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R2075/DeconvolutionLab2/src/deconvolutionlab/module/PreprocessingModule.java
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PreprocessingModule.java
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/*
* 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.module;
import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import signal.RealSignal;
import signal.apodization.AbstractApodization;
import signal.apodization.Apodization;
import signal.apodization.UniformApodization;
import signal.padding.AbstractPadding;
import signal.padding.NoPadding;
import signal.padding.Padding;
import bilib.component.GridPanel;
import bilib.component.SpinnerRangeInteger;
import bilib.tools.NumFormat;
import deconvolution.Command;
import deconvolution.Deconvolution;
import deconvolutionlab.Config;
import deconvolutionlab.monitor.Monitors;
public class PreprocessingModule extends AbstractModule implements ActionListener, ChangeListener {
private JComboBox<String> cmbPadXY;
private JComboBox<String> cmbPadZ;
private JComboBox<String> cmbApoXY;
private JComboBox<String> cmbApoZ;
private SpinnerRangeInteger spnExtensionXY;
private SpinnerRangeInteger spnExtensionZ;
private JLabel lblPad;
private JLabel lblApo;
private JComboBox<String> cmbNormalization;
private JButton bnTest;
public PreprocessingModule() {
super("Preprocessing", "", "Default", "");
}
@Override
public String getCommand() {
AbstractPadding pxy = Padding.getByName((String) cmbPadXY.getSelectedItem());
AbstractPadding paz = Padding.getByName((String) cmbPadZ.getSelectedItem());
AbstractApodization axy = Apodization.getByName((String) cmbApoXY.getSelectedItem());
AbstractApodization apz = Apodization.getByName((String) cmbApoZ.getSelectedItem());
boolean ext = spnExtensionXY.get() + spnExtensionZ.get() > 0;
String extXY = (ext ? "" + spnExtensionXY.get() : "") + " ";
String extZ = ext ? "" + spnExtensionZ.get() : "";
String cmd = "";
if (!(pxy instanceof NoPadding) || !(paz instanceof NoPadding) || spnExtensionXY.get() > 0 || spnExtensionZ.get() > 0)
cmd += " -pad " + pxy.getShortname() + " " + paz.getShortname() + " " + extXY + extZ;
if (!(axy instanceof UniformApodization) || !(apz instanceof UniformApodization))
cmd += " -apo " + axy.getShortname() + " " + apz.getShortname() + " ";
if (cmbNormalization.getSelectedIndex() != 0)
cmd += " -norm " + NumFormat.parseNumber((String)cmbNormalization.getSelectedItem(), 1);
return cmd;
}
@Override
public JPanel buildExpandedPanel() {
bnTest = new JButton("Test");
lblPad = new JLabel("Information on padding size");
lblPad.setBorder(BorderFactory.createEtchedBorder());
lblApo = new JLabel("Information on apodization energy");
lblApo.setBorder(BorderFactory.createEtchedBorder());
cmbPadXY = new JComboBox<String>(Padding.getPaddingsAsArray());
cmbPadZ = new JComboBox<String>(Padding.getPaddingsAsArray());
cmbApoXY = new JComboBox<String>(Apodization.getApodizationsAsArray());
cmbApoZ = new JComboBox<String>(Apodization.getApodizationsAsArray());
spnExtensionXY = new SpinnerRangeInteger(0, 0, 99999, 1);
spnExtensionZ = new SpinnerRangeInteger(0, 0, 99999, 1);
cmbNormalization = new JComboBox<String>(new String[] { "1", "10", "1000", "1E+6", "1E+9", "no" });
cmbNormalization.addActionListener(this);
cmbNormalization.setSelectedIndex(0);
cmbNormalization.removeActionListener(this);
GridPanel pnBorder = new GridPanel(false, 2);
pnBorder.place(0, 0, "<html><b>Image</b>");
pnBorder.place(0, 1, "Lateral (XY)");
pnBorder.place(0, 2, "Axial (Z)");
pnBorder.place(1, 0, "Apodization");
pnBorder.place(1, 1, cmbApoXY);
pnBorder.place(1, 2, cmbApoZ);
pnBorder.place(2, 0, "Padding Extension");
pnBorder.place(2, 1, spnExtensionXY);
pnBorder.place(2, 2, spnExtensionZ);
pnBorder.place(3, 0, "Padding Constraint");
pnBorder.place(3, 1, cmbPadXY);
pnBorder.place(3, 2, cmbPadZ);
pnBorder.place(4, 0, 3, 1, lblPad);
pnBorder.place(5, 0, 3, 1, lblApo);
pnBorder.place(6, 2, 3, 1, bnTest);
pnBorder.place(7, 0, " ");
pnBorder.place(8, 0, "<html><b>PSF</b>");
pnBorder.place(9, 0, "Normalization");
pnBorder.place(9, 1, cmbNormalization);
pnBorder.place(9, 2, "recommended: 1");
JScrollPane scroll = new JScrollPane(pnBorder);
scroll.setBorder(BorderFactory.createEmptyBorder());
scroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scroll.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
JPanel panel = new JPanel(new BorderLayout());
panel.setBorder(BorderFactory.createEtchedBorder());
panel.add(scroll, BorderLayout.CENTER);
Config.register(getName(), "padxy", cmbPadXY, Padding.getDefault().getName());
Config.register(getName(), "padz", cmbPadZ, Padding.getDefault().getName());
Config.register(getName(), "apoxy", cmbApoXY, Apodization.getDefault().getName());
Config.register(getName(), "apoz", cmbApoZ, Apodization.getDefault().getName());
Config.register(getName(), "extxy", spnExtensionXY, "0");
Config.register(getName(), "extz", spnExtensionZ, "0");
Config.register(getName(), "normalization", cmbNormalization, cmbNormalization.getItemAt(0));
cmbNormalization.addActionListener(this);
spnExtensionXY.addChangeListener(this);
spnExtensionZ.addChangeListener(this);
cmbPadXY.addActionListener(this);
cmbPadZ.addActionListener(this);
cmbApoXY.addActionListener(this);
cmbApoZ.addActionListener(this);
bnTest.addActionListener(this);
getAction1Button().addActionListener(this);
return panel;
}
private void update() {
setCommand(getCommand());
boolean ext = spnExtensionXY.get() + spnExtensionZ.get() > 0;
boolean pad = cmbPadXY.getSelectedIndex() + cmbPadZ.getSelectedIndex() > 0;
boolean apo = cmbApoXY.getSelectedIndex() + cmbApoZ.getSelectedIndex() > 0;
if (pad || apo || ext) {
setSynopsis("" + " " + (pad ? "Padding" : "") + " " + (ext ? "Extension" : "") + " " + (apo ? "Apodization" : ""));
}
else {
setSynopsis("Default options");
}
Command.command();
}
@Override
public void stateChanged(ChangeEvent e) {
update();
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
if (e.getSource() == getAction1Button()) {
cmbPadXY.removeActionListener(this);
cmbPadZ.removeActionListener(this);
cmbApoXY.removeActionListener(this);
cmbApoZ.removeActionListener(this);
cmbPadXY.setSelectedIndex(0);
cmbPadZ.setSelectedIndex(0);
cmbApoXY.setSelectedIndex(0);
cmbApoZ.setSelectedIndex(0);
spnExtensionXY.set(0);
spnExtensionZ.set(0);
cmbNormalization.setSelectedIndex(0);
cmbPadXY.addActionListener(this);
cmbPadZ.addActionListener(this);
cmbApoXY.addActionListener(this);
cmbApoZ.addActionListener(this);
update();
return;
}
if (e.getSource() == bnTest) {
Thread thread = new Thread(new Runnable() {
@Override
public void run() {
getAction1Button().setEnabled(false);
getAction2Button().setEnabled(false);
Deconvolution d = new Deconvolution("CheckImage", Command.command());
Apodization apo = d.getController().getApodization();
if (apo == null) {
lblApo.setText("Error in Apodization");
return;
}
Padding pad = d.getController().getPadding();
if (pad == null) {
lblPad.setText("Error in Padding");
return;
}
RealSignal x = d.openImage();
if (x == null) {
lblPad.setText("Error in input image");
lblApo.setText("Error in input image");
return;
}
Monitors m = Monitors.createDefaultMonitor();
RealSignal y = pad.pad(m, x);
apo.apodize(m, y);
lblPad.setText(x.dimAsString() + " > " + y.dimAsString());
lblApo.setText(NumFormat.nice(x.getStats()[5]) + " > " + NumFormat.nice(y.getStats()[5]));
getAction1Button().setEnabled(true);
getAction2Button().setEnabled(true);
}
});
thread.setPriority(Thread.MIN_PRIORITY);
thread.start();
return;
}
update();
}
@Override
public void close() {
cmbPadXY.removeActionListener(this);
cmbPadZ.removeActionListener(this);
cmbApoXY.removeActionListener(this);
cmbApoZ.removeActionListener(this);
getAction1Button().removeActionListener(this);
spnExtensionXY.removeChangeListener(this);
spnExtensionZ.removeChangeListener(this);
cmbNormalization.removeActionListener(this);
bnTest.removeActionListener(this);
}
}
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