[ImageJ-bugs] [Bug 1059] New: Analyze Particles and Bug Report not working
bugzilla at fiji.sc
bugzilla at fiji.sc
Thu Apr 23 16:23:32 CDT 2015
http://fiji.sc/bugzilla/show_bug.cgi?id=1059
Bug ID: 1059
Summary: Analyze Particles and Bug Report not working
Product: Fiji
Version: unspecified
Hardware: Macintosh
OS: Mac OS
Status: NEW
Severity: enhancement
Priority: P5
Component: Other
Assignee: imagej-bugs at imagej.net
Reporter: esf at stanford.edu
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:
--------------------------
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<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:
http://update.imagej.net/ (last check:20150421185343)
Fiji:
http://fiji.sc/update/ (last check:20150422041240)
Files not
up-to-date:
1ad3be0d (LOCAL_ONLY) 20140902085109
jars/jpedalSTD.jar
">
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Please help!
Thanks,
ESF
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