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Re: AnalyzeSkeleton in JavaScript: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException

Posted by Ignacio Arganda-Carreras-2 on Feb 14, 2016; 8:35pm
URL: http://imagej.273.s1.nabble.com/AnalyzeSkeleton-in-JavaScript-Exception-in-thread-AWT-EventQueue-0-java-lang-NullPointerException-tp5015617p5015630.html

Hello Sarah,

In this line:

var skelResult = skel.run(AnalyzeSkeleton_.NONE, false, true, null, true,
false);

You should replace the "null" parameter by the image (ImagePlus object) you
want to analyze.

Cheers!

ignacio

On Fri, Feb 12, 2016 at 7:35 PM, SarahBerlin <[hidden email]> wrote:

> Hello.
>
> I want to use AnalyzeSkeleton in a JavaScript. But it produces
> java.lang.NullPointerException. What happens here? How can I avoid that?
>
> Thank you
> Sarah
>
> A code sniplet looks like that (cp.
> http://fiji.sc/AnalyzeSkeleton#Using_silent_mode_from_scripts):
>
> importPackage(Packages.ij);
> importPackage(Packages.ij.plugin);
> importPackage(Packages.ij.process );
> importPackage(Packages.ij.measure );
> importPackage(Packages.sc.fiji.analyzeSkeleton);
> importClass(Packages.ij.plugin.frame.RoiManager);
>
> imp = IJ.getImage();
> IJ.run(imp, "Skeletonize (2D/3D)", "");
>
> //ROIs
> roi_manager = RoiManager.getInstance();
> roi_list    = roi_manager.getRoisAsArray();
> for (var roi = 0; roi < roi_list.length; roi++) {
>         ip = imp.getProcessor();
>         imp.setRoi(roi_list[roi]); // set current ROI
>
>         // Initialize AnalyzeSkeleton_
>         var skel = new AnalyzeSkeleton_();  // works w/o error message
>
>         // each of the following produces error messages
>         var skelResult = skel.run(AnalyzeSkeleton_.NONE, false, true, null,
> true, false);
>         skel.calculateShortestPath = true;
>         skel.setup("", imp);
>         }
>
> Error messages:
>
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>         at javax.swing.JComponent._paintImmediately(JComponent.java:5087)
>         at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
>         at
> javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
>         at
>
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
>         at
> java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>         at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
>         at java.awt.EventQueue.access$000(EventQueue.java:85)
>         at java.awt.EventQueue$1.run(EventQueue.java:603)
>         at java.awt.EventQueue$1.run(EventQueue.java:601)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>         at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
>         at
>
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>         at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>         at javax.swing.JComponent._paintImmediately(JComponent.java:5087)
>         at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
>         at
> javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
>         at
>
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
>         at
> java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>         at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
>         at java.awt.EventQueue.access$000(EventQueue.java:85)
>         at java.awt.EventQueue$1.run(EventQueue.java:603)
>         at java.awt.EventQueue$1.run(EventQueue.java:601)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>         at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
>         at
>
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>         at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>         at javax.swing.JComponent._paintImmediately(JComponent.java:5087)
>         at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
>         at
> javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
>         at
>
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
>         at
> java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>         at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
>         at java.awt.EventQueue.access$000(EventQueue.java:85)
>         at java.awt.EventQueue$1.run(EventQueue.java:603)
>         at java.awt.EventQueue$1.run(EventQueue.java:601)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>         at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
>         at
>
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>         at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>         at javax.swing.JComponent._paintImmediately(JComponent.java:5087)
>         at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
>         at
> javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
>         at
>
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
>         at
> java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>         at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
>         at java.awt.EventQueue.access$000(EventQueue.java:85)
>         at java.awt.EventQueue$1.run(EventQueue.java:603)
>         at java.awt.EventQueue$1.run(EventQueue.java:601)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>         at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
>         at
>
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>         at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>         at javax.swing.JComponent._paintImmediately(JComponent.java:5087)
>         at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
>         at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
>         at
> javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
>         at
>
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
>         at
> java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
>         at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
>         at java.awt.EventQueue.access$000(EventQueue.java:85)
>         at java.awt.EventQueue$1.run(EventQueue.java:603)
>         at java.awt.EventQueue$1.run(EventQueue.java:601)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>         at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
>         at
>
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>         at
>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>         at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "Run$_AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "Run$_AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "Run$_AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "Run$_AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> [WARNING] Ignoring unsupported output: result [java.lang.Integer]
> [WARNING] Ignoring unsupported output: result [java.lang.Integer]
> [WARNING] Ignoring unsupported output: result [java.lang.Integer]
> [WARNING] Ignoring unsupported output: result [java.lang.Double]
> [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
> [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
> [WARNING] Ignoring unsupported output: result [java.lang.Integer]
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>
>
>
>
> --
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> http://imagej.1557.x6.nabble.com/AnalyzeSkeleton-in-JavaScript-Exception-in-thread-AWT-EventQueue-0-java-lang-NullPointerException-tp5015617.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencias de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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