macro/batch issue

[David Gene Morgan]

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Hi,

        I've written a macro that strips the metadata out of Digital Micrograph
image.  I use a self-written wrapper to start imageJ and the following
command works well:

        imageJ -macro getMetaData FILE.dm3

I have a second macro that should work in batch mode (no GUI, so no open
windows) but when I run it

        imageJ -batch getMetaDataBatch FILE.dm3

I get an error that indicates an inability to find/use the plugin to
read DM3 files.  This seems to be specific for the DM3 plugin since I
can run the batch process using a few other "more standard" file types.

        I may be able to solve this by mucking about with the java environment,
but I figure someone else may know exactly what to do.  Thanks for any help.


- --
                 David Gene Morgan
                  cryoEM Facility
                  005B Simon Hall
           Indiana University Bloomington
               812 856 1457 (office)
               812 856 3221 (EM lab)
            http://bio.indiana.edu/~cryo
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[Wayne Rasband]

> Hi,
>
> I've written a macro that strips the metadata out of Digital  
> Micrograph
> image.  I use a self-written wrapper to start imageJ and the following
> command works well:
>
> imageJ -macro getMetaData FILE.dm3
>
> I have a second macro that should work in batch mode (no GUI, so no  
> open
> windows) but when I run it
>
> imageJ -batch getMetaDataBatch FILE.dm3
>
> I get an error that indicates an inability to find/use the plugin to
> read DM3 files.  This seems to be specific for the DM3 plugin since I
> can run the batch process using a few other "more standard" file  
> types.
>
> I may be able to solve this by mucking about with the java  
> environment,
> but I figure someone else may know exactly what to do.  Thanks for  
> any help.

This bug is fixed in the 1.43f daily build or you can work around it  
by generating a full path in the macro using

     name = getArgument();
     dir = getInfo("user.dir");
     path = dir+File.separator+name;

-wayne