<html>
<head>
<base href="http://fiji.sc/bugzilla/" />
</head>
<body><table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - bUnwarpJ completely crashes Fiji"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=993">993</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>bUnwarpJ completely crashes Fiji
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>PC
</td>
</tr>
<tr>
<th>OS</th>
<td>Windows
</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>vbindoka@bsd.uchicago.edu
</td>
</tr>
<tr>
<th>CC</th>
<td>vbindoka@bsd.uchicago.edu
</td>
</tr></table>
<p>
<div>
<pre>the following macro will crash Fiji to desktop in win7-64 every few runs,
randomly. I will upload a sample file ["wiggly.tif"]
macro text:
/*macro to register images to median of Z slices per timepoint
* uses FIJI garbage code to try to correct random major crashes!
* V.Bindokas, Univ of Chicago, JAN 2015
*/
ti=getTitle();
Stack.getDimensions(width, height, channels, slices, frames);
//waitForUser("ref","select reference slice and then hit OK");
for(z=1;z<=slices; z++){
selectWindow(ti);
Stack.setSlice(z);
Stack.setFrame(1);
run("Z Project...", "projection=Median");
run("Unsharp Mask...", "radius=11 mask=0.60");
//run("Duplicate...", "title=ref");
rename("ref");
for (i=1; i<=frames; i++){
selectWindow(ti);
Stack.setFrame(i);
run("Duplicate...", "title=wrk");
// Fine [Very Fine] [Very Coarse] [Super Fine]
run("bUnwarpJ", "source_image=wrk target_image=ref registration=Mono
image_subsample_factor=0 initial_deformation=[Coarse] final_deformation=[Very
Fine] divergence_weight=0.7 curl_weight=0 landmark_weight=0 image_weight=0.8
consistency_weight=20 stop_threshold=0.001");
while(isOpen("Registered Source Image")==false) wait(800);
selectWindow("wrk");
close();
selectWindow("Registered Source Image");
run("Copy");
close();
selectWindow(ti);
run("Paste");
run("Collect Garbage");
}
selectWindow("ref");
close();
run("Collect Garbage");
}
Information about your version of Java:
os.arch => amd64
os.name => Windows 7
os.version => 6.1
java.version => 1.6.0_24
java.vendor => Sun Microsystems Inc.
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.6.0_24-b07
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 19.1-b02
java.vm.vendor => Sun Microsystems Inc.
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.6
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: E:\DEC201~1/java/win64/jdk1.6.0_24//jre
imagej.dir => E:\DEC201~1
Information about the version of each plugin:
Activated update sites:
ImageJ: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20150122044514)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150122030708)
3D ImageJ Suite: <a href="http://sites.imagej.net/Tboudier/">http://sites.imagej.net/Tboudier/</a> (last check:20141208015245)
FFMPEG: <a href="http://fiji.sc/~schindelin/ffmpeg-plugins/">http://fiji.sc/~schindelin/ffmpeg-plugins/</a> (last check:20130606102449)
GDSC-SMLM: <a href="http://sites.imagej.net/GDSC-SMLM/">http://sites.imagej.net/GDSC-SMLM/</a> (last check:20140918051334)
HDF5: <a href="http://sites.imagej.net/Ronneber/">http://sites.imagej.net/Ronneber/</a> (last check:20140827114014)
Morphology: <a href="http://sites.imagej.net/Landini/">http://sites.imagej.net/Landini/</a> (last check:20140723095558)
OpenSPIM: <a href="http://openspim.org/update/">http://openspim.org/update/</a> (last check:20140630085101)
Files not up-to-date:
1ad3be0d (LOCAL_ONLY) 20141222042830 jars/jpedalSTD.jar
6d337b7a (LOCAL_ONLY) 20140730142734 plugins/Accurate_Gaussian_Blur.class
6e9d50db (LOCAL_ONLY) 20140320051924 plugins/Adjustable_Watershed.class
12ec0761 (LOCAL_ONLY) 20120224100622 plugins/Align_RGB_planes.class
0c575fd1 (LOCAL_ONLY) 20141209160514 plugins/BioVoxxel_Plugins.jar
52ff6766 (LOCAL_ONLY) 20150115075008 plugins/Create_Template.jar
55de57f2 (LOCAL_ONLY) 20050408121420 plugins/DecCredits$1.class
66a64476 (LOCAL_ONLY) 20050408121420 plugins/DecCredits.class
fd4ce3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionFFT.class
b0398adb (LOCAL_ONLY) 20141028073350
plugins/DeconvolutionLab/DeconvolutionLab_.jar
8866a3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionSolution.class
ce989b93 (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionWavelets.class
13072662 (LOCAL_ONLY) 20050408121420 plugins/Deconvolution_.class
11326750 (LOCAL_ONLY) 20050408103628 plugins/FFT1D.class
18f23277 (LOCAL_ONLY) 20050408103628 plugins/FourierSpace.class
348da731 (LOCAL_ONLY) 20141126044659 plugins/GHT_.jar
15a0aac2 (LOCAL_ONLY) 20050408150536 plugins/GibsonPSF.class
52861b7c (LOCAL_ONLY) 20050408150244 plugins/GibsonPSFF.class
f481dc68 (LOCAL_ONLY) 20120817074900 plugins/Hybrid_2D_Filters.class
6b2de3e5 (LOCAL_ONLY) 20120817084143 plugins/Hybrid_3D_Filters.class
e9cb6eb7 (LOCAL_ONLY) 20150115083713 plugins/Image_CorrelationJ_1o.class
d6bc39b9 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins.jar
04b38ca7 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins2.jar
71ae5c42 (LOCAL_ONLY) 20140509130342 plugins/KalmanOpenStackFilter_.class
44f1acfa (LOCAL_ONLY) 20121128135145 plugins/Mexican_Hat_Filter.class
53c5c1ad (LOCAL_ONLY) 20141103073745 plugins/NL_Means_.jar
4ed208ff (LOCAL_ONLY) 20140929064046 plugins/NanoTrackJ_.jar
21927175 (LOCAL_ONLY) 20140808090713 plugins/PIV_.jar
b3b13b1f (LOCAL_ONLY) 20050408150244 plugins/PSFCredits$1.class
cb99705d (LOCAL_ONLY) 20050408150244 plugins/PSFCredits.class
de90b917 (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG$1.class
e33950eb (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG.class
9f2412ff (LOCAL_ONLY) 20141028082626 plugins/PSF_Generator.jar
5a3abd78 (LOCAL_ONLY) 20050408150536 plugins/PSF_Gibson_.class
65b190f7 (LOCAL_ONLY) 20121002063426 plugins/PSF_Simple_.class
0c89ccf5 (LOCAL_ONLY) 20140507100709 plugins/PoissonNMF_.jar
12289f6e (LOCAL_ONLY) 20110916093010 plugins/PureDenoise_.jar
33ca5f87 (LOCAL_ONLY) 20141215122204 plugins/Thunder_STORM.jar
69b16199 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4.class
f0990b22 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4Filter.class
27901023 (LOCAL_ONLY) 20050408152652 plugins/Wavelet_Deconvolution_.class
71331805 (LOCAL_ONLY) 20140314082430 plugins/jacop_.jar
9bbfb280 (LOCAL_ONLY) 20140225135257 plugins/octane2_.jar</pre>
</div>
</p>
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