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<head>
<base href="http://fiji.sc/bugzilla/" />
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<body><table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - TrakEM2-View Volume fails"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1020">1020</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>TrakEM2-View Volume fails
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>Macintosh
</td>
</tr>
<tr>
<th>OS</th>
<td>Mac OS
</td>
</tr>
<tr>
<th>Status</th>
<td>NEW
</td>
</tr>
<tr>
<th>Severity</th>
<td>normal
</td>
</tr>
<tr>
<th>Priority</th>
<td>P4
</td>
</tr>
<tr>
<th>Component</th>
<td>Plugins
</td>
</tr>
<tr>
<th>Assignee</th>
<td>imagej-bugs@imagej.net
</td>
</tr>
<tr>
<th>Reporter</th>
<td>glenmac@uw.edu
</td>
</tr>
<tr>
<th>CC</th>
<td>glenmac@uw.edu
</td>
</tr></table>
<p>
<div>
<pre>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: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20150301202523)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150302145742)
Bio-Formats: <a href="http://sites.imagej.net/Bio-Formats/">http://sites.imagej.net/Bio-Formats/</a> (last check:20150303182651)
IMCF Uni Basel: <a href="http://sites.imagej.net/UniBas-IMCF/">http://sites.imagej.net/UniBas-IMCF/</a> (last
check:20150210143144)
Morphology: <a href="http://sites.imagej.net/Landini/">http://sites.imagej.net/Landini/</a> (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</pre>
</div>
</p>
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