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Batch measurements of the Cell-Tracking-Challenge metrics using TrackMate.

License: GNU Affero General Public License v3.0

Java 100.00%

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nick-kuang

trackmate-ctcrunner's Issues

Deploy to maven.scijava.org

The page https://imagej.net/plugins/trackmate/extensions/trackmate-helper is currently pointing to the wrong source code on GitHub, because the artifact is set as sc.fiji:TrackMate where it should be sc.fiji:TrackMate-CTCRunner. But the maven artifact of this repository here is not deployed.

I suggest:

adding CI via GitHub actions (i.e. running github-actionify.sh from scijava-scripts
transferring this repo to the fiji organization (or asking @ctrueden to add the maven secrets just for this repo in your personal space @tinevez)
fixing the artifact name on the wiki page.

That would have made it much easier for me to find the source code when troubleshooting for users of our core facility 🙂.

Ensure compatibility of TrackMate-Helper with TrackMate v8.

"All spots" table export for TrackMate Batcher

From maxadrian:

"The TrackMate batcher currently exports the results table from the tracks. It would be great if it could also have an extra option to export the "All spots table" that contains the localization data of spots that are not part of tracks.
Thanks for all the fantastic work on TrackMate!"

trackmate-sc/TrackMate#241

For SPT metrics, the maxDist parameter is hardcoded to 1.

https://github.com/trackmate-sc/TrackMate-CTCRunner/blob/master/src/main/java/fiji/plugin/trackmate/helper/spt/SPTMetricsRunner.java#L40

This parameter controls what is the distance candidate spots must be from ground-truth to be accepted as 'good'.
In situations where we have many spurious spots, it would be nice to let the user controls and sets this distance explicitly.
Add a UI element that allows setting it, and save it in the config file.

Add an exporter for the simple XML format.

This way we can use the tracking results with the @msdananalyzer.
https://forum.image.sc/t/new-version-of-the-trackmate-helper-v1-2-1-with-a-batcher-and-the-spt-metrics/68180/8?u=tinevez

TrackMate Batcher not working

Hi,

On a freshly new installed Fiji today, just updated and with the following extra plugins installed:

TrackMate-Cellpose
TrackMate-ExTrack
TrackMate-Helper
TrackMate-Ilastik
TrackMate-MorphoLibJ
TrackMate-Oneat
TrackMate-Pairing
TrackMate-StarDist
TrackMate-Weka
TrackMateCSVImporter
CellTrackingChallenge

On the following system:

ImageJ version : 1.54f
Windows 10 Pro
with the following jars installed in Fiji.app\jars:
TrackMate-7.11.1.jar
TrackMate-Cellpose-0.1.1.jar
TrackMate-CSVImporter-3.1.3.jar
TrackMate-CTCRunner-1.2.4.jar
TrackMate-ExTrack-1.3.0.jar
TrackMate-Ilastik-1.3.2.jar
TrackMate-MorphoLibJ-1.2.0.jar
TrackMate-StarDist-1.2.0.jar
TrackMate-Weka-1.3.0.jar

When I try to start TrackMate Batcher via the menu Plugins › Tracking › TrackMate Batcher, I get the following error:

[ERROR] Command errored: TrackMate Batcher
java.io.UncheckedIOException: java.nio.charset.MalformedInputException: Input length = 1
	at java.io.BufferedReader$1.hasNext(BufferedReader.java:574)
	at java.util.Iterator.forEachRemaining(Iterator.java:115)
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
	at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
	at fiji.plugin.trackmate.batcher.ui.BatcherModelIO.readFrom(BatcherModelIO.java:89)
	at fiji.plugin.trackmate.batcher.ui.BatcherModelIO.readFromDefault(BatcherModelIO.java:114)
	at fiji.plugin.trackmate.batcher.ui.BatcherController.<init>(BatcherController.java:65)
	at fiji.plugin.trackmate.batcher.TrackMateBatcherPlugin.run(TrackMateBatcherPlugin.java:36)
	at ij.IJ.runUserPlugIn(IJ.java:244)
	at ij.IJ.runPlugIn(IJ.java:210)
	at ij.IJ.runPlugIn(IJ.java:199)
	at net.imagej.legacy.command.LegacyCommand.run(LegacyCommand.java:57)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)
Caused by: java.nio.charset.MalformedInputException: Input length = 1
	at java.nio.charset.CoderResult.throwException(CoderResult.java:281)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:339)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at java.io.BufferedReader$1.hasNext(BufferedReader.java:571)
	... 24 more
[INFO] Reading available sites from https://imagej.net/
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at javax.swing.JTable.columnMarginChanged(JTable.java:4599)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
	at java.awt.Dialog.show(Dialog.java:1084)
	at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:869)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:666)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:637)
	at net.imagej.ui.swing.updater.SwingTools.lambda$showMessageBox$0(SwingTools.java:240)
	at net.imagej.ui.swing.updater.SwingTools.invokeOnEDT(SwingTools.java:288)
	at net.imagej.ui.swing.updater.SwingTools.showMessageBox(SwingTools.java:236)
	at net.imagej.ui.swing.updater.SitesDialog.error(SitesDialog.java:688)
	at net.imagej.ui.swing.updater.SitesDialog$1$1.stopCellEditing(SitesDialog.java:154)
	at javax.swing.JTable.columnMarginChanged(JTable.java:4598)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
	at java.awt.Dialog.show(Dialog.java:1084)
	at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:869)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:666)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:637)
	at net.imagej.ui.swing.updater.SwingTools.lambda$showMessageBox$0(SwingTools.java:240)
	at net.imagej.ui.swing.updater.SwingTools.invokeOnEDT(SwingTools.java:288)
	at net.imagej.ui.swing.updater.SwingTools.showMessageBox(SwingTools.java:236)
	at net.imagej.ui.swing.updater.SitesDialog.error(SitesDialog.java:688)
	at net.imagej.ui.swing.updater.SitesDialog$1$1.stopCellEditing(SitesDialog.java:154)
	at javax.swing.JTable.columnMarginChanged(JTable.java:4598)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
	at java.awt.Dialog.show(Dialog.java:1084)
	at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:869)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:666)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:637)
	at net.imagej.ui.swing.updater.SwingTools.lambda$showMessageBox$0(SwingTools.java:240)
	at net.imagej.ui.swing.updater.SwingTools.invokeOnEDT(SwingTools.java:288)
	at net.imagej.ui.swing.updater.SwingTools.showMessageBox(SwingTools.java:236)
	at net.imagej.ui.swing.updater.SitesDialog.error(SitesDialog.java:688)
	at net.imagej.ui.swing.updater.SitesDialog$1$1.stopCellEditing(SitesDialog.java:154)
	at javax.swing.JTable.columnMarginChanged(JTable.java:4598)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at javax.swing.JTable.columnMarginChanged(JTable.java:4599)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
	at java.awt.Dialog.show(Dialog.java:1084)
	at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:869)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:666)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:637)
	at net.imagej.ui.swing.updater.SwingTools.lambda$showMessageBox$0(SwingTools.java:240)
	at net.imagej.ui.swing.updater.SwingTools.invokeOnEDT(SwingTools.java:288)
	at net.imagej.ui.swing.updater.SwingTools.showMessageBox(SwingTools.java:236)
	at net.imagej.ui.swing.updater.SitesDialog.error(SitesDialog.java:688)
	at net.imagej.ui.swing.updater.SitesDialog$1$1.stopCellEditing(SitesDialog.java:154)
	at javax.swing.JTable.columnMarginChanged(JTable.java:4598)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
	at java.awt.Dialog.show(Dialog.java:1084)
	at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:869)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:666)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:637)
	at net.imagej.ui.swing.updater.SwingTools.lambda$showMessageBox$0(SwingTools.java:240)
	at net.imagej.ui.swing.updater.SwingTools.invokeOnEDT(SwingTools.java:288)
	at net.imagej.ui.swing.updater.SwingTools.showMessageBox(SwingTools.java:236)
	at net.imagej.ui.swing.updater.SitesDialog.error(SitesDialog.java:688)
	at net.imagej.ui.swing.updater.SitesDialog$1$1.stopCellEditing(SitesDialog.java:154)
	at javax.swing.JTable.columnMarginChanged(JTable.java:4598)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at javax.swing.JTable.columnMarginChanged(JTable.java:4599)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
	at java.awt.Dialog.show(Dialog.java:1084)
	at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:869)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:666)
	at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:637)
	at net.imagej.ui.swing.updater.SwingTools.lambda$showMessageBox$0(SwingTools.java:240)
	at net.imagej.ui.swing.updater.SwingTools.invokeOnEDT(SwingTools.java:288)
	at net.imagej.ui.swing.updater.SwingTools.showMessageBox(SwingTools.java:236)
	at net.imagej.ui.swing.updater.SitesDialog.error(SitesDialog.java:688)
	at net.imagej.ui.swing.updater.SitesDialog$1$1.stopCellEditing(SitesDialog.java:154)
	at javax.swing.JTable.columnMarginChanged(JTable.java:4598)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at javax.swing.JTable.columnMarginChanged(JTable.java:4599)
	at javax.swing.table.DefaultTableColumnModel.fireColumnMarginChanged(DefaultTableColumnModel.java:628)
	at javax.swing.table.DefaultTableColumnModel.propertyChange(DefaultTableColumnModel.java:691)
	at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
	at javax.swing.event.SwingPropertyChangeSupport.firePropertyChange(SwingPropertyChangeSupport.java:92)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:278)
	at javax.swing.table.TableColumn.firePropertyChange(TableColumn.java:284)
	at javax.swing.table.TableColumn.setWidth(TableColumn.java:514)
	at javax.swing.JTable$2.setSizeAt(JTable.java:3235)
	at javax.swing.JTable$4.setSizeAt(JTable.java:3316)
	at javax.swing.JTable.adjustSizes(JTable.java:3361)
	at javax.swing.JTable.adjustSizes(JTable.java:3329)
	at javax.swing.JTable.setWidthsFromPreferredWidths(JTable.java:3243)
	at javax.swing.JTable.doLayout(JTable.java:3131)
	at java.awt.Container.validateTree(Container.java:1698)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validateTree(Container.java:1707)
	at java.awt.Container.validate(Container.java:1633)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:711)
	at javax.swing.RepaintManager$3.run(RepaintManager.java:709)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Resulting in beeing able to start the TrackMate Batch processing interface

Any tips?

Best,
Benjamin

Do we crash if the json file for the batcher model changed of version?

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