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Bug 1020 - TrakEM2-View Volume fails
TrakEM2-View Volume fails
Status: NEW
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-03-04 12:53 CST by Glen MacDonald
Modified: 2015-03-04 12:53 CST
1 user (show)

See Also:
Description Glen MacDonald 2015-03-04 12:53:31 CST 
Attempting to view a 3D volume in TrakEM2.
select the dataset in the Patches tab
right click
Patches>View Volume results in
==================
ERROR:
java.lang.ArrayIndexOutOfBoundsException
==================
same if the pipe objects are selected by shift-click before attempting to view the Patches volume
Selecting only the pipes, without the Patches volume, can be viewed with right-click>Show in 3D 

I haven't used TrakEM2 in months, so don't know when problem started.  Fiji was freshly updated this morning.

at 1 point, this longer exception appeared:
==================
ERROR:
java.lang.ArrayIndexOutOfBoundsException: 661720
	at vib.NaiveResampler.getPixel(NaiveResampler.java:15)
	at vib.NaiveResampler.resample(NaiveResampler.java:226)
	at vib.NaiveResampler.resample(NaiveResampler.java:155)
	at vib.NaiveResampler.resample(NaiveResampler.java:159)
	at voltex.VoltexGroup.<init>(VoltexGroup.java:79)
	at ij3d.ContentInstant.displayAs(ContentInstant.java:128)
	at ij3d.ContentCreator.createContent(ContentCreator.java:104)
	at ij3d.ContentCreator.createContent(ContentCreator.java:62)
	at ij3d.Image3DUniverse.addContent(Image3DUniverse.java:848)
	at ij3d.Image3DUniverse.addVoltex(Image3DUniverse.java:954)
	at ini.trakem2.display.Display3D.showVolume(Display3D.java:587)
	at ini.trakem2.display.Display$46.run(Display.java:5405)
	at ini.trakem2.utils.Dispatcher$Task.run(Dispatcher.java:44)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:695)
==================

Regards,
Glen

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.5
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150301202523)
Fiji: http://fiji.sc/update/ (last check:20150302145742)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150303182651)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last check:20150210143144)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723075558)

Files not up-to-date:
  9ad834b2 (MODIFIED) 20141219113019 Contents/Info.plist
  1ad3be0d (LOCAL_ONLY) 20140602022601 jars/jpedalSTD.jar
  b18d577c (LOCAL_ONLY) 20100916121922 macros/Import_Channel_Order3.8a.txt
  f4074bbb (LOCAL_ONLY) 20120702084321 macros/toolsets/BPCounting3g.ijm
  40b911a7 (LOCAL_ONLY) 20150218114830 macros/toolsets/FV_Montage_ACDC3.ijm
  a26f9668 (LOCAL_ONLY) 20150226131700 macros/toolsets/FV_Montage_ACDC4.ijm
  b92791c5 (LOCAL_ONLY) 20150226144514 macros/toolsets/FV_Montage_ACDC5.ijm
  3c6a36df (LOCAL_ONLY) 20150226163247 macros/toolsets/FV_Montage_ACDC6.ijm
  2fe75fec (LOCAL_ONLY) 20131107171559 macros/toolsets/FWHM3.ijm
  77158612 (LOCAL_ONLY) 20150102131424 macros/toolsets/Import Channel Order3.98c.ijm
  17d1aba0 (LOCAL_ONLY) 20140404113537 macros/toolsets/Merge HuPro Quadrants_3b.ijm
  82d9a278 (LOCAL_ONLY) 20131031121151 macros/toolsets/Open and rescale.ijm
  4651471a (LOCAL_ONLY) 20121116153428 macros/toolsets/PIMP_3_Batch.ijm
  0c5c4a4c (LOCAL_ONLY) 20121116153510 macros/toolsets/PIMP_3_Single file.ijm
  7dbe7422 (LOCAL_ONLY) 20120708135042 macros/toolsets/Placenta_macro3.ijm
  a4ed32f3 (LOCAL_ONLY) 20130919160119 macros/toolsets/Read tomography log.ijm
  cb9c4438 (LOCAL_ONLY) 20141104113030 macros/toolsets/Stereology_grid2_6.ijm
  269efdaa (LOCAL_ONLY) 20130903082641 macros/toolsets/Time3D.ijm
  3f09c23b (LOCAL_ONLY) 20130814161408 macros/toolsets/Time_rescale.ijm
  d955a886 (LOCAL_ONLY) 20131218150852 macros/toolsets/Utricle_RGB_merge2_1.ijm
  978e3d7d (LOCAL_ONLY) 20150218093125 macros/toolsets/WSR_testmontage.ijm
  e9126f03 (LOCAL_ONLY) 20120925154335 macros/toolsets/jv.ijm
  6c9b7e82 (LOCAL_ONLY) 20150226150346 macros/toolsets/sortfiles_.ijm
  88650aa3 (LOCAL_ONLY) 20150130171537 macros/toolsets/testmontage_.ijm
  20e2cec7 (LOCAL_ONLY) 20140925095705 plugins/Analyze/ICTN_1_6_.jar