Re: Thresholder in headless macro mode results in NullPointerException

Posted by Rasband, Wayne (NIH/NIMH) [E] on Oct 08, 2014; 8:04pm
URL: http://imagej.273.s1.nabble.com/Thresholder-in-headless-macro-mode-results-in-NullPointerException-tp5009940p5009968.html

On Oct 7, 2014, at 10:32 AM, Konrad Rokicki wrote:

> Hi all,
>
> I'm trying to run a macro on a cluster. I can use Xvfb, but it's very hard
> to debug problems when dialog boxes popup while this is running on a
> cluster. So I thought I'd try Fiji's headless mode:
>
> ImageJ-linux64 --headless -macro macro.ijm
>
> Most of the macro works well, but I can't seem to get the Thresholder to
> work. I reduced the problem to a very simple macro:
>
> open("test.tif");
> setThreshold(77, 173);
> run("Convert to Mask", "method=Default background=Dark black");
>
> This results in a strange exception:
>
> java.lang.NullPointerException
>    at ij.plugin.Thresholder.convertStack(Thresholder.java:75)

This bug is fixed in the latest ImageJ daily build (1.49i13). The GenericDialog.getChoices() method call at line 74 in Thresholder.java returns null in headless mode.

-wayne

>    at ij.plugin.Thresholder.run(Thresholder.java:48)
>    at ij.IJ.runPlugIn(IJ.java:172)
>    at ij.Executer.runCommand(Executer.java:131)
>    at ij.Executer.run(Executer.java:64)
>    at ij.IJ.run(IJ.java:272)
>    at ij.macro.Functions.doRun(Functions.java:591)
>    at ij.macro.Functions.doFunction(Functions.java:89)
>    at ij.macro.Interpreter.doStatement(Interpreter.java:227)
>    at ij.macro.Interpreter.doStatements(Interpreter.java:215)
>    at ij.macro.Interpreter.run(Interpreter.java:112)
>    at ij.macro.Interpreter.run(Interpreter.java:82)
>    at ij.macro.Interpreter.run(Interpreter.java:93)
>    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:133)
>    at net.imagej.legacy.IJ1Helper.runMacroFile(IJ1Helper.java:802)
>    at
> net.imagej.legacy.LegacyCommandline$Macro.handle(LegacyCommandline.java:178)
>    at
> org.scijava.console.DefaultConsoleService.processArgs(DefaultConsoleService.java:75)
>    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:39)
>    at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>    at java.lang.reflect.Method.invoke(Method.java:597)
>    at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>    at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>    at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>
> After inspecting the Plugin's source code, I can't find any reason this
> exception might occur at that location. I'm guessing this has to do with
> the way Fiji is instrumenting the dialog portions of the plugin to remove
> the dependency on AWT?
>
> The exception seems very similar to the one I was getting when I was trying
> to use run("Colors...", "background=black"). I was able to fix that by
> switching to setBackgroundColor(), so I wonder if there's also a workaround
> for running the thresholder.
>
> I should mention that I've tried using various versions of Fiji, including
> the lifeline versions and the latest build.
>
> Thank you,
> Konrad
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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