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Bug 540 - exception runnig maccro
exception runnig maccro
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2012-12-20 23:42 CST by bugzilla-fiji
Modified: 2013-01-29 23:47 CST
2 users (show)

See Also:
Description bugzilla-fiji 2012-12-20 23:42:30 CST 
I had a macro running fine interactively, from the command line with a display, but not from the command line headless. 
I came here to file a bug report, but when I saw that the up-to-date check said "needs upgrade", I've upgraded and now the problem is even worse.

I invoke fiji/imagej, start plugins/macro/record then call one of the stitching functions.  Everything works fine, produces the proper output. I then save the macro, which consists of one line:

run("Grid/Collection stitching", "type=[Grid: row-by-row] order=[Right & Down                ] grid_size_x=3 grid_size_y=11 tile_overlap=10 first_file_index_i=1 directory=/tmp/tiles file_names=tile_{ii}.jpg output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=5 absolute_displacement_threshold=10 compute_overlap subpixel_accuracy computation_parameters=[Save memory (but be slower)] image_output=[Write to disk] output_directory=/tmp/tiles");

If I immediately, or in any subsequent runs, try to invoke that macro, from Plugins/Macro/run I get an exception:

java.lang.reflect.InvocationTargetException
	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 ij.Command.runPlugIn(Command.java:146)
	at ij.Command.runCommand(Command.java:95)
	at ij.Executer.run(Executer.java:64)
	at ij.IJ.run(IJ.java:250)
	at ij.macro.Functions.doRun(Functions.java:580)
	at ij.macro.Functions.doFunction(Functions.java:83)
	at ij.macro.Interpreter.doStatement(Interpreter.java:219)
	at ij.macro.Interpreter.doStatements(Interpreter.java:207)
	at ij.macro.Interpreter.run(Interpreter.java:104)
	at ij.macro.Interpreter.run(Interpreter.java:74)
	at ij.macro.Interpreter.run(Interpreter.java:85)
	at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:105)
	at ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:90)
	at ij.plugin.Macro_Runner.run(Macro_Runner.java:28)
	at ij.IJ.runPlugIn(IJ.java:157)
	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 ij.Command.runPlugIn(Command.java:146)
	at ij.Command.runCommand(Command.java:95)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.NullPointerException: cannot add null item to Choice
	at java.awt.Choice.insertNoInvalidate(Choice.java:208)
	at java.awt.Choice.addItem(Choice.java:189)
	at ij.gui.GenericDialog.addChoice(GenericDialog.java:445)
	at plugin.GridType.<init>(GridType.java:94)
	at plugin.Stitching_Grid.run(Stitching_Grid.java:96)
	at ij.IJ.runUserPlugIn(IJ.java:184)
	at ij.IJ.runPlugIn(IJ.java:151)
	... 27 more

Confused ...



Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => amd64
  os.name => Linux
  os.version => 3.6.10-2.fc17.x86_64
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /usr/local/bin/fiji/java/linux-amd64/jdk1.6.0_24/jre/
  ij.dir => /usr/local/bin/fiji

Information about the version of each plugin:

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Comment 1 bugzilla-fiji 2012-12-20 23:57:02 CST 
This seems to be a problem with the stitching plugin as I can record and run other macros fine...
Comment 2 Curtis Rueden 2013-01-28 19:43:10 CST 
This may be the same issue as bug #551. Are you still having the problem?
Comment 3 bugzilla-fiji 2013-01-29 22:40:17 CST 
Just downloaded the latest fiji and it seems to work.
My recorded macro that calls the stitching plugin still doesn't run in headless mode, but at least it runs again.
I use it weekly to process a bunch of scans, if the problem shows up again at the next run I'll report back.
Thanks