1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
| 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();
}
}
} |
