Re: error in Fiji headless mode at convolve step

Posted by Mark Hiner on Feb 11, 2016; 3:28pm
URL: http://imagej.273.s1.nabble.com/error-in-Fiji-headless-mode-at-convolve-step-tp5015595p5015606.html

Hello,

>It makes me think the convolve step is failing. Thoughts?

Based on the line number, it looks like the kernel is null[1]. The kernel
is only set in the dialogItemChanged method[2] - which means I do not think
there is a way to perform convolution headlessly with this class.

If you open up the Script Editor[3] in Fiji, under "Templates > Tutorials >
Create and Convolve Points" there is actually an example of convolution
using ImageJ Ops - part of the ImageJ2 framework, which emphasizes
decoupling algorithms from user interface.

If you give it a try and have any questions, most Ops discussion takes
place on the ImageJ forum.[4]

Hope that helps.

Regards,
Mark Hiner
ImageJ2 developer
LOCI, UW-Madison


[1]
https://github.com/imagej/ImageJA/blob/40afa1d8cf4b4ca74a16f25fba711dd7fd4d2142/src/main/java/ij/plugin/filter/Convolver.java#L177
[2]
https://github.com/imagej/ImageJA/blob/40afa1d8cf4b4ca74a16f25fba711dd7fd4d2142/src/main/java/ij/plugin/filter/Convolver.java#L83
[3] http://imagej.net/Using_the_Script_Editor
[4] http://forum.imagej.net/



On Wed, Feb 10, 2016 at 2:20 PM, samjlord <[hidden email]> wrote:

> Hi all,
>
> I have a macro that at one step convolves the image with a kernel. When I
> run the macro from Fiji, everything works fine. When I run it in headless
> mode, something goes wrong: instead of convolving like it does in normal
> mode, it seems to skip that step.
>
> I see the following message when I run in headless mode:
>
>
> > ERROR: java.lang.NullPointerException
> > in Convolve... 600-899
> > at ij.plugin.filter.Convolver.convolve(Convolver.java:177)
> > from ij.plugin.filter.Convolver.run(Convolver.java:63)
> > java.lang.NullPointerException
> >       at ij.plugin.filter.Convolver.convolve(Convolver.java:177)
> >       at ij.plugin.filter.Convolver.run(Convolver.java:63)
> >       at
> >
> ij.plugin.filter.PlugInFilterRunner.processChannelUsingThreads(PlugInFilterRunner.java:330)
> >       at
> >
> ij.plugin.filter.PlugInFilterRunner.processImageUsingThreads(PlugInFilterRunner.java:299)
> >       at
> >
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:234)
> >       at ij.plugin.filter.PlugInFilterRunner.
> > <init>
> > (PlugInFilterRunner.java:112)
> >       at ij.IJ.runPlugIn(IJ.java:184)
> >       at ij.Executer.runCommand(Executer.java:136)
> >       at ij.Executer.run(Executer.java:65)
> >       at ij.IJ.run(IJ.java:292)
> >       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:153)
> >       at ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:137)
> >       at ij.IJ.runMacroFile(IJ.java:143)
> >       at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:952)
> >       at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:949)
> >       at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:899)
> >       at net.imagej.legacy.IJ1Helper.runMacroFile(IJ1Helper.java:949)
> >       at
> >
> net.imagej.legacy.LegacyCommandline$Macro.handle(LegacyCommandline.java:188)
> >       at
> >
> org.scijava.console.DefaultConsoleService.processArgs(DefaultConsoleService.java:93)
> >       at
> >
> net.imagej.legacy.LegacyConsoleService.processArgs(LegacyConsoleService.java:76)
> >       at net.imagej.Main.launch(Main.java:64)
> >       at net.imagej.Main.main(Main.java:73)
> >       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >       at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> >       at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> >       at java.lang.reflect.Method.invoke(Method.java:497)
> >       at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
> >       at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
> >       at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
>
> It makes me think the convolve step is failing. Thoughts? (This is on a
> Mac,
> but also fails on a PC. Fiji updated.)
>
> Here's a shortened version of the macro that also fails the same way with
> some comparative images:
> https://www.dropbox.com/sh/gaf2hgvnjlge53y/AAAucdebIHDfjwC56W5iysjIa?dl=0
>
>
>
> --
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> Sent from the ImageJ mailing list archive at Nabble.com.
>
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