<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 - Analyze Particles and Bug Report not working"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1059">1059</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Analyze Particles and Bug Report not working
</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>enhancement
</td>
</tr>
<tr>
<th>Priority</th>
<td>P5
</td>
</tr>
<tr>
<th>Component</th>
<td>Other
</td>
</tr>
<tr>
<th>Assignee</th>
<td>imagej-bugs@imagej.net
</td>
</tr>
<tr>
<th>Reporter</th>
<td>esf@stanford.edu
</td>
</tr></table>
<p>
<div>
<pre>Hi,
I recently updated FIJI, and now analyze particles isn't working on single
images. It works on stacks. I've tried with a macro and manually, and neither
way is working. Here's what I'm doing:
Macro:
run("Set Measurements...", "area mean standard median limit redirect=None
decimal=3");
setAutoThreshold("Default dark");
//run("Threshold...");
setThreshold(0.0100, 10);
run("Analyze Particles...", "size=10-infinity pixel display summarize");
run("Distribution...", "parameter=Median or=20 and=0-3");
Exception:
(Fiji Is Just) ImageJ 2.0.0-rc-29/1.49r; Java 1.6.0_65 [64-bit]; Mac OS X
10.10.2; 27MB of 2279MB (1%)
java.lang.ArrayIndexOutOfBoundsException: -1
at ij.process.FloatStatistics.getMedian(FloatStatistics.java:240)
at ij.process.FloatStatistics.<init>(FloatStatistics.java:38)
at
ij.plugin.filter.ParticleAnalyzer.getStatistics(ParticleAnalyzer.java:888)
at
ij.plugin.filter.ParticleAnalyzer.analyzeParticle(ParticleAnalyzer.java:838)
at ij.plugin.filter.ParticleAnalyzer.analyze(ParticleAnalyzer.java:572)
at ij.plugin.filter.ParticleAnalyzer.run(ParticleAnalyzer.java:254)
at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:112)
at ij.IJ.runPlugIn(IJ.java:171)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:695)\
ALSO, when I tried to submit the bug report through FIJI, I got the following
error messages:
--------------------------
Submission Reply Page:
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"<a href="http://www.w3.org/TR/html4/loose.dtd">http://www.w3.org/TR/html4/loose.dtd</a>">
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It looks like you didn't come from the right page (you have no valid token
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<li>You clicked the "Back" button of your web browser after having
successfully
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<li>You entered the URL in the address bar of your web browser directly,
which should be safe.</li>
<li>You clicked on a URL which redirected you here <b>without your
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<form name="check" id="check" method="post" action="post_bug.cgi"><input
type="hidden" name="priority"
value="P4">
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value="http://">
<input type="hidden" name="cc"
value="esf@stanford.edu">
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value="Macintosh">
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value="">
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value="">
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value="Analyze particles not working">
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value="unspecified">
<input type="hidden" name="estimated_time"
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<input type="hidden" name="deadline"
value="">
<input type="hidden" name="comment"
value="Hi, 

I recently updated FIJI, and now analyze
particles isn't working on single images. It works on stacks. I've tried with a
macro and manually, and neither way is working. Here's what I'm
doing:

Macro:

run("Set Measurements...",
"area mean standard median limit redirect=None
decimal=3");
setAutoThreshold("Default
dark");
//run("Threshold...");
setThreshold(0.0100,
10);
run("Analyze Particles...", "size=10-infinity pixel
display summarize");
run("Distribution...",
"parameter=Median or=20
and=0-3");

Exception:

(Fiji Is Just) ImageJ
2.0.0-rc-29/1.49r; Java 1.6.0_65 [64-bit]; Mac OS X 10.10.2; 27MB of 2279MB
(1%)
 
java.lang.ArrayIndexOutOfBoundsException: -1
 at
ij.process.FloatStatistics.getMedian(FloatStatistics.java:240)
 at
ij.process.FloatStatistics.<init>(FloatStatistics.java:38)
 at
ij.plugin.filter.ParticleAnalyzer.getStatistics(ParticleAnalyzer.java:888)
at
ij.plugin.filter.ParticleAnalyzer.analyzeParticle(ParticleAnalyzer.java:838)
at
ij.plugin.filter.ParticleAnalyzer.analyze(ParticleAnalyzer.java:572)
at ij.plugin.filter.ParticleAnalyzer.run(ParticleAnalyzer.java:254)
 at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)
at
ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:112)
at ij.IJ.runPlugIn(IJ.java:171)
 at
ij.Executer.runCommand(Executer.java:131)
 at
ij.Executer.run(Executer.java:64)
 at
java.lang.Thread.run(Thread.java:695)

Information about your version
of Java:

 os.arch => x86_64
 os.name => Mac OS X
os.version => 10.10.2
 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-b14-466.1-11M4716
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
 java.vm.version
=> 20.65-b04-466.1
 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:20150421185343)
Fiji:
<a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150422041240)

Files not
up-to-date:
 1ad3be0d (LOCAL_ONLY) 20140902085109
jars/jpedalSTD.jar
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Please help!
Thanks,
ESF</pre>
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