Macro Instability?

[AdamC]

I'm writing a simple macro to take a 4D dataset, separate three channels,
project one, and merge two channels into a composite hyperstack, then save
all of the results (5 files). The macro works fine for a while, but after
2-5 runs it stops saving the last file (the composite hyperstack). It also
produces the following java error.

java.lang.NullPointerException
        at ij.CompositeImage.getChannelLut(CompositeImage.java:456)
        at ij.io.FileSaver.saveDisplayRangesAndLuts(FileSaver.java:132)
        at ij.io.FileSaver.saveAsTiffStack(FileSaver.java:112)
        at ij.io.FileSaver.saveAsTiff(FileSaver.java:69)
        at ij.plugin.filter.Writer.run(Writer.java:20)
        at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:243)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
        at ij.IJ.runPlugIn(IJ.java:133)
        at ij.Executer.runCommand(Executer.java:104)
        at ij.Executer.run(Executer.java:58)
        at ij.IJ.run(IJ.java:247)
        at ij.IJ.saveAs(IJ.java:1196)
        at ij.macro.Functions.saveAs(Functions.java:2268)
        at ij.macro.Functions.doFunction(Functions.java:136)
        at ij.macro.Interpreter.doStatement(Interpreter.java:205)
        at ij.macro.Interpreter.doBlock(Interpreter.java:515)
        at ij.macro.Interpreter.runMacro(Interpreter.java:119)
        at ij.macro.MacroRunner.run(MacroRunner.java:105)
        at java.lang.Thread.run(Thread.java:619)

Does anyone know what might cause a macro to behave differently at different
times? Restarting ImageJ seems to solve the problem (for a few iterations).

Thanks

Adam

[jmutterer]

This issue has been fixed in version 1.41a.
http://rsb.info.nih.gov/ij/notes.html

Jerome


On Mon, Apr 28, 2008 at 5:15 AM, Adam Cliffe <[hidden email]> wrote:

> I'm writing a simple macro to take a 4D dataset, separate three channels,
> project one, and merge two channels into a composite hyperstack, then save
> all of the results (5 files). The macro works fine for a while, but after
> 2-5 runs it stops saving the last file (the composite hyperstack). It also
> produces the following java error.
>
> java.lang.NullPointerException
>        at ij.CompositeImage.getChannelLut(CompositeImage.java:456)
>        at ij.io.FileSaver.saveDisplayRangesAndLuts(FileSaver.java:132)
>        at ij.io.FileSaver.saveAsTiffStack(FileSaver.java:112)
>        at ij.io.FileSaver.saveAsTiff(FileSaver.java:69)
>        at ij.plugin.filter.Writer.run(Writer.java:20)
>        at
>
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:243)
>        at
> ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
>        at ij.IJ.runPlugIn(IJ.java:133)
>        at ij.Executer.runCommand(Executer.java:104)
>        at ij.Executer.run(Executer.java:58)
>        at ij.IJ.run(IJ.java:247)
>        at ij.IJ.saveAs(IJ.java:1196)
>        at ij.macro.Functions.saveAs(Functions.java:2268)
>        at ij.macro.Functions.doFunction(Functions.java:136)
>        at ij.macro.Interpreter.doStatement(Interpreter.java:205)
>        at ij.macro.Interpreter.doBlock(Interpreter.java:515)
>        at ij.macro.Interpreter.runMacro(Interpreter.java:119)
>        at ij.macro.MacroRunner.run(MacroRunner.java:105)
>        at java.lang.Thread.run(Thread.java:619)
>
> Does anyone know what might cause a macro to behave differently at
> different
> times? Restarting ImageJ seems to solve the problem (for a few
> iterations).
>
> Thanks
>
> Adam
>

[AdamC]

Nope, my problem still exists using 1.41a (I've tried most of the  
versions from 1.39d-1.41a)

It somehow seems to be affected by the length of the file name (or at  
least it seems to work ok sometimes with relatively short file names).
ImageJ does manage to run the macro without problems some of the  
time, which makes it less obvious (to me) what is going wrong.

adam

On 28 Apr 2008, at 14:13, Jerome Mutterer wrote:

> This issue has been fixed in version 1.41a.
> http://rsb.info.nih.gov/ij/notes.html
>
> Jerome
>
>
> On Mon, Apr 28, 2008 at 5:15 AM, Adam Cliffe <[hidden email]>  
> wrote:
>
>> I'm writing a simple macro to take a 4D dataset, separate three  
>> channels,
>> project one, and merge two channels into a composite hyperstack,  
>> then save
>> all of the results (5 files). The macro works fine for a while,  
>> but after
>> 2-5 runs it stops saving the last file (the composite hyperstack).  
>> It also
>> produces the following java error.
>>
>> java.lang.NullPointerException
>>        at ij.CompositeImage.getChannelLut(CompositeImage.java:456)
>>        at ij.io.FileSaver.saveDisplayRangesAndLuts(FileSaver.java:
>> 132)
>>        at ij.io.FileSaver.saveAsTiffStack(FileSaver.java:112)
>>        at ij.io.FileSaver.saveAsTiff(FileSaver.java:69)
>>        at ij.plugin.filter.Writer.run(Writer.java:20)
>>        at
>>
>> ij.plugin.filter.PlugInFilterRunner.processOneImage
>> (PlugInFilterRunner.java:243)
>>        at
>> ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:
>> 102)
>>        at ij.IJ.runPlugIn(IJ.java:133)
>>        at ij.Executer.runCommand(Executer.java:104)
>>        at ij.Executer.run(Executer.java:58)
>>        at ij.IJ.run(IJ.java:247)
>>        at ij.IJ.saveAs(IJ.java:1196)
>>        at ij.macro.Functions.saveAs(Functions.java:2268)
>>        at ij.macro.Functions.doFunction(Functions.java:136)
>>        at ij.macro.Interpreter.doStatement(Interpreter.java:205)
>>        at ij.macro.Interpreter.doBlock(Interpreter.java:515)
>>        at ij.macro.Interpreter.runMacro(Interpreter.java:119)
>>        at ij.macro.MacroRunner.run(MacroRunner.java:105)
>>        at java.lang.Thread.run(Thread.java:619)
>>
>> Does anyone know what might cause a macro to behave differently at
>> different
>> times? Restarting ImageJ seems to solve the problem (for a few
>> iterations).
>>
>> Thanks
>>
>> Adam
>>

Dr Adam Cliffe
Research Fellow
Rørth Lab
Cell Migration Group
Temasek Lifescience Laboratory
1 Research Link
National University of Singapore
Singapore 117604

tel: [phone]
fax: [phone]

[Wayne Rasband]

This bug is fixed in ImageJ 1.41b. You can upgrade by running the  
Plugins>Utilities>Update ImageJ command and selecting "daily build"  
from the drop down menu.

-wayne

On Apr 27, 2008, at 11:15 PM, Adam Cliffe wrote:

> I'm writing a simple macro to take a 4D dataset, separate three  
> channels,
> project one, and merge two channels into a composite hyperstack, then  
> save
> all of the results (5 files). The macro works fine for a while, but  
> after
> 2-5 runs it stops saving the last file (the composite hyperstack). It  
> also
> produces the following java error.
>
> java.lang.NullPointerException
> at ij.CompositeImage.getChannelLut(CompositeImage.java:456)
> at ij.io.FileSaver.saveDisplayRangesAndLuts(FileSaver.java:132)
> at ij.io.FileSaver.saveAsTiffStack(FileSaver.java:112)
> at ij.io.FileSaver.saveAsTiff(FileSaver.java:69)
> at ij.plugin.filter.Writer.run(Writer.java:20)
> at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.
> java:243)
> at  
> ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:
> 102)
> at ij.IJ.runPlugIn(IJ.java:133)
> at ij.Executer.runCommand(Executer.java:104)
> at ij.Executer.run(Executer.java:58)
> at ij.IJ.run(IJ.java:247)
> at ij.IJ.saveAs(IJ.java:1196)
> at ij.macro.Functions.saveAs(Functions.java:2268)
> at ij.macro.Functions.doFunction(Functions.java:136)
> at ij.macro.Interpreter.doStatement(Interpreter.java:205)
> at ij.macro.Interpreter.doBlock(Interpreter.java:515)
> at ij.macro.Interpreter.runMacro(Interpreter.java:119)
> at ij.macro.MacroRunner.run(MacroRunner.java:105)
> at java.lang.Thread.run(Thread.java:619)
>
> Does anyone know what might cause a macro to behave differently at  
> different
> times? Restarting ImageJ seems to solve the problem (for a few  
> iterations).
>
> Thanks
>
> Adam
>