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diff --git a/DeconvolutionLab2/src/imagej/IJImager.java b/DeconvolutionLab2/src/imagej/IJImager.java
index 335fc91..8c3bc13 100644
--- a/DeconvolutionLab2/src/imagej/IJImager.java
+++ b/DeconvolutionLab2/src/imagej/IJImager.java
@@ -1,353 +1,353 @@
/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package imagej;
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowEvent;
import java.awt.event.WindowListener;
import javax.swing.BorderFactory;
import javax.swing.DefaultListModel;
import javax.swing.JButton;
import javax.swing.JDialog;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.ListSelectionModel;
import deconvolutionlab.Imager;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.gui.GUI;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import signal.ComplexComponent;
import signal.ComplexSignal;
import signal.RealSignal;
public class IJImager extends Imager {
@Override
public Platform getPlatform() {
return Imager.Platform.IMAGEJ;
}
@Override
public void setVisible(JDialog dialog, boolean modal) {
if (modal) {
dialog.setModal(modal);
GUI.center(dialog);
}
dialog.pack();
dialog.setVisible(true);
}
public static RealSignal create(ImagePlus imp) {
int nx = imp.getWidth();
int ny = imp.getHeight();
int nz = imp.getStackSize();
RealSignal signal = new RealSignal(imp.getTitle(), nx, ny, nz);
for (int k = 0; k < nz; k++) {
ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
signal.setXY(k, (float[]) ip.getPixels());
}
return signal;
}
@Override
public RealSignal getActiveImage() {
return build(WindowManager.getCurrentImage());
}
@Override
public RealSignal getImageByName(String name) {
ImagePlus imp = null;
if (name.equalsIgnoreCase("active"))
imp = WindowManager.getCurrentImage();
else
imp = WindowManager.getImage(name);
if (imp == null)
- imp = WindowManager.getCurrentImage();
+ return null;
return build(imp);
}
@Override
public RealSignal open(String filename) {
Opener opener = new Opener();
ImagePlus imp = opener.openImage(filename);
if (imp == null)
return null;
return build(imp);
}
@Override
public void show(RealSignal signal, String title, Imager.Type type, int z) {
ImagePlus imp = build(signal, type);
if (imp != null) {
imp.setTitle(title);
int nz = imp.getStackSize();
imp.show();
imp.setSlice(Math.max(1, Math.min(nz, z)));
imp.getProcessor().resetMinAndMax();
}
}
@Override
public ContainerImage createContainer(String title) {
return new ContainerImage();
}
@Override
public void append(ContainerImage container, RealSignal signal, String title, Imager.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, Imager.Type type) {
ImagePlus imp = build(signal, type);
if (imp != null) {
if (imp.getStackSize() == 1) {
new FileSaver(imp).saveAsTiff(filename);
}
else {
new FileSaver(imp).saveAsTiffStack(filename);
}
}
}
@Override
public void show(ComplexSignal signal, String title, ComplexComponent complex) {
ImageStack stack = new ImageStack(signal.nx, signal.ny);
for (int k = 0; k < signal.nz; k++) {
float[] plane = null;
switch (complex) {
case REAL:
plane = signal.getRealXY(k);
break;
case IMAGINARY:
plane = signal.getImagXY(k);
break;
case MODULE:
plane = signal.getModuleXY(k);
break;
default:
plane = signal.getModuleXY_dB(k);
}
stack.addSlice(new FloatProcessor(signal.nx, signal.ny, plane));
}
new ImagePlus(title, stack).show();
}
private RealSignal build(ImagePlus imp) {
if (imp == null)
return null;
int nx = imp.getWidth();
int ny = imp.getHeight();
int nz = imp.getStackSize();
RealSignal signal = new RealSignal("ij-" + imp.getTitle(), nx, ny, nz);
for (int k = 0; k < nz; k++) {
ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
signal.setXY(k, (float[]) ip.getPixels());
}
return signal;
}
private ImagePlus build(RealSignal signal, Imager.Type type) {
if (signal == null)
return null;
ImageStack stack = new ImageStack(signal.nx, signal.ny);
for (int k = 0; k < signal.nz; k++) {
ImageProcessor ip = new FloatProcessor(signal.nx, signal.ny, signal.getXY(k));
switch (type) {
case BYTE:
stack.addSlice(ip.convertToByteProcessor(false));
break;
case SHORT:
stack.addSlice(ip.convertToShortProcessor(false));
break;
case FLOAT:
stack.addSlice(ip);
default:
break;
}
}
return new ImagePlus("", stack);
}
@Override
public String getName() {
return "ImageJ";
}
@Override
public boolean isSelectable() {
return true;
}
@Override
public String getSelectedImage() {
Dialog dialog = new Dialog();
dialog.setVisible(true);
if (dialog.wasCancel())
return "";
return dialog.getName();
}
public class Dialog extends JDialog implements ActionListener, WindowListener {
private JList<String> list;
private JButton bnOK = new JButton("OK");
private JButton bnCancel = new JButton("Cancel");
private boolean cancel = false;
private String name = "";
public Dialog() {
super(new JFrame(), "Image Selection");
JPanel bn = new JPanel(new GridLayout(1, 2));
bn.add(bnCancel);
bn.add(bnOK);
JPanel panel = new JPanel(new BorderLayout());
int[] ids = WindowManager.getIDList();
if (ids != null) {
DefaultListModel listModel = new DefaultListModel();
list = new JList(listModel);
for (int id : ids) {
ImagePlus idp = WindowManager.getImage(id);
if (idp != null) {
((DefaultListModel) listModel).addElement(idp.getTitle());
}
}
list.setSelectionMode(ListSelectionModel.SINGLE_INTERVAL_SELECTION);
JScrollPane listScroller = new JScrollPane(list);
listScroller.setPreferredSize(new Dimension(250, 80));
panel.add(listScroller, BorderLayout.CENTER);
}
else {
panel.add(new JLabel("No open images."));
}
panel.add(bn, BorderLayout.SOUTH);
panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
bnOK.addActionListener(this);
bnCancel.addActionListener(this);
add(panel);
pack();
addWindowListener(this);
GUI.center(this);
setModal(true);
}
@Override
public void actionPerformed(ActionEvent e) {
bnOK.removeActionListener(this);
bnCancel.removeActionListener(this);
if (e.getSource() == bnCancel) {
cancel = true;
name = "";
dispose();
return;
}
else if (e.getSource() == bnOK) {
cancel = false;
name = (String) list.getSelectedValue();
dispose();
}
}
@Override
public String getName() {
return name;
}
public boolean wasCancel() {
return cancel;
}
@Override
public void windowOpened(WindowEvent e) {
}
@Override
public void windowClosing(WindowEvent e) {
dispose();
cancel = true;
name = "";
return;
}
@Override
public void windowClosed(WindowEvent e) {
}
@Override
public void windowIconified(WindowEvent e) {
}
@Override
public void windowDeiconified(WindowEvent e) {
}
@Override
public void windowActivated(WindowEvent e) {
}
@Override
public void windowDeactivated(WindowEvent e) {
}
}
}

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