Java exception error related to extended particle analyzer

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Java exception error related to extended particle analyzer

Volko Straub
Dear All,

I am a bit stumped by a Java exception error that appears to be related to the Advanced Particle Analyzer. It doesn't appear to affect the function of the Advanced Particle Analyzer, but it generates a window with an error message. I have written the following small macro code to illustrate the problem:

for (k=0; k<3; k++) {

newImage("Test"+k, "8-bit black", 1000, 1000, 1);
for (i=1;i<11;i++){
makeOval(random*1000, random*1000, random*50, random*50);
run("Fill", "slice");
makeLine(random*1000, random*1000,random*1000, random*1000);
  run("Fill", "slice");
};
run("Extended Particle Analyzer", "pixel solidity=0.5-1.00 aspect=0-100 show=Masks redirect=None keep=None display reset");
wait(2000);
rename("Blobs"+k);
imageCalculator("Subtract  create", "Test"+k,"Blobs"+k);
rename("Lines"+k);
close("Blobs"+k);
close("Test"+k);
};



The macro code creates an image containing random lines and ovals. It then use the Advanced Particle Analyzer to find 'blob' like structures and subtract them from the original image. Carrying out all the commands manually (or just once using the macro code without the outer for loop) produces the expected result without any exceptions.


However, putting the code inside the for-loop to carry it out multiple times (i.e. to batch process a series of images) throws a Java exception (I have copied the error message below) on the second and all subsequent images.


I thought that this may be a timing issue and added a wait command after the Extended Particle Analyzer command, but it didn't solve the problem.


I have updated ImageJ to the latest version (v1.51r) and also updated the Biovoxxel tools via the Fiji update site, but the issue persists.


Any idea what might be going on?


Thanks,

Volko




Java error message text (doesn't appear to be terminal as code continues):


(Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 97MB of 5938MB (1%)

java.lang.IllegalArgumentException: "Label" column not found
at ij.measure.ResultsTable.getValue(ResultsTable.java:376)
at Extended_Particle_Analyzer.particleAnalysis(Extended_Particle_Analyzer.java:680)
at Extended_Particle_Analyzer.run(Extended_Particle_Analyzer.java:340)
at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:265)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
at ij.IJ.runUserPlugIn(IJ.java:219)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:297)
at ij.macro.Functions.doRun(Functions.java:601)
at ij.macro.Functions.doFunction(Functions.java:96)
at ij.macro.Interpreter.doStatement(Interpreter.java:230)
at ij.macro.Interpreter.doBlock(Interpreter.java:608)
at ij.macro.Interpreter.doStatement(Interpreter.java:272)
at ij.macro.Interpreter.doFor(Interpreter.java:530)
at ij.macro.Interpreter.doStatement(Interpreter.java:254)
at ij.macro.Interpreter.doStatements(Interpreter.java:218)
at ij.macro.Interpreter.run(Interpreter.java:115)
at ij.macro.Interpreter.run(Interpreter.java:85)
at ij.macro.Interpreter.run(Interpreter.java:96)
at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
at ij.IJ.runMacro(IJ.java:134)
at ij.IJ.runMacro(IJ.java:123)
at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052)
at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048)
at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:999)
at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048)
at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:136)
at org.scijava.script.ScriptModule.run(ScriptModule.java:159)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:237)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)






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Re: Java exception error related to extended particle analyzer

ctrueden
Hi Volko,

When I run your example code in the Script Editor, I got the error message:
"works with 8-bit binary images only". I then changed my foreground color
to white (Edit > Options > Colors), and then your macro ran, including
generation of the same error message you are seeing.

Unfortunately, I am out of time for today to dig further into the issue.

Did you post this on the ImageJ Forum? There you can specifically mention
@BioVoxxel, increasing the chance that the author will see it. Or you could
file an issue directly in the BioVoxxel Toolbox GitHub Issues here:
https://github.com/biovoxxel/BioVoxxel_Toolbox/issues

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Sun, Oct 22, 2017 at 2:55 AM, Straub, Volko A. (Dr.) <
[hidden email]> wrote:

> Dear All,
>
> I am a bit stumped by a Java exception error that appears to be related to
> the Advanced Particle Analyzer. It doesn't appear to affect the function of
> the Advanced Particle Analyzer, but it generates a window with an error
> message. I have written the following small macro code to illustrate the
> problem:
>
> for (k=0; k<3; k++) {
>
> newImage("Test"+k, "8-bit black", 1000, 1000, 1);
> for (i=1;i<11;i++){
> makeOval(random*1000, random*1000, random*50, random*50);
> run("Fill", "slice");
> makeLine(random*1000, random*1000,random*1000, random*1000);
>   run("Fill", "slice");
> };
> run("Extended Particle Analyzer", "pixel solidity=0.5-1.00 aspect=0-100
> show=Masks redirect=None keep=None display reset");
> wait(2000);
> rename("Blobs"+k);
> imageCalculator("Subtract  create", "Test"+k,"Blobs"+k);
> rename("Lines"+k);
> close("Blobs"+k);
> close("Test"+k);
> };
>
>
>
> The macro code creates an image containing random lines and ovals. It then
> use the Advanced Particle Analyzer to find 'blob' like structures and
> subtract them from the original image. Carrying out all the commands
> manually (or just once using the macro code without the outer for loop)
> produces the expected result without any exceptions.
>
>
> However, putting the code inside the for-loop to carry it out multiple
> times (i.e. to batch process a series of images) throws a Java exception (I
> have copied the error message below) on the second and all subsequent
> images.
>
>
> I thought that this may be a timing issue and added a wait command after
> the Extended Particle Analyzer command, but it didn't solve the problem.
>
>
> I have updated ImageJ to the latest version (v1.51r) and also updated the
> Biovoxxel tools via the Fiji update site, but the issue persists.
>
>
> Any idea what might be going on?
>
>
> Thanks,
>
> Volko
>
>
>
>
> Java error message text (doesn't appear to be terminal as code continues):
>
>
> (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; Windows
> 10 10.0; 97MB of 5938MB (1%)
>
> java.lang.IllegalArgumentException: "Label" column not found
> at ij.measure.ResultsTable.getValue(ResultsTable.java:376)
> at Extended_Particle_Analyzer.particleAnalysis(Extended_Particl
> e_Analyzer.java:680)
> at Extended_Particle_Analyzer.run(Extended_Particle_Analyzer.java:340)
> at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFi
> lterRunner.java:265)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
> at ij.IJ.runUserPlugIn(IJ.java:219)
> at ij.IJ.runPlugIn(IJ.java:181)
> at ij.Executer.runCommand(Executer.java:137)
> at ij.Executer.run(Executer.java:66)
> at ij.IJ.run(IJ.java:297)
> at ij.macro.Functions.doRun(Functions.java:601)
> at ij.macro.Functions.doFunction(Functions.java:96)
> at ij.macro.Interpreter.doStatement(Interpreter.java:230)
> at ij.macro.Interpreter.doBlock(Interpreter.java:608)
> at ij.macro.Interpreter.doStatement(Interpreter.java:272)
> at ij.macro.Interpreter.doFor(Interpreter.java:530)
> at ij.macro.Interpreter.doStatement(Interpreter.java:254)
> at ij.macro.Interpreter.doStatements(Interpreter.java:218)
> at ij.macro.Interpreter.run(Interpreter.java:115)
> at ij.macro.Interpreter.run(Interpreter.java:85)
> at ij.macro.Interpreter.run(Interpreter.java:96)
> at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
> at ij.IJ.runMacro(IJ.java:134)
> at ij.IJ.runMacro(IJ.java:123)
> at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052)
> at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048)
> at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:999)
> at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048)
> at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:136)
> at org.scijava.script.ScriptModule.run(ScriptModule.java:159)
> at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
> at org.scijava.thread.DefaultThreadService$3.call(DefaultThread
> Service.java:237)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
> Executor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
> lExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Java exception error related to extended particle analyzer

Volko Straub
Thanks Curtis for the suggestion - I should have thought about reporting it directly on the Biovoxxel Toolbox GitHub site.
I have now reported it on the site.
Cheers,
Volko


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: 06 November 2017 22:49
To: [hidden email]
Subject: Re: Java exception error related to extended particle analyzer

Hi Volko,

When I run your example code in the Script Editor, I got the error message:
"works with 8-bit binary images only". I then changed my foreground color to white (Edit > Options > Colors), and then your macro ran, including generation of the same error message you are seeing.

Unfortunately, I am out of time for today to dig further into the issue.

Did you post this on the ImageJ Forum? There you can specifically mention @BioVoxxel, increasing the chance that the author will see it. Or you could file an issue directly in the BioVoxxel Toolbox GitHub Issues here:
https://github.com/biovoxxel/BioVoxxel_Toolbox/issues

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/


On Sun, Oct 22, 2017 at 2:55 AM, Straub, Volko A. (Dr.) < [hidden email]> wrote:

> Dear All,
>
> I am a bit stumped by a Java exception error that appears to be
> related to the Advanced Particle Analyzer. It doesn't appear to affect
> the function of the Advanced Particle Analyzer, but it generates a
> window with an error message. I have written the following small macro
> code to illustrate the
> problem:
>
> for (k=0; k<3; k++) {
>
> newImage("Test"+k, "8-bit black", 1000, 1000, 1); for (i=1;i<11;i++){
> makeOval(random*1000, random*1000, random*50, random*50); run("Fill",
> "slice"); makeLine(random*1000, random*1000,random*1000, random*1000);
>   run("Fill", "slice");
> };
> run("Extended Particle Analyzer", "pixel solidity=0.5-1.00
> aspect=0-100 show=Masks redirect=None keep=None display reset");
> wait(2000); rename("Blobs"+k); imageCalculator("Subtract  create",
> "Test"+k,"Blobs"+k); rename("Lines"+k); close("Blobs"+k);
> close("Test"+k); };
>
>
>
> The macro code creates an image containing random lines and ovals. It
> then use the Advanced Particle Analyzer to find 'blob' like structures
> and subtract them from the original image. Carrying out all the
> commands manually (or just once using the macro code without the outer
> for loop) produces the expected result without any exceptions.
>
>
> However, putting the code inside the for-loop to carry it out multiple
> times (i.e. to batch process a series of images) throws a Java
> exception (I have copied the error message below) on the second and
> all subsequent images.
>
>
> I thought that this may be a timing issue and added a wait command
> after the Extended Particle Analyzer command, but it didn't solve the problem.
>
>
> I have updated ImageJ to the latest version (v1.51r) and also updated
> the Biovoxxel tools via the Fiji update site, but the issue persists.
>
>
> Any idea what might be going on?
>
>
> Thanks,
>
> Volko
>
>
>
>
> Java error message text (doesn't appear to be terminal as code continues):
>
>
> (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit];
> Windows
> 10 10.0; 97MB of 5938MB (1%)
>
> java.lang.IllegalArgumentException: "Label" column not found at
> ij.measure.ResultsTable.getValue(ResultsTable.java:376)
> at Extended_Particle_Analyzer.particleAnalysis(Extended_Particl
> e_Analyzer.java:680)
> at Extended_Particle_Analyzer.run(Extended_Particle_Analyzer.java:340)
> at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFi
> lterRunner.java:265)
> at
> ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114
> )
> at ij.IJ.runUserPlugIn(IJ.java:219)
> at ij.IJ.runPlugIn(IJ.java:181)
> at ij.Executer.runCommand(Executer.java:137)
> at ij.Executer.run(Executer.java:66)
> at ij.IJ.run(IJ.java:297)
> at ij.macro.Functions.doRun(Functions.java:601)
> at ij.macro.Functions.doFunction(Functions.java:96)
> at ij.macro.Interpreter.doStatement(Interpreter.java:230)
> at ij.macro.Interpreter.doBlock(Interpreter.java:608)
> at ij.macro.Interpreter.doStatement(Interpreter.java:272)
> at ij.macro.Interpreter.doFor(Interpreter.java:530)
> at ij.macro.Interpreter.doStatement(Interpreter.java:254)
> at ij.macro.Interpreter.doStatements(Interpreter.java:218)
> at ij.macro.Interpreter.run(Interpreter.java:115)
> at ij.macro.Interpreter.run(Interpreter.java:85)
> at ij.macro.Interpreter.run(Interpreter.java:96)
> at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
> at ij.IJ.runMacro(IJ.java:134)
> at ij.IJ.runMacro(IJ.java:123)
> at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052)
> at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048)
> at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:999)
> at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048)
> at
> net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:136)
> at org.scijava.script.ScriptModule.run(ScriptModule.java:159)
> at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
> at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
> at org.scijava.thread.DefaultThreadService$3.call(DefaultThread
> Service.java:237)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
> Executor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
> lExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Java exception error related to extended particle analyzer

gankaku
Dear Volko,

I have seen the issue you filed and will have a look at this. Hopefully I
can provide a solution by next week.

Kind regards,
Jan

2017-11-07 10:36 GMT+01:00 Straub, Volko A. (Dr.) <[hidden email]>:

> Thanks Curtis for the suggestion - I should have thought about reporting
> it directly on the Biovoxxel Toolbox GitHub site.
> I have now reported it on the site.
> Cheers,
> Volko
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: 06 November 2017 22:49
> To: [hidden email]
> Subject: Re: Java exception error related to extended particle analyzer
>
> Hi Volko,
>
> When I run your example code in the Script Editor, I got the error message:
> "works with 8-bit binary images only". I then changed my foreground color
> to white (Edit > Options > Colors), and then your macro ran, including
> generation of the same error message you are seeing.
>
> Unfortunately, I am out of time for today to dig further into the issue.
>
> Did you post this on the ImageJ Forum? There you can specifically mention
> @BioVoxxel, increasing the chance that the author will see it. Or you could
> file an issue directly in the BioVoxxel Toolbox GitHub Issues here:
> https://github.com/biovoxxel/BioVoxxel_Toolbox/issues
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
> know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Sun, Oct 22, 2017 at 2:55 AM, Straub, Volko A. (Dr.) <
> [hidden email]> wrote:
>
> > Dear All,
> >
> > I am a bit stumped by a Java exception error that appears to be
> > related to the Advanced Particle Analyzer. It doesn't appear to affect
> > the function of the Advanced Particle Analyzer, but it generates a
> > window with an error message. I have written the following small macro
> > code to illustrate the
> > problem:
> >
> > for (k=0; k<3; k++) {
> >
> > newImage("Test"+k, "8-bit black", 1000, 1000, 1); for (i=1;i<11;i++){
> > makeOval(random*1000, random*1000, random*50, random*50); run("Fill",
> > "slice"); makeLine(random*1000, random*1000,random*1000, random*1000);
> >   run("Fill", "slice");
> > };
> > run("Extended Particle Analyzer", "pixel solidity=0.5-1.00
> > aspect=0-100 show=Masks redirect=None keep=None display reset");
> > wait(2000); rename("Blobs"+k); imageCalculator("Subtract  create",
> > "Test"+k,"Blobs"+k); rename("Lines"+k); close("Blobs"+k);
> > close("Test"+k); };
> >
> >
> >
> > The macro code creates an image containing random lines and ovals. It
> > then use the Advanced Particle Analyzer to find 'blob' like structures
> > and subtract them from the original image. Carrying out all the
> > commands manually (or just once using the macro code without the outer
> > for loop) produces the expected result without any exceptions.
> >
> >
> > However, putting the code inside the for-loop to carry it out multiple
> > times (i.e. to batch process a series of images) throws a Java
> > exception (I have copied the error message below) on the second and
> > all subsequent images.
> >
> >
> > I thought that this may be a timing issue and added a wait command
> > after the Extended Particle Analyzer command, but it didn't solve the
> problem.
> >
> >
> > I have updated ImageJ to the latest version (v1.51r) and also updated
> > the Biovoxxel tools via the Fiji update site, but the issue persists.
> >
> >
> > Any idea what might be going on?
> >
> >
> > Thanks,
> >
> > Volko
> >
> >
> >
> >
> > Java error message text (doesn't appear to be terminal as code
> continues):
> >
> >
> > (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit];
> > Windows
> > 10 10.0; 97MB of 5938MB (1%)
> >
> > java.lang.IllegalArgumentException: "Label" column not found at
> > ij.measure.ResultsTable.getValue(ResultsTable.java:376)
> > at Extended_Particle_Analyzer.particleAnalysis(Extended_Particl
> > e_Analyzer.java:680)
> > at Extended_Particle_Analyzer.run(Extended_Particle_Analyzer.java:340)
> > at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFi
> > lterRunner.java:265)
> > at
> > ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114
> > )
> > at ij.IJ.runUserPlugIn(IJ.java:219)
> > at ij.IJ.runPlugIn(IJ.java:181)
> > at ij.Executer.runCommand(Executer.java:137)
> > at ij.Executer.run(Executer.java:66)
> > at ij.IJ.run(IJ.java:297)
> > at ij.macro.Functions.doRun(Functions.java:601)
> > at ij.macro.Functions.doFunction(Functions.java:96)
> > at ij.macro.Interpreter.doStatement(Interpreter.java:230)
> > at ij.macro.Interpreter.doBlock(Interpreter.java:608)
> > at ij.macro.Interpreter.doStatement(Interpreter.java:272)
> > at ij.macro.Interpreter.doFor(Interpreter.java:530)
> > at ij.macro.Interpreter.doStatement(Interpreter.java:254)
> > at ij.macro.Interpreter.doStatements(Interpreter.java:218)
> > at ij.macro.Interpreter.run(Interpreter.java:115)
> > at ij.macro.Interpreter.run(Interpreter.java:85)
> > at ij.macro.Interpreter.run(Interpreter.java:96)
> > at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
> > at ij.IJ.runMacro(IJ.java:134)
> > at ij.IJ.runMacro(IJ.java:123)
> > at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052)
> > at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048)
> > at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:999)
> > at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048)
> > at
> > net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:136)
> > at org.scijava.script.ScriptModule.run(ScriptModule.java:159)
> > at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
> > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
> > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
> > at org.scijava.thread.DefaultThreadService$3.call(DefaultThread
> > Service.java:237)
> > at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
> > Executor.java:1142)
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
> > lExecutor.java:617)
> > at java.lang.Thread.run(Thread.java:745)
> >
> >
> >
> >
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Java exception error related to extended particle analyzer

gankaku
In reply to this post by Volko Straub
Dear Volko and all others using the Extended Particle Analyzer,

the bug reported by Volko regarding a java error regarding the results
table label column when analyzing multiple images and collecting results
should be fixed in the new version of the BioVoxxel Toolbox version 1.1.8.
So, all interested, please update the toolbox.

Kind regards,
Jan

2017-11-07 10:36 GMT+01:00 Straub, Volko A. (Dr.) <[hidden email]>:

> Thanks Curtis for the suggestion - I should have thought about reporting
> it directly on the Biovoxxel Toolbox GitHub site.
> I have now reported it on the site.
> Cheers,
> Volko
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: 06 November 2017 22:49
> To: [hidden email]
> Subject: Re: Java exception error related to extended particle analyzer
>
> Hi Volko,
>
> When I run your example code in the Script Editor, I got the error message:
> "works with 8-bit binary images only". I then changed my foreground color
> to white (Edit > Options > Colors), and then your macro ran, including
> generation of the same error message you are seeing.
>
> Unfortunately, I am out of time for today to dig further into the issue.
>
> Did you post this on the ImageJ Forum? There you can specifically mention
> @BioVoxxel, increasing the chance that the author will see it. Or you could
> file an issue directly in the BioVoxxel Toolbox GitHub Issues here:
> https://github.com/biovoxxel/BioVoxxel_Toolbox/issues
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
> know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Sun, Oct 22, 2017 at 2:55 AM, Straub, Volko A. (Dr.) <
> [hidden email]> wrote:
>
> > Dear All,
> >
> > I am a bit stumped by a Java exception error that appears to be
> > related to the Advanced Particle Analyzer. It doesn't appear to affect
> > the function of the Advanced Particle Analyzer, but it generates a
> > window with an error message. I have written the following small macro
> > code to illustrate the
> > problem:
> >
> > for (k=0; k<3; k++) {
> >
> > newImage("Test"+k, "8-bit black", 1000, 1000, 1); for (i=1;i<11;i++){
> > makeOval(random*1000, random*1000, random*50, random*50); run("Fill",
> > "slice"); makeLine(random*1000, random*1000,random*1000, random*1000);
> >   run("Fill", "slice");
> > };
> > run("Extended Particle Analyzer", "pixel solidity=0.5-1.00
> > aspect=0-100 show=Masks redirect=None keep=None display reset");
> > wait(2000); rename("Blobs"+k); imageCalculator("Subtract  create",
> > "Test"+k,"Blobs"+k); rename("Lines"+k); close("Blobs"+k);
> > close("Test"+k); };
> >
> >
> >
> > The macro code creates an image containing random lines and ovals. It
> > then use the Advanced Particle Analyzer to find 'blob' like structures
> > and subtract them from the original image. Carrying out all the
> > commands manually (or just once using the macro code without the outer
> > for loop) produces the expected result without any exceptions.
> >
> >
> > However, putting the code inside the for-loop to carry it out multiple
> > times (i.e. to batch process a series of images) throws a Java
> > exception (I have copied the error message below) on the second and
> > all subsequent images.
> >
> >
> > I thought that this may be a timing issue and added a wait command
> > after the Extended Particle Analyzer command, but it didn't solve the
> problem.
> >
> >
> > I have updated ImageJ to the latest version (v1.51r) and also updated
> > the Biovoxxel tools via the Fiji update site, but the issue persists.
> >
> >
> > Any idea what might be going on?
> >
> >
> > Thanks,
> >
> > Volko
> >
> >
> >
> >
> > Java error message text (doesn't appear to be terminal as code
> continues):
> >
> >
> > (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit];
> > Windows
> > 10 10.0; 97MB of 5938MB (1%)
> >
> > java.lang.IllegalArgumentException: "Label" column not found at
> > ij.measure.ResultsTable.getValue(ResultsTable.java:376)
> > at Extended_Particle_Analyzer.particleAnalysis(Extended_Particl
> > e_Analyzer.java:680)
> > at Extended_Particle_Analyzer.run(Extended_Particle_Analyzer.java:340)
> > at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFi
> > lterRunner.java:265)
> > at
> > ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114
> > )
> > at ij.IJ.runUserPlugIn(IJ.java:219)
> > at ij.IJ.runPlugIn(IJ.java:181)
> > at ij.Executer.runCommand(Executer.java:137)
> > at ij.Executer.run(Executer.java:66)
> > at ij.IJ.run(IJ.java:297)
> > at ij.macro.Functions.doRun(Functions.java:601)
> > at ij.macro.Functions.doFunction(Functions.java:96)
> > at ij.macro.Interpreter.doStatement(Interpreter.java:230)
> > at ij.macro.Interpreter.doBlock(Interpreter.java:608)
> > at ij.macro.Interpreter.doStatement(Interpreter.java:272)
> > at ij.macro.Interpreter.doFor(Interpreter.java:530)
> > at ij.macro.Interpreter.doStatement(Interpreter.java:254)
> > at ij.macro.Interpreter.doStatements(Interpreter.java:218)
> > at ij.macro.Interpreter.run(Interpreter.java:115)
> > at ij.macro.Interpreter.run(Interpreter.java:85)
> > at ij.macro.Interpreter.run(Interpreter.java:96)
> > at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
> > at ij.IJ.runMacro(IJ.java:134)
> > at ij.IJ.runMacro(IJ.java:123)
> > at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1052)
> > at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1048)
> > at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:999)
> > at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1048)
> > at
> > net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:136)
> > at org.scijava.script.ScriptModule.run(ScriptModule.java:159)
> > at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
> > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
> > at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
> > at org.scijava.thread.DefaultThreadService$3.call(DefaultThread
> > Service.java:237)
> > at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
> > Executor.java:1142)
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
> > lExecutor.java:617)
> > at java.lang.Thread.run(Thread.java:745)
> >
> >
> >
> >
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
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>
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>



--

CEO: Dr. Jan Brocher
phone: +49 (0)176 705 746 81
e-mail: [hidden email]
info: [hidden email]
inquiries: [hidden email]
web: www.biovoxxel.de

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