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| package plugins.nchenouard.particletracking;
import icy.file.FileUtil;
import icy.gui.frame.IcyFrame;
import icy.gui.frame.IcyInternalFrame;
import icy.gui.frame.progress.AnnounceFrame;
import icy.gui.frame.progress.ProgressFrame;
import icy.image.ImageUtil;
import icy.main.Icy;
import icy.plugin.abstract_.PluginActionable;
import icy.resource.ResourceUtil;
import icy.sequence.Sequence;
import icy.swimmingPool.SwimmingObject;
import icy.system.SystemUtil;
import icy.util.XMLUtil;
import java.awt.BorderLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Vector;
import java.util.concurrent.locks.Condition;
import java.util.concurrent.locks.Lock;
import java.util.concurrent.locks.ReentrantLock;
import javax.swing.ButtonGroup;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JEditorPane;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.SwingUtilities;
import javax.swing.filechooser.FileFilter;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import plugins.fab.trackmanager.TrackGroup;
import plugins.fab.trackmanager.TrackManager;
import plugins.fab.trackmanager.TrackSegment;
import plugins.nchenouard.particletracking.MHTracker.HMMMHTracker;
import plugins.nchenouard.particletracking.filtering.IMM2D;
import plugins.nchenouard.particletracking.filtering.IMM3D;
import plugins.nchenouard.particletracking.filtering.KF2dDirected;
import plugins.nchenouard.particletracking.filtering.KF2dRandomWalk;
import plugins.nchenouard.particletracking.filtering.KF3dDirected;
import plugins.nchenouard.particletracking.filtering.KF3dRandomWalk;
import plugins.nchenouard.particletracking.filtering.Predictor;
import plugins.nchenouard.particletracking.filtering.Predictor2D;
import plugins.nchenouard.particletracking.filtering.Predictor3D;
import plugins.nchenouard.particletracking.gui.TrackingMainPanel;
import plugins.nchenouard.particletracking.legacytracker.StoppableTracker;
import plugins.nchenouard.particletracking.legacytracker.Tracker;
import plugins.nchenouard.particletracking.legacytracker.associationMethod.InstantaneousTracker;
import plugins.nchenouard.particletracking.legacytracker.associationMethod.SolveMLAssociation;
import plugins.nchenouard.particletracking.legacytracker.associationMethod.Track;
import plugins.nchenouard.particletracking.legacytracker.gui.PanelTracking;
import plugins.nchenouard.particletracking.simplifiedMHT.SimplifiedMHTPanel;
import plugins.nchenouard.spot.Detection;
import plugins.nchenouard.spot.DetectionResult;
import plugins.nchenouard.spot.Spot;
/**
* Particle tracking plugin for ICY that uses the multiple hypothesis tracking algorithm
* described in:
* Nicolas Chenouard, Isabelle Bloch, Jean-Christophe Olivo-Marin,
* "Multiple Hypothesis Tracking for Cluttered Biological Image Sequences," IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 35, no. 11, pp. 2736-3750, Nov., 2013
* Pubmed link: http://www.ncbi.nlm.nih.gov/pubmed/23689865
*
* Part of the Spot Tracking plugin for ICY: http://icy.bioimageanalysis.org/plugin/Spot_Tracking
*
* @author Nicolas Chenouard (nicolas.chenouard@gmail.com)
* @version 3.1
* @date 2013-11-13
* @license gpl v3.0
*/
public class SpotTrackingPlugin extends PluginActionable implements ActionListener
{
public static String MHT_PLUGIN_CONFIGURATION = "MHTconfiguration";
private enum GUIStateEnum {ADVANCED, SIMPLE, LEGACY};
GUIStateEnum currentGUISate = GUIStateEnum.SIMPLE;
IcyFrame mainFrame;
JMenuBar menuBar;
JMenu guiMenu, fileMenu, infoMenu;
JMenuItem menuItem;
JPanel mainPanel;
final String SIMPLEGUI = "Simple interface";
final String ADVANCEDGUI = "Avanced interface";
final String LEGACYGUI = "Legacy plugin";
TrackingMainPanel advancedGUIPanel;
SimplifiedMHTPanel simpleGUIPanel;
PanelTracking legacyGUIPanel;
LegacyTrackerManager legacyTrackerManager;
MHTrackerManager mhTrackerManager;
MHTparameterSet mhtParameterSet = null;
boolean defaultParameterSet = true;
Thread computationThread = null;
ProgressFrame trackingAnnounce;
public static boolean optimizationLibraryLoaded = false;
boolean useMultithreading = true;
boolean useLPSolve = true;
public SpotTrackingPlugin()
{
if (!optimizationLibraryLoaded)
{
try
{
if (!loadLibrary("lpsolve55"))
{
System.err.println("Library cannot be loaded");
throw (new Exception("lpsolve55 could not be loaded"));
}
if (extractLibrary("lpsolve55j") == null)
{
System.err.println("Library cannot be extracted");
throw (new Exception("lpsolve55 could not be loaded"));
}
}
catch (Exception e)
{
e.printStackTrace();
optimizationLibraryLoaded = false;
JOptionPane.showMessageDialog(Icy.getMainInterface().getMainFrame(),
"The lpsolve55 optimization library has failed to load.\n" +
"The plugin is now using a slower library.\n" +
"Please, consider switching to another platform (eg. windows) for improved performance,\nor contact the developper.",
"Library loading error",
JOptionPane.ERROR_MESSAGE);
return;
}
optimizationLibraryLoaded = true;
}
}
public File extractLibrary(String libName)
{
try
{
// get mapped library name
String mappedlibName = System.mapLibraryName(libName);
// get base resource path for native library
final String basePath = getResourceLibraryPath() + ResourceUtil.separator;
// search for library in resource
URL libUrl = getResource(basePath + mappedlibName);
// not found ?
if (libUrl == null)
{
// jnilib extension may not work, try with "dylib" extension instead
if (mappedlibName.endsWith(".jnilib"))
{
mappedlibName = mappedlibName.substring(0, mappedlibName.length() - 7) + ".dylib";
libUrl = getResource(basePath + mappedlibName);
}
}
// resource not found --> error
if (libUrl == null)
throw new IOException("Couldn't find resource " + basePath + mappedlibName);
// extract resource
return extractResource(SystemUtil.getTempLibraryDirectory() + FileUtil.separator + mappedlibName, libUrl);
}
catch (IOException e)
{
System.err.println("Error while loading packed library " + libName + ": " + e);
}
return null;
}
@Override
public void run() {
mhTrackerManager = new MHTrackerManager();
mainPanel = new JPanel();
mainFrame = new IcyFrame("Spot Tracking", true, true, true, true);
mainFrame.getContentPane().add(mainPanel);
// set up the tracking plugin panels
mainPanel.setLayout(new BorderLayout());
int iconSize = 100;
ImageIcon detectionIcon = ResourceUtil.getImageIcon( ImageUtil.load( getResourceAsStream( "plugins/nchenouard/particletracking/simplifiedMHT/detectionIcon.png" ) ), iconSize );
ImageIcon mhtIcon = ResourceUtil.getImageIcon( ImageUtil.load( getResourceAsStream( "plugins/nchenouard/particletracking/simplifiedMHT/MHTIcon.png" ) ), iconSize );
ImageIcon outputIcon = ResourceUtil.getImageIcon( ImageUtil.load( getResourceAsStream( "plugins/nchenouard/particletracking/simplifiedMHT/trackPoolIcon.png" ) ), iconSize );
ImageIcon workingIcon = ResourceUtil.getImageIcon( ImageUtil.load( getResourceAsStream( "plugins/nchenouard/particletracking/simplifiedMHT/workingIcon.png" ) ), iconSize );
simpleGUIPanel = new SimplifiedMHTPanel(detectionIcon, mhtIcon, outputIcon, workingIcon);
mainPanel.add(simpleGUIPanel, BorderLayout.CENTER);
simpleGUIPanel.loadParametersButton.addActionListener(this);
simpleGUIPanel.runTrackingButton.addActionListener(mhTrackerManager);
simpleGUIPanel.detectionChooser.addItemListener(new ItemListener() {
@Override
public void itemStateChanged(ItemEvent e) {
if (simpleGUIPanel.detectionChooser.getSelectedDetectionResult() != null && mhtParameterSet != null)
mhtParameterSet.detectionResults = simpleGUIPanel.detectionChooser.getSelectedDetectionResult();
}
});
simpleGUIPanel.trackGroupNameTF.addKeyListener(new KeyListener() {
@Override
public void keyTyped(KeyEvent e) {
}
@Override
public void keyReleased(KeyEvent e) {
mhtParameterSet.trackGroupName = simpleGUIPanel.trackGroupNameTF.getText();
}
@Override
public void keyPressed(KeyEvent e) {
}
});
simpleGUIPanel.estimateParametersButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0)
{
estimateTrackingParameters();
}
});
advancedGUIPanel = new TrackingMainPanel();
advancedGUIPanel.startTrackingButton.addActionListener(mhTrackerManager);
advancedGUIPanel.configFilePanel.exportConfigurationFileButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e)
{
mhtParameterSet = advancedGUIPanel.getParameterSet();
exportConfiguration();
}
});
advancedGUIPanel.configFilePanel.loadConfigurationFileButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e)
{
loadMHTParameters();
}
});
// advancedGUIPanel.configFilePanel.runMultipleConfigurationFileButton.addActionListener(new ActionListener() {
// @Override
// public void actionPerformed(ActionEvent e)
// {
// }
// });
refreshMainPanel(currentGUISate);
// legacy tracker
legacyGUIPanel = new PanelTracking();
legacyTrackerManager = new LegacyTrackerManager(legacyGUIPanel);
// set up the menu bar
menuBar = new JMenuBar();
mainFrame.setJMenuBar(menuBar);
fileMenu = new JMenu("File");
menuBar.add(fileMenu);
JMenuItem saveConfigurationItem = new JMenuItem("Save parameters");
fileMenu.add(saveConfigurationItem);
saveConfigurationItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
exportConfiguration();
}
});
JMenuItem loadConfigurationItem = new JMenuItem("Load parameters");
fileMenu.add(loadConfigurationItem);
loadConfigurationItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
loadMHTParameters();
}
});
JMenuItem configurationItem = new JMenuItem("Plugin configuration");
fileMenu.add(configurationItem);
configurationItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String title = "Plugin configuration";
boolean resizable = false;
boolean closable = true;
boolean maximizable = false;
boolean iconifiable = true;
final IcyInternalFrame configFrame = new IcyInternalFrame(title, resizable, closable, maximizable, iconifiable);
JPanel configFramePanel = new JPanel();
configFrame.setContentPane(configFramePanel);
configFramePanel.setLayout(new GridLayout(3, 1));
final JCheckBox multithreadingBox = new JCheckBox("Multithreaded computation.");
multithreadingBox.setSelected(useMultithreading);
final JCheckBox lpSolveBox = new JCheckBox("Optimization library in C (faster).");
lpSolveBox.setSelected(useLPSolve);
final JButton closeButton = new JButton("Apply");
configFramePanel.add(multithreadingBox);
configFramePanel.add(lpSolveBox);
configFramePanel.add(closeButton);
closeButton.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent e) {
useMultithreading = multithreadingBox.isSelected();
useLPSolve = lpSolveBox.isSelected();
configFrame.close(false);
}});
configFrame.pack();
configFrame.setVisible(true);
Icy.getMainInterface().addToDesktopPane(configFrame);
}
});
guiMenu = new JMenu("Interface");
menuBar.add(guiMenu);
JMenuItem simplifiedGUIItem = new JMenuItem(SIMPLEGUI);
guiMenu.add(simplifiedGUIItem);
simplifiedGUIItem.addActionListener(this);
JMenuItem advancedGUIItem = new JMenuItem(ADVANCEDGUI);
guiMenu.add(advancedGUIItem);
advancedGUIItem.addActionListener(this);
JMenuItem legacyInterfaceItem = new JMenuItem(LEGACYGUI);
guiMenu.add(legacyInterfaceItem);
legacyInterfaceItem.addActionListener(this);
infoMenu = new JMenu("Info");
menuBar.add(infoMenu);
JMenuItem manualItem = new JMenuItem("Manual");
infoMenu.add(manualItem);
manualItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e)
{
IcyFrame manualFrame = new IcyFrame("Spot Tracking Plugin Manual");
manualFrame.setResizable(true);
manualFrame.setClosable(true);
JEditorPane descriptionPane = new JEditorPane();
descriptionPane.setEditable(false);
descriptionPane.setContentType("text/html");
descriptionPane.setText( "<html><p>For a full description, please read the <a href=http://icy.bioimageanalysis.org/plugin/Spot_Tracking#documentation>online manual</a> on ICY website:<br> http://icy.bioimageanalysis.org/plugin/Spot_Tracking#documentation"
+ "<p><b>Quick description:</b>"
+"<br><html>The usual way of using the software is to follow indications given by the interface from top to bottom.<br> Tool tip text on each graphical element gives useful information about the use." +
"<br>In general, the following sequence of operations will be performed: <ol><li>Select a set of locations in space and over time (detections) for the spots to track.<br> This can be done with the Spot Detector plugin. (Section 1)</li> <li>Estimate parameters for the tracking steps or load a set of existing parameters from a local file. (Section 2)</li><li>Specify a unique name for the tracking results. (Section 3)</li><li>Run the track construction process. (Section 4)</li><li>Analyze and save tracking results with the Track Manager plugin.</li><li>Save the tracking parameters via the File menu of the plugin for future re-use.</li></ol>"
+ "<br>Exhaustive control of the tracking parameters is accessible by switching to the advanced interface.<br> (Menu Interface/Advanced Interface).</html>");
manualFrame.setContentPane(descriptionPane);
manualFrame.pack();
addIcyFrame(manualFrame);
manualFrame.setVisible(true);
}
});
JMenuItem aboutItem = new JMenuItem("About");
infoMenu.add(aboutItem);
aboutItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
IcyFrame aboutFrame = new IcyFrame("About Spot Tracking Plugin");
aboutFrame.setResizable(true);
aboutFrame.setClosable(true);
JEditorPane descriptionPane = new JEditorPane();
descriptionPane.setEditable(false);
descriptionPane.setContentType("text/html");
descriptionPane.setText("<html><p>The Spot Tracking Plugin is a essentially an implementation of the methods described in the article:" +
"<br>Nicolas Chenouard, Isabelle Bloch, Jean-Christophe Olivo-Marin,<br> <b>Multiple Hypothesis Tracking for Cluttered Biological Image Sequences</b>, <br>IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 35, no. 11, pp. 2736-3750, Nov., 2013" +
"<br>Pubmed link: http://www.ncbi.nlm.nih.gov/pubmed/23689865" +
"<br><p>By using the software for data analysis you agree to properly cite and reference this work<br> in any communication regarding results obtained by using it." +
"<br><p>Author: Nicolas Chenouard. Institut Pasteur, Paris, France." +
"<br>Version 3.1, 2013-11-13.</html>");
aboutFrame.setContentPane(descriptionPane);
aboutFrame.pack();
addIcyFrame(aboutFrame);
aboutFrame.setVisible(true);
}
});
mainFrame.pack();
mainFrame.addToDesktopPane();
mainFrame.center();
mainFrame.setVisible(true);
mainFrame.requestFocus();
defaultParameterSet = true;
simpleGUIPanel.setUsingDefaultParameters(defaultParameterSet);
}
private void refreshMHTParameterSetFromGUI()
{
if (advancedGUIPanel != null)
{
MHTparameterSet parameters = advancedGUIPanel.getParameterSet();
if (parameters != null)
{
mhtParameterSet = parameters;
simpleGUIPanel.setParameter(mhtParameterSet);
defaultParameterSet = false;
simpleGUIPanel.setUsingDefaultParameters(defaultParameterSet);
}
}
}
private void setMHTParameterSetToGUI()
{
if (advancedGUIPanel != null && mhtParameterSet != null)
{
advancedGUIPanel.setParameterset(mhtParameterSet);
simpleGUIPanel.setParameter(mhtParameterSet);
defaultParameterSet = false;
}
}
private void refreshMainPanel(final GUIStateEnum guiState)
{
mainPanel.removeAll();
switch(guiState)
{
case ADVANCED:
setMHTParameterSetToGUI(); // set the current parameters to the advanced GUI
mainPanel.add(advancedGUIPanel, BorderLayout.CENTER);
break;
case LEGACY:
mainPanel.add(legacyGUIPanel, BorderLayout.CENTER);
break;
case SIMPLE:
refreshMHTParameterSetFromGUI(); // load parameters from advanced GUI
mainPanel.add(simpleGUIPanel, BorderLayout.CENTER);
break;
default:
break;
}
mainFrame.pack();
mainFrame.updateUI();
currentGUISate = guiState;
}
@Override
public void actionPerformed(ActionEvent e) {
if (e.getSource() instanceof JMenuItem)
{
if (((JMenuItem)e.getSource()).getText().equals(SIMPLEGUI))
refreshMainPanel(GUIStateEnum.SIMPLE); // switch to simple GUI
if (((JMenuItem)e.getSource()).getText().equals(ADVANCEDGUI))
refreshMainPanel(GUIStateEnum.ADVANCED); // switch to advanced GUI
if (((JMenuItem)e.getSource()).getText().equals(LEGACYGUI))
refreshMainPanel(GUIStateEnum.LEGACY); // switch to legacy GUI
}
if (e.getSource() == simpleGUIPanel.loadParametersButton)
loadMHTParameters();
}
public void loadMHTParameters()
{
MHTparameterSet parameters = loadConfiguration();
if (parameters != null)
{
mhtParameterSet = parameters;
advancedGUIPanel.setParameterset(mhtParameterSet);
}
}
private void exportConfigurationToFile(File file) {
Document document = XMLUtil.createDocument( true );
Element configurationElement = document.createElement(MHT_PLUGIN_CONFIGURATION);
XMLUtil.getRootElement( document ).appendChild(configurationElement);
if (mhtParameterSet != null)
{
mhtParameterSet.saveToXML(configurationElement);
}
XMLUtil.saveDocument( document , file );
}
public void exportConfiguration() {
JFileChooser fileChooser = new JFileChooser();
fileChooser.setFileFilter(new FileFilter() {
@Override
public String getDescription() {
return "XML file filter";
}
@Override
public boolean accept(File file) {
if (file.isDirectory())
return true;
return file.getName().endsWith(".xml");
}
});
fileChooser.setMultiSelectionEnabled(false);
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
fileChooser.setName("Output xml file selection");
int returnVal = fileChooser.showOpenDialog(mainPanel);
if (returnVal == JFileChooser.APPROVE_OPTION) {
File file = fileChooser.getSelectedFile();
if(!file.getName().endsWith(".xml"))
file = new File(file.getAbsolutePath() + ".xml");
exportConfigurationToFile(file);
}
}
public MHTparameterSet loadConfiguration() {
MHTparameterSet parameterSet = null;
JFileChooser fileChooser = new JFileChooser();
fileChooser.setFileFilter(new FileFilter() {
@Override
public String getDescription() {
return "XML file filter";
}
@Override
public boolean accept(File file) {
if (file.isDirectory())
return true;
return file.getName().endsWith(".xml");
}
});
fileChooser.setMultiSelectionEnabled(false);
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
fileChooser.setName("Input xml file selection");
int returnVal = fileChooser.showOpenDialog(mainPanel);
if (returnVal == JFileChooser.APPROVE_OPTION) {
File file = fileChooser.getSelectedFile();
parameterSet = loadConfigurationFromFile(file);
}
return parameterSet;
}
private MHTparameterSet loadConfigurationFromFile(File file)
{
Document document = XMLUtil.loadDocument( file );
Element root = XMLUtil.getRootElement( document );
if ( root == null )
{
throw new IllegalArgumentException( "can't find: <root> tag." );
}
Element configurationElement = XMLUtil.getElements( root , MHT_PLUGIN_CONFIGURATION ).get( 0 );
if ( configurationElement == null )
{
throw new IllegalArgumentException( "can't find: <root><" + MHT_PLUGIN_CONFIGURATION + "> tag." ) ;
}
MHTparameterSet parameterSet = MHTparameterSet.loadFromXML(configurationElement);
return parameterSet;
}
public static void sendTracksToPool(final TrackGroup trackGroup,
final Sequence sequence) {
SwingUtilities.invokeLater(new Runnable()
{
public void run() {
// Add the given trackGroup
SwimmingObject result = new SwimmingObject(trackGroup);
Icy.getMainInterface().getSwimmingPool().add(result);
TrackManager manager = new TrackManager();
if (sequence != null)
manager.setDisplaySequence(sequence );
new AnnounceFrame("Tracking results exported to Track manager plugin");
}
});
}
double squaredDistance(Spot s1, Spot s2)
{
return (s1.mass_center.x - s2.mass_center.x)*(s1.mass_center.x - s2.mass_center.x) + (s1.mass_center.y - s2.mass_center.y)*(s1.mass_center.y - s2.mass_center.y) + (s1.mass_center.z - s2.mass_center.z)*(s1.mass_center.z - s2.mass_center.z);
}
void estimateTrackingParameters()
{
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
ParameterEstimationFrame estimationFrame = new ParameterEstimationFrame();
addIcyFrame(estimationFrame);
estimationFrame.setVisible(true);
}
});
}
class MHTrackerManager implements ActionListener
{
boolean isRunning = false;
boolean stopTracking = false;
boolean stopped = false;
HMMMHTracker runningTracker;
private Lock stopLock = new ReentrantLock();
private Condition stopCondition = stopLock.newCondition();
@Override
public void actionPerformed(ActionEvent e)
{
if (e.getSource() == advancedGUIPanel.startTrackingButton || e.getSource() == simpleGUIPanel.runTrackingButton)
{
if (e.getSource() == advancedGUIPanel.startTrackingButton)
mhtParameterSet = advancedGUIPanel.getParameterSet();
startSoppableMHTracking();
}
}
public void startSoppableMHTracking()
{
if (isRunning)
{
stopLock.lock();
if (runningTracker != null)
runningTracker.stopComputing();
stopTracking = true;
try {
while (isRunning)
stopCondition.await();
} catch (InterruptedException ie) {
ie.printStackTrace();
}
finally
{
stopLock.unlock();
}
stopTracking = false;
}
else
{
enableTracking(false);
startMHTracking();
}
}
private void enableTracking(final boolean isEnableTracking)
{
SwingUtilities.invokeLater(new Runnable(){
@Override
public void run() {
simpleGUIPanel.changeTrackingState(!isEnableTracking);
advancedGUIPanel.changeTrackingState(!isEnableTracking);
}});
}
public HMMMHTracker buildMHTracker(DetectionResult dr)
{
HMMMHTracker tracker = null;
int dim = 2;
double volume = 256*256;
if (dr.getSequence() != null)
{
if (dr.getSequence().getSizeZ() > 1)
dim = 3;
volume = dr.getSequence().getSizeX()*dr.getSequence().getSizeY()*dr.getSequence().getSizeZ();
}
else
{
// check detections to see if they all have the same z coordinate
// double minX = Double.MAX_VALUE;
// double minY = Double.MAX_VALUE;
// double minZ = Double.MAX_VALUE;
double minX = 0; // assume the sequence coordinates start at 0
double minY = 0;
double minZ = 0;
double maxX = 0;
double maxY = 0;
double maxZ = 0;
for (int t = dr.getFirstFrameTime(); t <= dr.getLastFrameTime(); t++)
{
for (Spot s:dr.getDetectionsAtT(t))
{
minX = Math.min(minX, s.mass_center.x);
minY = Math.min(minY, s.mass_center.y);
minZ = Math.min(minZ, s.mass_center.z);
maxX = Math.max(maxX, s.mass_center.x);
maxY = Math.max(maxY, s.mass_center.y);
maxZ = Math.max(maxZ, s.mass_center.z);
}
}
if (maxZ > minZ)
{
dim = 3;
volume = (maxX - minX +1)*(maxY - minY +1)*(maxZ - minZ +1);
}
else
{
dim = 2;
volume = (maxX - minX +1)*(maxY - minY +1);
}
}
try {
tracker = advancedGUIPanel.buildTracker(dim, volume, useLPSolve && optimizationLibraryLoaded, useMultithreading);
} catch (Exception e) {
e.printStackTrace();
}
return tracker;
}
private void startMHTracking()
{
final DetectionResult dr = mhtParameterSet.detectionResults;// advancedGUIPanel.getSelectedDetectionResult();
if (dr == null)
{
enableTracking(true);
new AnnounceFrame("Tracking requires to specify a set of detections. You can use the Spot Detector plugin to create some.", 10);
return;
}
if (dr.getNumberOfDetection() < 1)
{
enableTracking(true);
new AnnounceFrame("A non empty set of detections needs to be used");
return;
}
final HMMMHTracker mhtracker = buildMHTracker(dr);
computationThread = new Thread(){
@Override
public void run()
{
trackingAnnounce.setLength(dr.getLastFrameTime());
for (int t = dr.getFirstFrameTime(); t <= dr.getLastFrameTime(); t++)
{
if (!stopTracking)
{
trackingAnnounce.setMessage("Track extraction at frame " + t);
trackingAnnounce.setPosition(t);
mhtracker.track(t, dr.getDetectionsAtT(t));
}
else
{
stopped = true;
break;
}
}
trackingAnnounce.close();
ArrayList<TrackSegment> tracks = mhtracker.getCompleteTracks();
TrackGroup tg = new TrackGroup(dr.getSequence());
tg.setDescription(mhtParameterSet.trackGroupName);
for (TrackSegment ts:tracks)
tg.addTrackSegment(ts);
sendTracksToPool(tg, tg.getSequence());
isRunning = false;
enableTracking(true);
if (stopped)
{
stopLock.lock();
isRunning = false;
stopCondition.signalAll();
stopLock.unlock();
}
computationThread = null;
runningTracker = null;
}
};
trackingAnnounce = new ProgressFrame("Tracking progress started");
computationThread.start();
}
}
class LegacyTrackerManager implements ActionListener
{
private StoppableTracker runningTracker = null;
private boolean stopTracking = false;
private boolean isRunning = false;
private Thread runningThread = null;
private Lock stopLock = new ReentrantLock();
private Condition stopCondition = stopLock.newCondition();
PanelTracking panelTracking;
public LegacyTrackerManager(PanelTracking legacyGUIPanel)
{
legacyGUIPanel.trackingStartButton.addActionListener(this);
this.panelTracking = legacyGUIPanel;
}
private void enableTracking(final boolean isEnableTracking)
{
SwingUtilities.invokeLater(new Runnable(){
@Override
public void run() {
panelTracking.changeTrackingState(!isEnableTracking);
}});
}
public void actionPerformed(ActionEvent e)
{
if (e.getSource() == panelTracking.trackingStartButton)
{
if (isRunning)
{
stopLock.lock();
if (runningTracker != null)
runningTracker.stopComputing();
stopTracking = true;
try {
while (isRunning)
stopCondition.await();
} catch (InterruptedException ie) {
ie.printStackTrace();
}
finally
{
stopLock.unlock();
}
stopTracking = false;
}
else
{
DetectionResult detections = panelTracking.getDetectionResults();
if (detections != null) {
enableTracking(false);
trackingRun(detections, detections.getSequence());
} else
new AnnounceFrame("Please first select a detection set.");
}
}
}
private synchronized void trackingRun(final DetectionResult detections, final Sequence sequence) {
if (detections != null) {
isRunning = true;
Thread trackThread = new Thread() {
public void run() {
int dim = 2;
if (sequence.getSizeZ() > 1)
dim = 3;
Tracker tracker = panelTracking.buildTracker(dim);
if (tracker instanceof StoppableTracker)
runningTracker = (StoppableTracker)tracker;
int firstT = detections.getFirstFrameTime();
int lastT = detections.getLastFrameTime();
String message = "Tracking at frame ";
ProgressFrame announceFrame = new ProgressFrame("");
announceFrame.setLength(lastT - firstT + 1);
boolean stopped = false;
for (int t = firstT; t <= lastT; t++) {
if (!stopTracking)
{
announceFrame.setPosition(t);
announceFrame.setMessage(message+" "+t);
tracker.track(t, detections.getDetectionsAtT(t));
}
else
{
stopped = true;
break;
}
}
announceFrame.close();
if (tracker instanceof InstantaneousTracker) {
TrackGroup trackGroup = new TrackGroup(sequence);
trackGroup.setDescription(panelTracking.getTrackGroupName());
for (Track track : ((InstantaneousTracker) tracker)
.getTracks()) {
TrackSegment ts = convertTrack2TrackSegment(track,
null);
if (ts != null && ts.getDetectionList().size() > 1)
trackGroup.addTrackSegment(ts);
}
sendTracksToPool(trackGroup, sequence);
new AnnounceFrame("Tracks exported as "+trackGroup.getDescription()+" in TrackEditor");
}
isRunning = false;
enableTracking(true);
if (stopped)
{
stopLock.lock();
isRunning = false;
stopCondition.signalAll();
stopLock.unlock();
}
runningThread = null;
runningTracker = null;
}
};
runningThread = trackThread;
trackThread.start();
}
}
public TrackSegment convertTrack2TrackSegment(Track track, Object detectionEditor) {
int firstIndex = track.getFirstIndex();
int lastIndex = track.getLastIndex();
for (int i = lastIndex; i > firstIndex; i--)
{
if (track.isPredictionAtFrame(i))
lastIndex = i-1;
else
break;
}
if (firstIndex <= lastIndex)
{
ArrayList<Detection> detections = new ArrayList<Detection>(lastIndex - firstIndex + 1);
for (int i = firstIndex; i <= lastIndex; i++)
{
Spot s = track.getSpotAtFrame(i);
Detection detect = new DetectionSpotTrack(s, i);
if (track.isPredictionAtFrame(i))
detect.setDetectionType(Detection.DETECTIONTYPE_VIRTUAL_DETECTION);
detections.add(detect);
}
return new TrackSegment(detections);
}
else
return null;
}
}
class ParameterEstimationFrame extends IcyFrame
{
public ParameterEstimationFrame()
{
super("Parameters estimation", true, true, true, true);
JPanel mainPanel = new JPanel();
this.setContentPane(mainPanel);
mainPanel.setLayout(new GridBagLayout());
GridBagConstraints gc = new GridBagConstraints();
gc.fill = GridBagConstraints.HORIZONTAL;
gc.gridy = 0;
mainPanel.add(new JLabel("Target motion"), gc);
gc.gridy++;
final JRadioButton diffusiveButton = new JRadioButton("is mainly diffusive (default).");
mainPanel.add(diffusiveButton, gc);
gc.gridy++;
final JRadioButton directedButton = new JRadioButton("is mainly directed.");
mainPanel.add(directedButton, gc);
gc.gridy++;
final JRadioButton directedDiffusiveButton = new JRadioButton("is both diffusive and directed.");
mainPanel.add(directedDiffusiveButton, gc);
gc.gridy++;
ButtonGroup motionGroup = new ButtonGroup();
motionGroup.add(diffusiveButton);
motionGroup.add(directedButton);
motionGroup.add(directedDiffusiveButton);
diffusiveButton.setSelected(true);
mainPanel.add(new JLabel("Parameters for target motion"), gc);
gc.gridy++;
final JRadioButton noUpdateMotionButton = new JRadioButton("are kept to their initial values (default).");
mainPanel.add(noUpdateMotionButton, gc);
gc.gridy++;
final JRadioButton updateMotionButton = new JRadioButton("are re-estimated online.");
mainPanel.add(updateMotionButton, gc);
gc.gridy++;
ButtonGroup updateGroup = new ButtonGroup();
updateGroup.add(noUpdateMotionButton);
updateGroup.add(updateMotionButton);
noUpdateMotionButton.setSelected(true);
JButton estimateParametersButton = new JButton("Run parameter estimation procedure");
mainPanel.add(estimateParametersButton, gc);
estimateParametersButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0)
{
estimateParameters(directedButton.isSelected(), !directedDiffusiveButton.isSelected(), updateMotionButton.isSelected());
close();
}
});
this.pack();
}
public void estimateParameters(final boolean isDirectedMotion, final boolean isSingleMotion, final boolean isUpdateMotion)
{
computationThread = new Thread()
{
@Override
public void run()
{
mhtParameterSet.isDirectedMotion = isDirectedMotion;
mhtParameterSet.isSingleMotion = isSingleMotion;
mhtParameterSet.isUpdateMotion = isUpdateMotion;
// first get an estimation of parameters based on analysis of distance between detections
if (mhtParameterSet.detectionResults == null)
return;
// fill the detection distance list between subsequent detections
int maxNumDetections = 10000;
int numDetections = 0;
int numT = 0;
for (int t = mhtParameterSet.detectionResults.getFirstFrameTime(); t < mhtParameterSet.detectionResults.getLastFrameTime(); t++)
{
numDetections += mhtParameterSet.detectionResults.getDetectionsAtT(t).size();
numT++;
if (numDetections > maxNumDetections)
break;
}
int t = mhtParameterSet.detectionResults.getFirstFrameTime();
double[] distTabXY = new double[numDetections];
double[] distTabZ = new double[numDetections];
int cntDist = 0;
while (t < mhtParameterSet.detectionResults.getFirstFrameTime() + numT)
{
Vector<Spot> dList1 = mhtParameterSet.detectionResults.getDetectionsAtT(t);
Vector<Spot> dList2 = mhtParameterSet.detectionResults.getDetectionsAtT(t + 1);
if (!dList1.isEmpty() && !dList2.isEmpty())
{
for (Spot s1:dList1)
{
double minDist = Double.MAX_VALUE;
Spot minSpot = null;
for (Spot s2:dList2)
{
double d = squaredDistance(s1, s2);
if (d < minDist)
{
minDist = d;
minSpot = s2;
}
}
if (minDist < Double.MAX_VALUE)
{
///distTab[cntDist] = minDist;
distTabXY[cntDist] = (s1.mass_center.x - minSpot.mass_center.x)*(s1.mass_center.x - minSpot.mass_center.x) + (s1.mass_center.y - minSpot.mass_center.y)*(s1.mass_center.y - minSpot.mass_center.y);
distTabZ[cntDist] += (s1.mass_center.z - minSpot.mass_center.z)*(s1.mass_center.z - minSpot.mass_center.z);
cntDist++;
}
}
}
t++;
}
// get a first estimation of the diffusion as the underestimated median of the squared distances
Arrays.sort(distTabXY);
Arrays.sort(distTabZ);
double varDiffXY = distTabXY[(int)(distTabXY.length*0.45)];
double varDiffZ = distTabZ[(int)(distTabXY.length*0.45)];
// then run the legacy tracker to get a refined estimation
int maxConsecutivePred = 1;
int gateFactor = 3;
boolean gateLikelihood = true;
Predictor predictor = null;
if (isSingleMotion)
{
if (varDiffZ > 0)
{
if (isDirectedMotion)
predictor = new KF3dDirected();
else
predictor = new KF3dRandomWalk();
predictor.setTrackingCovariances(new double[]{varDiffXY, varDiffXY, varDiffZ});
}
else
{
if (isDirectedMotion)
predictor = new KF2dDirected();
else
predictor = new KF2dRandomWalk();
predictor.setTrackingCovariances(new double[]{varDiffXY, varDiffXY});
}
}
else
{
if (varDiffZ > 0)
{
ArrayList<Predictor3D> predictors = new ArrayList<Predictor3D>();
predictors.add(new KF3dRandomWalk());
predictors.add(new KF3dDirected());
predictors.get(0).setTrackingCovariances(new double[]{varDiffXY, varDiffXY, varDiffZ});
predictors.get(1).setTrackingCovariances(new double[]{varDiffXY, varDiffXY, varDiffZ});
if (mhtParameterSet.useMostLikelyModel)
predictor = new IMM3D(IMM3D.LikelihoodTypes.IMM_MAX_LIKELIHOOD, new Double(mhtParameterSet.immInertia), predictors);
else
predictor = new IMM3D(IMM3D.LikelihoodTypes.IMM_WEIGHTED_LIKELIHOOD, mhtParameterSet.immInertia, predictors);
}
else
{
ArrayList<Predictor2D> predictors = new ArrayList<Predictor2D>();
predictors.add(new KF2dRandomWalk());
predictors.add(new KF2dDirected());
predictors.get(0).setTrackingCovariances(new double[]{varDiffXY, varDiffXY});
predictors.get(1).setTrackingCovariances(new double[]{varDiffXY, varDiffXY});
if (mhtParameterSet.useMostLikelyModel)
predictor = new IMM2D(IMM2D.LikelihoodTypes.IMM_MAX_LIKELIHOOD, new Double(mhtParameterSet.immInertia), predictors);
else
predictor = new IMM2D(IMM2D.LikelihoodTypes.IMM_WEIGHTED_LIKELIHOOD, mhtParameterSet.immInertia, predictors);
}
}
SolveMLAssociation assignementSolver = new SolveMLAssociation(true);
InstantaneousTracker tracker = new InstantaneousTracker(assignementSolver, predictor, gateLikelihood, gateFactor, maxConsecutivePred);
for (int tt = mhtParameterSet.detectionResults.getFirstFrameTime(); tt < mhtParameterSet.detectionResults.getLastFrameTime(); tt++)
tracker.track(tt, mhtParameterSet.detectionResults.getDetectionsAtT(tt));
ArrayList<Track> tracks = tracker.getTracks();
// consider tracks with length < 3 to be wrong
ArrayList<Track> trueTracks = new ArrayList<Track>();
ArrayList<Track> falseTracks = new ArrayList<Track>();
for (Track tr:tracks)
{
if (tr.getLastIndex() - tr.getFirstIndex() > 2)
trueTracks.add(tr);
else
falseTracks.add(tr);
}
if (trueTracks.isEmpty())
return;
// compute track length
int sumTrackLength = 0;
for (Track tr:trueTracks)
sumTrackLength += (tr.getLastIndex() - tr.getFirstIndex() + 1);
mhtParameterSet.meanTrackLength = sumTrackLength/trueTracks.size();
// compute number of tracks at first frame, and number of new tracks in other frames
int numTrackFirstFrame = 0;
int numNewTracks = 0;
for (Track tr:trueTracks)
{
if (tr.getFirstIndex() == 0)
numTrackFirstFrame ++;
else
numNewTracks ++;
}
mhtParameterSet.numberInitialObjects = numTrackFirstFrame;
mhtParameterSet.numberNewObjects = (numNewTracks/(1d + mhtParameterSet.detectionResults.getLastFrameTime() - mhtParameterSet.detectionResults.getFirstFrameTime()));
// compute number of false detections per frame
int numFalseDetections = 0;
for (Track tr:falseTracks)
{
for (int tt = tr.getFirstIndex(); tt < tr.getLastIndex() + 1; tt++)
{
if (tr.isPredictionAtFrame(tt))
numFalseDetections++;
}
}
mhtParameterSet.numberOfFalseDetections = (int) (Math.round(numFalseDetections/(1d + mhtParameterSet.detectionResults.getLastFrameTime() - mhtParameterSet.detectionResults.getFirstFrameTime())));
// re estimate diffusion //TODO: do this with MSDs to account for directed periods
// if (isSingleMotion && !isDirectedMotion)
{
// just use squared displacement
double sumDistSq = 0;
double sumDistSqZ = 0;
int numDist = 0;
for (Track tr:trueTracks)
{
for (int f = tr.getFirstIndex(); f < tr.getLastIndex(); f++)
{
if(!tr.isPredictionAtFrame(f) && !tr.isPredictionAtFrame(f +1))
{
Spot s1 = tr.getSpotAtFrame(f);
Spot s2 = tr.getSpotAtFrame(f + 1);
sumDistSq += (s1.mass_center.x - s2.mass_center.x)*(s1.mass_center.x - s2.mass_center.x) + (s1.mass_center.y - s2.mass_center.y)*(s1.mass_center.y - s2.mass_center.y);
sumDistSqZ += (s1.mass_center.z - s2.mass_center.z)*(s1.mass_center.z - s2.mass_center.z);
numDist++;
if (numDist > maxNumDetections)
break;
}
}
if (numDist > maxNumDetections)
break;
}
mhtParameterSet.displacementXY = Math.sqrt(sumDistSq/((double) numDist));
mhtParameterSet.displacementZ = Math.sqrt(sumDistSqZ/((double) numDist));
}
// estimate detection rate
int numTrueDetections = 0;
int numVirtualDetections = 0;
for (Track tr:trueTracks)
{
for (int f = tr.getFirstIndex(); f < tr.getLastIndex(); f++)
if (tr.isPredictionAtFrame(f))
numVirtualDetections++;
else
numTrueDetections++;
}
mhtParameterSet.detectionRate = numTrueDetections/((double)numTrueDetections + numVirtualDetections);
SwingUtilities.invokeLater(new Runnable(){
@Override
public void run() {
simpleGUIPanel.changeTrackingState(false);
advancedGUIPanel.changeTrackingState(false);
if (trackingAnnounce != null)
trackingAnnounce.close();
}});
// computationThread = null;
}
};
trackingAnnounce = new ProgressFrame("Parameter estimation in progress");
simpleGUIPanel.changeTrackingState(true);
advancedGUIPanel.changeTrackingState(true);
computationThread.start();
}
}
} |
Utiliser une sous classe d'une classe.
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