Hello there,
You need to add a wait in your macro after calling the plugin so the GUI
has time to get loaded. Have a look at the example in the wiki (line 6):
https://imagej.net/Morphological_Segmentation# Complete_macro_example:
Cheers!
On Wed, Jun 28, 2017 at 12:43 AM, GP <[hidden email]> wrote:
> Hie!
>
> On normal execution of 'Morphological Segmentation' plugin from
> 'MorphoLibJ'
> works fine but on execution via macro with exact same settings leads to the
> following two exception error windows:
>
> 1) Exception Error Window:
> (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51p; Java 1.8.0_66 [64-bit]; Mac OS X
> 10.12.5; 62MB of 2854MB (2%)
>
> java.lang.reflect.InvocationTargetException
> 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 ij.macro.Functions.call(Functions.java:4131)
> at ij.macro.Functions.getStringFunction(Functions. java:272)
> at ij.macro.Interpreter.getStringTerm(Interpreter. java:1307)
> at ij.macro.Interpreter.getString(Interpreter.java: 1286)
> at ij.macro.Interpreter.doStatement(Interpreter.java: 294)
> at ij.macro.Interpreter.doStatements(Interpreter.java: 231)
> at ij.macro.Interpreter.run(Interpreter.java:115)
> at ij.macro.Interpreter.run(Interpreter.java:86)
> at ij.macro.Interpreter.run(Interpreter.java:97)
> 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)
> Caused by: java.lang.NullPointerException
> at
> inra.ijpb.plugins.MorphologicalSegmentation$ CustomWindow.
> getResultDisplayOption(MorphologicalSegmentation. java:1450)
> at
> inra.ijpb.plugins.MorphologicalSegmentation. createResultImage(
> MorphologicalSegmentation.java:1763)
> ... 30 more
>
>
> 2) Exception Error Window:
> (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51p; Java 1.8.0_66 [64-bit]; Mac OS X
> 10.12.5; 61MB of 2854MB (2%)
>
> java.lang.reflect.InvocationTargetException
> 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 ij.macro.Functions.call(Functions.java:4131)
> at ij.macro.Functions.getStringFunction(Functions. java:272)
> at ij.macro.Interpreter.getStringTerm(Interpreter. java:1307)
> at ij.macro.Interpreter.getString(Interpreter.java: 1286)
> at ij.macro.Interpreter.doStatement(Interpreter.java: 294)
> at ij.macro.Interpreter.doStatements(Interpreter.java: 231)
> at ij.macro.Interpreter.run(Interpreter.java:115)
> at ij.macro.Interpreter.run(Interpreter.java:86)
> at ij.macro.Interpreter.run(Interpreter.java:97)
> 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)
> Caused by: java.lang.NullPointerException
> at
> inra.ijpb.plugins.MorphologicalSegmentation$ CustomWindow.
> setResultDisplayOption(MorphologicalSegmentation. java:1441)
> at
> inra.ijpb.plugins.MorphologicalSegmentation. setDisplayFormat(
> MorphologicalSegmentation.java:1829)
> ... 30 more
>
>
> And following message is displayed in the log window:
> Error: Morphological Segmentation GUI not detected
>
> Macro code used is as follows:
>
> run("Morphological Segmentation");
> call("inra.ijpb.plugins.MorphologicalSegmentation. setInputImageType",
> "object");
> call("inra.ijpb.plugins.MorphologicalSegmentation. setGradientRadius",
> "1");
> call("inra.ijpb.plugins.MorphologicalSegmentation. segment",
> "tolerance=10",
> "calculateDams=true", "connectivity=4");
> call("inra.ijpb.plugins.MorphologicalSegmentation. setDisplayFormat",
> "Catchment basins");
> call("inra.ijpb.plugins.MorphologicalSegmentation. createResultImage");
>
> Thank you so much for your help.
> Best Regards,
>
>
>
>
>
>
> --
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> com/Re-Exception-Error-on-MorphologicalSegmentation-
> Plugin-Execution-from-Macro-tp5018975.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain
Phone : <a href="tel:+34%20943%2001%2073%2025" value="+34943017325" target="_blank">+34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html >
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