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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 15, 2016; 11:25am
URL: http://imagej.273.s1.nabble.com/AnalyzeSkeleton-in-JavaScript-Exception-in-thread-AWT-EventQueue-0-java-lang-NullPointerException-tp5015617p5015634.html

Sorry, Sarah. I was wrong on my remark. As nicely pointed out by Richard
Domander, the fourth parameter of that run method is not input skeleton
image but the original grayscale image (for lowest pixel intensity pruning
mode). So setting to null is fine. What you need to do is to call setup
with the input image before calling run, or the plugin will crash with a
NullPointerException.

Best,

ignacio

On Sun, Feb 14, 2016 at 9:35 PM, Ignacio Arganda-Carreras <
[hidden email]> wrote:

> 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
>>
>>
>>
>>
>> --
>> View this message in context:
>> 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>
>



--
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>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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