Timeline

No OneTemporary
Actions