Re: Using UnwarpJ in a macro

Posted by Herbie on Mar 22, 2017; 9:43am
URL: http://imagej.273.s1.nabble.com/Using-UnwarpJ-in-a-macro-tp5018342p5018346.html

Dear Ron,

I guess the character following "UnwarpJ" is not a blank but an
underscore -- no?

HTH

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Am 21.03.17 um 20:33 schrieb Paletzki, Ron (NIH/NIMH) [E]:

> I am trying to register multichannel images and I’ve tried most of
> the plugins in Fiji’s registration plugins folder.   Using UnwarpJ I
> can take the channel containing a nissl stain and register it to our
> reference images (target) and save the transformation which I can
> then apply individually to the other channels containing different
> fluorescent signals.  This works but we have 1000 of images so I need
> to write a macro to automate this task.  So I read the UnwarpJ web
> page and copied and ran a one line macro to try and align two open
> images (target_299.tif and source_299.tif).  I get the Exception
> listed below.  Any ideas or help would be greatly appreciated.
>
> The macro line is run("UnwarpJ","-align target_299.tif NULL
> source_299.tif NULL 0 2 0 0 1 output.tif");
>
> By the way on all examples I could find of macros using UnwarpJ, the
> run(“UnwarpJ “ call always has a space after UnwarpJ right before the
> quotation mark.  If I run that I get an “Unrecognized command:
> “UnwarpJ “” error, but if I remove the space it appears to start the
> command but some other error occurs.
>
> Thanks for any help Ron
>
> EXCEPTION (Fiji Is Just) ImageJ 2.0.0-rc-59/1.51j; Java 1.8.0_66
> [64-bit]; Mac OS X 10.12.3; 127MB of 17339MB (<1%)
>
> java.lang.NullPointerException at
> UnwarpJ_.alignImagesMacro(UnwarpJ_.java:244) at
> UnwarpJ_.run(UnwarpJ_.java:152) at ij.IJ.runUserPlugIn(IJ.java:217)
> 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.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:1039) at
> net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1035) at
> net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:986) at
> net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1035) at
> net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:97)
> at
> net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:144)
>
>

at org.scijava.script.ScriptModule.run(ScriptModule.java:177)
> 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$2.call(DefaultThreadService.java:191)
>
>
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>
>
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
>
>
>
>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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