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diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java b/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
index 632ec12..cbc399c 100644
--- a/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
@@ -1,135 +1,164 @@
/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package deconvolution.algorithm;
import java.util.ArrayList;
public class Algorithm {
private static ArrayList<AbstractAlgorithmPanel> list;
static {
list = new ArrayList<AbstractAlgorithmPanel>();
list.add(new RegularizedInverseFilterPanel());
list.add(new TikhonovRegularizationInverseFilterPanel());
list.add(new NaiveInverseFilterPanel());
list.add(new FISTAPanel());
list.add(new ISTAPanel());
list.add(new LandweberPanel());
list.add(new LandweberPositivityPanel());
list.add(new RichardsonLucyPanel());
list.add(new RichardsonLucyTVPanel());
list.add(new TikhonovMillerPanel());
list.add(new ICTMPanel());
list.add(new VanCittertPanel());
list.add(new IdentityPanel());
list.add(new ConvolutionPanel());
list.add(new SimulationPanel());
list.add(new NonStabilizedDivisionPanel());
}
public static ArrayList<AbstractAlgorithmPanel> getAvailableAlgorithms() {
return list;
}
+
+ public static ArrayList<AbstractAlgorithmPanel> getAvailableDeconvolutionAlgorithms() {
+ ArrayList<AbstractAlgorithmPanel> list = new ArrayList<AbstractAlgorithmPanel>();
+ list = new ArrayList<AbstractAlgorithmPanel>();
+ list.add(new RegularizedInverseFilterPanel());
+ list.add(new TikhonovRegularizationInverseFilterPanel());
+ list.add(new NaiveInverseFilterPanel());
+ list.add(new FISTAPanel());
+ list.add(new ISTAPanel());
+ list.add(new LandweberPanel());
+ list.add(new LandweberPositivityPanel());
+ list.add(new RichardsonLucyPanel());
+ list.add(new RichardsonLucyTVPanel());
+ list.add(new TikhonovMillerPanel());
+ list.add(new ICTMPanel());
+ list.add(new VanCittertPanel());
+ return list;
+ }
+
+ public static ArrayList<AbstractAlgorithmPanel> getAvailableSimulationAlgorithms() {
+ ArrayList<AbstractAlgorithmPanel> list = new ArrayList<AbstractAlgorithmPanel>();
+ list.add(new IdentityPanel());
+ list.add(new ConvolutionPanel());
+ list.add(new SimulationPanel());
+ list.add(new NonStabilizedDivisionPanel());
+ return list;
+ }
+
+
public static AbstractAlgorithm getDefaultAlgorithm() {
return new Identity();
}
public static AbstractAlgorithm createAlgorithm(String name) {
if (name == null)
return getDefaultAlgorithm();
String n = name.trim().toLowerCase();
int i = 0;
if (list.get(i++).isNamed(n))
return new RegularizedInverseFilter(0.1);
if (list.get(i++).isNamed(n))
return new TikhonovRegularizationInverseFilter(1.0);
if (list.get(i++).isNamed(n))
return new NaiveInverseFilter();
if (list.get(i++).isNamed(n))
return new FISTA(10, 1, 1, "Haar", 3);
if (list.get(i++).isNamed(n))
return new ISTA(10, 1, 1, "Haar", 3);
if (list.get(i++).isNamed(n))
return new Landweber(10, 1);
if (list.get(i++).isNamed(n))
return new LandweberPositivity(10, 1);
if (list.get(i++).isNamed(n))
return new RichardsonLucy(10);
if (list.get(i++).isNamed(n))
return new RichardsonLucyTV(10, 1);
if (list.get(i++).isNamed(n))
return new TikhonovMiller(10, 1, 0.1);
if (list.get(i++).isNamed(n))
return new ICTM(10, 1, 0.1);
if (list.get(i++).isNamed(n))
return new VanCittert(10, 1);
if (list.get(i++).isNamed(n))
return new Identity();
if (list.get(i++).isNamed(n))
return new Convolution();
if (list.get(i++).isNamed(n))
return new Simulation(0, 1, 0);
if (list.get(i++).isNamed(n))
return new NonStabilizedDivision();
return getDefaultAlgorithm();
}
public static AbstractAlgorithmPanel getPanel(String name) {
for (AbstractAlgorithmPanel panel : getAvailableAlgorithms()) {
if (panel.getShortname().equals(name.trim()))
return panel;
if (panel.getName().equals(name.trim()))
return panel;
}
return null;
}
public static ArrayList<String> getShortnames() {
ArrayList<String> list = new ArrayList<String>();
for (AbstractAlgorithmPanel algo : getAvailableAlgorithms()) {
list.add(algo.getShortname());
}
return list;
}
public static String getDocumentation(String name) {
for (AbstractAlgorithmPanel algo : getAvailableAlgorithms()) {
if (name.equals(algo.getName()))
return algo.getDocumentation();
}
return "Unknown Algorithm";
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
index 4e2162e..0200308 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
@@ -1,143 +1,145 @@
/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package deconvolutionlab.modules;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import javax.swing.BorderFactory;
import javax.swing.BoxLayout;
import javax.swing.JComboBox;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.JSeparator;
import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import lab.component.HTMLPane;
import deconvolution.Command;
import deconvolution.algorithm.AbstractAlgorithmPanel;
import deconvolution.algorithm.Algorithm;
import deconvolutionlab.Config;
public class AlgorithmModule extends AbstractModule implements ActionListener, ChangeListener {
private JComboBox<String> cmb;
private HTMLPane doc;
private JPanel cards;
public AlgorithmModule(boolean expanded) {
super("Algorithm", "-algorithm", "", "", expanded);
- ArrayList<AbstractAlgorithmPanel> panels = Algorithm.getAvailableAlgorithms();
- for (AbstractAlgorithmPanel panel : panels)
+ ArrayList<AbstractAlgorithmPanel> deconv = Algorithm.getAvailableAlgorithms();
+ for (AbstractAlgorithmPanel panel : deconv)
cmb.addItem(panel.getName());
cmb.addActionListener(this);
}
@Override
public String getCommand() {
String name = (String) cmb.getSelectedItem();
AbstractAlgorithmPanel algo = Algorithm.getPanel(name);
String cmd = "-algorithm " + algo.getShortname() + " " + algo.getCommand();
String synopsis = name;
setSynopsis(synopsis);
setCommand(cmd);
return cmd;
}
@Override
public JPanel buildExpandedPanel() {
cmb = new JComboBox<String>();
JPanel pnc = new JPanel();
pnc.add(cmb);
doc = new HTMLPane(100, 1000);
cards = new JPanel(new CardLayout());
ArrayList<AbstractAlgorithmPanel> panels = Algorithm.getAvailableAlgorithms();
+
for (AbstractAlgorithmPanel panel : panels) {
JScrollPane scroll = new JScrollPane(panel.getPanelParameters());
scroll.setBorder(BorderFactory.createEmptyBorder());
scroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scroll.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
cards.add(panel.getName(), scroll);
}
cmb.setMaximumRowCount(panels.size());
JPanel control = new JPanel();
control.setLayout(new BoxLayout(control, BoxLayout.PAGE_AXIS));
Border b1 = BorderFactory.createEtchedBorder();
Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);
control.setBorder(BorderFactory.createCompoundBorder(b1, b2));
control.add(cmb);
control.add(cards);
doc.append("h1", "Documentation");
JPanel panel = new JPanel(new BorderLayout());
panel.add(control, BorderLayout.NORTH);
panel.add(doc.getPane(), BorderLayout.CENTER);
// cmb.addActionListener(this);
Config.register(getName(), "algorithm", cmb, Algorithm.getDefaultAlgorithm());
panel.setBorder(BorderFactory.createEtchedBorder());
return panel;
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
if (e.getSource() == cmb) {
doc.clear();
String name = (String) cmb.getSelectedItem();
AbstractAlgorithmPanel algo = Algorithm.getPanel(name);
doc.append(algo.getDocumentation());
CardLayout cl = (CardLayout) (cards.getLayout());
cl.show(cards, name);
}
setSynopsis((String) cmb.getSelectedItem());
setCommand(getCommand());
Command.command();
}
@Override
public void stateChanged(ChangeEvent e) {
setSynopsis((String) cmb.getSelectedItem());
setCommand(getCommand());
Command.command();
}
@Override
public void close() {
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
index 705ea4c..9a47c62 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
@@ -1,352 +1,350 @@
/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package deconvolutionlab.modules;
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", "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()) {
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/OutputModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/OutputModule.java
index f256a35..146bff8 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/modules/OutputModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/OutputModule.java
@@ -1,240 +1,239 @@
/*
* 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.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.util.ArrayList;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JPanel;
import javax.swing.JToolBar;
import lab.component.CustomizedColumn;
import lab.component.CustomizedTable;
import deconvolution.Command;
import deconvolutionlab.Config;
import deconvolutionlab.Constants;
import deconvolutionlab.Output;
import deconvolutionlab.Output.View;
import deconvolutionlab.dialog.OutputDialog;
public class OutputModule extends AbstractModule implements ActionListener, MouseListener {
private CustomizedTable table;
private JButton bnStack;
private JButton bnSeries;
private JButton bnMIP;
private JButton bnOrtho;
private JButton bnPlanar;
private JButton bnFigure;
public OutputModule(boolean expanded) {
super("Output", "", "", "Default", expanded);
}
@Override
public String getCommand() {
String cmd = " ";
if (table == null)
return cmd;
for (int i = 0; i < table.getRowCount(); i++) {
String[] values = new String[table.getColumnCount()];
for(int c=0; c<table.getColumnCount(); c++)
values[c] = table.getCell(i, c) == null ? "" : table.getCell(i, c).trim();
cmd += " -out " + values[0] + " " + values[1] + " " + values[2] + " " + values[3] + " " + values[4];
if (values[5].equals(""))
cmd += " noshow";
if (values[6].equals(""))
cmd += " nosave";
}
return cmd;
}
public void update() {
setCommand(getCommand());
setSynopsis(table.getRowCount() + " output" + (table.getRowCount() > 1 ? "s" : ""));
Command.command();
getAction1Button().setEnabled(table.getRowCount() > 0);
}
@Override
public JPanel buildExpandedPanel() {
String[] dynamics = { "intact", "rescaled", "normalized", "clipped" };
String[] types = { "float", "short", "byte" };
ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
columns.add(new CustomizedColumn("Mode", String.class, 80, false));
columns.add(new CustomizedColumn("Name", String.class, Constants.widthGUI, true));
columns.add(new CustomizedColumn("Dynamic", String.class, 100, dynamics, "Select the dynamic range"));
columns.add(new CustomizedColumn("Type", String.class, 100, types, "Select the type"));
columns.add(new CustomizedColumn("Keypoint", String.class, 120, false));
columns.add(new CustomizedColumn("Show", String.class, 50, false));
columns.add(new CustomizedColumn("Save", String.class, 50, false));
columns.add(new CustomizedColumn("Del", String.class, 30, "\u232B", "Delete this image source"));
table = new CustomizedTable(columns, true);
table.getColumnModel().getColumn(5).setMaxWidth(50);
table.getColumnModel().getColumn(6).setMaxWidth(50);
table.getColumnModel().getColumn(7).setMaxWidth(30);
table.getColumnModel().getColumn(0).setMaxWidth(100);
table.getColumnModel().getColumn(2).setMaxWidth(100);
table.getColumnModel().getColumn(3).setMaxWidth(100);
table.addMouseListener(this);
bnStack = new JButton("\u2295 stack");
bnSeries = new JButton("\u2295 series");
bnMIP = new JButton("\u2295 mip");
bnOrtho = new JButton("\u2295 ortho");
bnPlanar = new JButton("\u2295 planar");
bnFigure = new JButton("\u2295 figure");
JToolBar pn = new JToolBar("Controls Image");
pn.setBorder(BorderFactory.createEmptyBorder());
pn.setLayout(new GridLayout(1, 6));
pn.setFloatable(false);
pn.add(bnStack);
pn.add(bnSeries);
pn.add(bnMIP);
pn.add(bnOrtho);
pn.add(bnPlanar);
pn.add(bnFigure);
JToolBar tool = new JToolBar("Path");
tool.setBorder(BorderFactory.createEmptyBorder());
tool.setLayout(new BorderLayout());
tool.setFloatable(false);
JPanel panel = new JPanel();
panel.setBorder(BorderFactory.createEtchedBorder());
panel.setLayout(new BorderLayout());
panel.add(tool, BorderLayout.NORTH);
panel.add(pn, BorderLayout.SOUTH);
panel.add(table.getMinimumPane(100, 100), BorderLayout.CENTER);
bnStack.addActionListener(this);
bnSeries.addActionListener(this);
bnMIP.addActionListener(this);
bnOrtho.addActionListener(this);
bnPlanar.addActionListener(this);
bnFigure.addActionListener(this);
getAction1Button().addActionListener(this);
Config.registerTable(getName(), "output", table);
return panel;
}
@Override
public void actionPerformed(ActionEvent e) {
-System.out.println("" + e);
super.actionPerformed(e);
View view = null;
if (e.getSource() == bnStack)
view = View.STACK;
else if (e.getSource() == bnSeries)
view = View.SERIES;
else if (e.getSource() == bnMIP)
view = View.MIP;
else if (e.getSource() == bnOrtho)
view = View.ORTHO;
else if (e.getSource() == bnPlanar)
view = View.PLANAR;
else if (e.getSource() == bnFigure)
view = View.FIGURE;
if (view != null) {
OutputDialog dlg = new OutputDialog(view);
if (dlg.wasCancel())
return;
Output out = dlg.getOut();
if (out == null)
System.out.println("Out is null");
else
table.insert(out.getAsString());
update();
}
if (e.getSource() == getAction1Button()) {
int n = table.getRowCount();
for (int i=0; i<n; i++)
table.removeRow(0);
String[] def = new String[] { "stack", "display", "intact", "float", "", "true", "false", "" };
System.out.println("Default " + n);
table.append(def);
}
}
@Override
public void mouseClicked(MouseEvent e) {
int row = table.getSelectedRow();
if (table.getSelectedColumn() == 7) {
table.removeRow(row);
if (table.getRowCount() > 0)
table.setRowSelectionInterval(0, 0);
}
update();
Command.command();
}
@Override
public void mousePressed(MouseEvent e) {
}
@Override
public void mouseReleased(MouseEvent e) {
}
@Override
public void mouseEntered(MouseEvent e) {
}
@Override
public void mouseExited(MouseEvent e) {
}
@Override
public void close() {
bnStack.removeActionListener(this);
bnSeries.removeActionListener(this);
bnMIP.removeActionListener(this);
bnOrtho.removeActionListener(this);
bnPlanar.removeActionListener(this);
bnFigure.removeActionListener(this);
getAction1Button().removeActionListener(this);
getAction2Button().removeActionListener(this);
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
index 2eeabc5..405b479 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
@@ -1,343 +1,341 @@
/*
* 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", "", "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/fft/fftw/FFTWLibrary.java b/DeconvolutionLab2/src/fft/fftw/FFTWLibrary.java
index d77ad82..726b107 100644
--- a/DeconvolutionLab2/src/fft/fftw/FFTWLibrary.java
+++ b/DeconvolutionLab2/src/fft/fftw/FFTWLibrary.java
@@ -1,193 +1,190 @@
/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package fft.fftw;
import java.io.File;
import java.security.CodeSource;
import deconvolutionlab.monitor.Monitors;
import fft.AbstractFFTLibrary;
-import fft.academic.AcademicLibrary;
import jfftw.complex.nd.Plan;
public class FFTWLibrary extends AbstractFFTLibrary {
private String location;
public FFTWLibrary(Monitors monitors) {
String path = "";
boolean found = false;
if (!found) {
try {
CodeSource code = FFTWLibrary.class.getProtectionDomain().getCodeSource();
File file = new File(code.getLocation().toURI().getPath());
path = file.getParentFile().getPath() + File.separator + "FFTW" + File.separator;
found = existsWidsom(monitors, path);
location = path;
}
catch (Exception ex) {
monitors.log("FFTW Widsom not found in : " + path);
location = "Not found in " + path;
found = false;
}
}
if (!found) {
try {
CodeSource code = FFTWLibrary.class.getProtectionDomain().getCodeSource();
File file = new File(code.getLocation().toURI().getPath());
path = file.getParentFile().getPath() + File.separator;
found = existsWidsom(monitors, path);
location = path;
}
catch (Exception ex) {
monitors.log("FFTW Widsom not found in : " + path);
location = "Not found in " + path;
found = false;
}
}
if (!found) {
try {
path = System.getProperty("user.home") + File.separator + "FFTW" + File.separator;
found = existsWidsom(monitors, path);
location = path;
}
catch (Exception ex) {
monitors.log("FFTW Widsom not found in : " + path);
location = "Not found in " + path;
found = false;
}
}
if (!found) {
try {
path = System.getProperty("user.home") + File.separator;
found = existsWidsom(monitors, path);
location = path;
}
catch (Exception ex) {
monitors.log("FFTW Widsom not found in : " + path);
location = "Not found in " + path;
found = false;
}
}
if (!found)
return;
loadLibraries(monitors, path);
try {
new Plan(new int[] { 20, 20, 20 }, Plan.FORWARD, Plan.ESTIMATE | Plan.IN_PLACE | Plan.USE_WISDOM);
ffts.add(new FFTW3D());
installed = true;
}
catch (UnsatisfiedLinkError ex) {
ex.printStackTrace();
installed = false;
}
}
@Override
public String getLocation() {
return location;
}
@Override
public boolean isMultithreadable() {
return true;
}
@Override
public String getCredit() {
return "http://www.fftw.org (FFTW Version 2)";
}
@Override
public String getLibraryName() {
return "FFTW2";
}
@Override
public String getLicence() {
return "<h1>FFTW Version 2, " + "<p>http://www.fftw.org" + "<p>FFTW is free software; you can redistribute it and/or modify it " + "under the terms of the GNU General Public License as published by "
+ "the Free Software Foundation; either version 2 of the License, or " + "(at your option) any later version.";
}
private static void loadLibraries(Monitors monitors, String path) {
try {
String osname = System.getProperty("os.name");
- System.out.println(" test " + osname + " " + path);
if (osname.startsWith("Windows")) {
String osarch = System.getProperty("os.arch");
if (osarch.contains("64")) {
System.load(path + "FFTWJNIWin64.dll");
monitors.log("Loading library FFTW for " + osarch + " " + osname + " " + path + "FFTWJNIWin64.dll");
}
else {
System.load(path + "FFTWJNIWin32.dll");
monitors.log("Loading library FFTW for " + osarch + " " + osname + " " + path + "FFTWJNIWin32.dll");
}
}
else if (osname.startsWith("Mac")) {
System.load(path + "libFFTWJNIMac.jnilib");
monitors.log("Loading library FFTW for " + osname + " " + path + "libFFTWJNIMac.jnilib");
}
else {
monitors.log("FFTW is not provided for the architecture : " + osname);
}
}
catch (Exception ex) {
monitors.log("FFTW not found in : " + path);
System.out.println(">>" + ex.toString());
}
}
private static boolean existsWidsom(Monitors monitors, String path) {
boolean found = false;
- System.out.println(" test " + path);
if (new File(path + "Wisdom").exists()) {
monitors.log("FFTW found in : " + path);
found = true;
}
else {
monitors.log("FFTW Widsom not found in : " + path);
found = false;
}
return found;
}
}
diff --git a/DeconvolutionLab2/src/lab/component/CustomizedTable.java b/DeconvolutionLab2/src/lab/component/CustomizedTable.java
index 85f70a2..2cae066 100644
--- a/DeconvolutionLab2/src/lab/component/CustomizedTable.java
+++ b/DeconvolutionLab2/src/lab/component/CustomizedTable.java
@@ -1,280 +1,284 @@
/*
* 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 lab.component;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Rectangle;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import javax.swing.DefaultCellEditor;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JScrollPane;
import javax.swing.JTable;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
public class CustomizedTable extends JTable {
private JScrollPane pane = null;
private ArrayList<CustomizedColumn> columns;
public CustomizedTable(String headers[], boolean sortable) {
ArrayList<CustomizedColumn> colums = new ArrayList<CustomizedColumn>();
for (int i = 0; i < headers.length; i++)
colums.add(new CustomizedColumn(headers[i], String.class, 150, false));
create(colums);
setAutoCreateRowSorter(sortable);
setRowHeight(20);
}
public CustomizedTable(ArrayList<CustomizedColumn> columns, boolean sortable) {
create(columns);
setAutoCreateRowSorter(sortable);
setRowHeight(20);
}
private void create(ArrayList<CustomizedColumn> column) {
columns = column;
DefaultTableModel model = new DefaultTableModel() {
@Override
public boolean isCellEditable(int row, int col) {
return columns.get(col).editable;
}
@Override
public Class<?> getColumnClass(int col) {
return columns.get(col).classe;
}
};
setModel(model);
int n = columns.size();
String headers[] = new String[n];
for (int col = 0; col < n; col++)
headers[col] = columns.get(col).header;
model.setColumnIdentifiers(headers);
setFillsViewportHeight(true);
for (int col = 0; col < n; col++) {
TableColumn tc = getColumnModel().getColumn(col);
tc.setPreferredWidth(columns.get(col).width);
if (columns.get(col).choices != null) {
JComboBox<String> cmb = new JComboBox<String>();
for (String p : columns.get(col).choices) {
cmb.addItem(p);
cmb.setToolTipText(columns.get(col).tooltip);
tc.setCellEditor(new DefaultCellEditor(cmb));
}
}
if (columns.get(col).button != null) {
ButtonRenderer bn = new ButtonRenderer();
bn.setToolTipText(columns.get(col).tooltip);
tc.setCellRenderer(bn);
}
}
}
public void setPreferredSize(int width, int height) {
if (pane != null)
pane.setPreferredSize(new Dimension(width, height));
}
public void removeRow(int row) {
if (row >= 0 && row < getRowCount())
((DefaultTableModel) getModel()).removeRow(row);
}
public String[] getRow(int row) {
if (row >= 0) {
int ncol = getColumnCount();
String items[] = new String[ncol];
for (int col = 0; col < ncol; col++)
items[col] = (String) getModel().getValueAt(row, col);
return items;
}
return new String[1];
}
public String getCell(int row, int col) {
if (row >= 0) {
return (String) getModel().getValueAt(row, col);
}
return "";
}
public String getRowCSV(int row, String seperator) {
if (row >= 0) {
int ncol = getColumnCount();
String items = "";
- for (int col = 0; col < ncol - 1; col++)
- items += (String) getModel().getValueAt(row, col) + seperator;
+ for (int col = 0; col < ncol - 1; col++) {
+ if ((String) getModel().getValueAt(row, col) == null)
+ items += "" + seperator;
+ else
+ items += (String) getModel().getValueAt(row, col) + seperator;
+ }
if (ncol >= 1)
items += (String) getModel().getValueAt(row, ncol - 1);
return items;
}
return "";
}
public void saveCSV(String filename) {
File file = new File(filename);
try {
BufferedWriter buffer = new BufferedWriter(new FileWriter(file));
int nrows = getRowCount();
int ncols = getColumnCount();
String row = "";
for (int c = 0; c < columns.size(); c++)
row += columns.get(c).header + (c == columns.size() - 1 ? "" : ", ");
buffer.write(row + "\n");
for (int r = 0; r < nrows; r++) {
row = "";
for (int c = 0; c < ncols; c++)
row += this.getCell(r, c) + (c == ncols - 1 ? "" : ", ");
buffer.write(row + "\n");
}
buffer.close();
}
catch (IOException ex) {
}
}
public String getSelectedAtColumn(int col) {
int row = getSelectedRow();
if (row >= 0)
return (String) getModel().getValueAt(row, col);
else
return "";
}
public void setSelectedAtColumn(int col, String selection) {
int nrows = this.getRowCount();
for (int i = 0; i < nrows; i++) {
String name = (String) getModel().getValueAt(i, col);
if (name.equals(selection))
this.setRowSelectionInterval(i, i + 1);
}
}
public void append(Object[] row) {
DefaultTableModel model = (DefaultTableModel) getModel();
int i = 0;
try {
model.addRow(row);
i = getRowCount() - 1;
if (i >= 0) {
getSelectionModel().setSelectionInterval(i, i);
scrollRectToVisible(new Rectangle(getCellRect(i, 0, true)));
}
}
catch (Exception e) {
}
repaint();
}
public void insert(Object[] row) {
DefaultTableModel model = (DefaultTableModel) getModel();
int i = 0;
try {
model.insertRow(0, row);
getSelectionModel().setSelectionInterval(i, i);
scrollRectToVisible(new Rectangle(getCellRect(i, 0, true)));
}
catch (Exception e) {
}
repaint();
}
@Override
public int getSelectedRow() {
int row = super.getSelectedRow();
if (row < 0) {
if (getRowCount() > 0) {
setRowSelectionInterval(0, 0);
row = super.getSelectedRow();
}
return row;
}
return row;
}
public void update(ArrayList<String[]> data) {
DefaultTableModel model = (DefaultTableModel) getModel();
model.getDataVector().removeAllElements();
for (String[] row : data)
model.addRow(row);
repaint();
}
public JScrollPane getPane(int width, int height) {
setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
setPreferredScrollableViewportSize(new Dimension(width, height));
setFillsViewportHeight(true);
pane = new JScrollPane(this);
return pane;
}
public JScrollPane getMinimumPane(int width, int height) {
setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
setMinimumSize(new Dimension(width, height));
setShowVerticalLines(true);
setPreferredScrollableViewportSize(new Dimension(width, height));
setFillsViewportHeight(true);
return new JScrollPane(this);
}
public JFrame show(String title, int w, int h) {
JFrame frame = new JFrame(title);
frame.add(getPane(w, h));
frame.pack();
frame.setVisible(true);
return frame;
}
public class ButtonRenderer extends JButton implements TableCellRenderer {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
setText(columns.get(column).button);
return this;
}
}
}
diff --git a/DeconvolutionLab2/src/signal/factory/GridSpots.java b/DeconvolutionLab2/src/signal/factory/GridSpots.java
index 57019b2..c8ab88c 100644
--- a/DeconvolutionLab2/src/signal/factory/GridSpots.java
+++ b/DeconvolutionLab2/src/signal/factory/GridSpots.java
@@ -1,117 +1,116 @@
/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package signal.factory;
import signal.RealSignal;
public class GridSpots extends SignalFactory {
private double radius = 3.0;
private double slope = 1;
private double spacing = 10.0;
public GridSpots(double radius, double slope, double spacing) {
super(new double[] {radius, spacing});
}
@Override
public String getName() {
return "GridSpots";
}
@Override
public String[] getParametersName() {
return new String[] { "Radius", "Sigmoid Curve Slope", "Spacing" };
}
@Override
public void setParameters(double[] parameters) {
if (parameters.length >= 1)
this.radius = parameters[0];
if (parameters.length >= 2)
this.slope = parameters[1];
if (parameters.length >= 3)
this.spacing = parameters[2];
}
@Override
public double[] getParameters() {
return new double[] { radius, slope, spacing };
}
@Override
public void fill(RealSignal signal) {
float b = (float) background;
for (int x = 0; x < nx; x++)
for (int y = 0; y < ny; y++)
for (int z = 0; z < nz; z++)
signal.data[z][x + nx * y] = b;
int nc = (int) ((nx - spacing) / spacing);
int nr = (int) ((2 * (ny - spacing)) / spacing);
double deltaY = spacing / nr;
int np = (int) ((2 * (nz - spacing)) / spacing);
double deltaZ = spacing / np;
- System.out.println(" " + spacing + " " + nr + " " + nc + " " + np + " " + deltaY + " " + deltaZ);
double y = 0;
double z = 0;
for (int j = 0; j < nr; j++) {
y += (spacing - j * deltaY);
z = 0;
for (int k = 0; k < np; k++) {
z += (spacing - k * deltaZ);
for (int i = 0; i < nc; i++) {
double x = spacing + i * spacing;
double A = amplitude- background; //i*(amplitude-background) / (nc+1);
spot(signal, x, y, z, A);
}
}
}
}
private void spot(RealSignal signal, double xc, double yc, double zc, double A) {
int x1 = (int) Math.max(0, Math.round(xc - radius - 3 * slope));
int x2 = (int) Math.min(nx - 1, Math.round(xc + radius + 3 * slope));
int y1 = (int) Math.max(0, Math.round(yc - radius - 3 * slope));
int y2 = (int) Math.min(ny - 1, Math.round(yc + radius + 3 * slope));
int z1 = (int) Math.max(0, Math.round(zc - radius - 3 * slope));
int z2 = (int) Math.min(nz - 1, Math.round(zc + radius + 3 * slope));
for (int x = x1; x <= x2; x++)
for (int y = y1; y <= y2; y++)
for (int z = z1; z <= z2; z++) {
double dr = Math.sqrt((x - xc) * (x - xc) + (y - yc) * (y - yc) + (z - zc) * (z - zc)) - radius;
signal.data[z][x + nx * y] = Math.max(signal.data[z][x + nx * y], (float) (A - A / (1.0 + Math.exp(-dr / slope))));
}
}
}
diff --git a/DeconvolutionLab2/src/signal/factory/SignalFactory.java b/DeconvolutionLab2/src/signal/factory/SignalFactory.java
index 32776a0..0bb23e6 100644
--- a/DeconvolutionLab2/src/signal/factory/SignalFactory.java
+++ b/DeconvolutionLab2/src/signal/factory/SignalFactory.java
@@ -1,213 +1,210 @@
/*
* 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 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 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;
}
}
}

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