Hi Damon,
The latest trunk build of Bio-Formats supports use of the "quiet" flag to
suppress errors and log output from the Bio-Formats Importer, for the most
part. Your colleague can try doing something like:
run("Bio-Formats Importer", "quiet open=/data/image.zvi view=Hyperstack
stack_order=XYCZT");
Using this command in a loop should allow the macro to continue, even if one
of the files is missing or has a problem opening. There may be exceptions --
the quiet flag is a bit of a hack -- but hopefully this helps.
If your colleague needs more sophisticated error handling, we advise to
write a Java plugin instead of using a macro, to take advantage of try/catch
constructs.
-Curtis
On Fri, May 15, 2009 at 1:51 AM, Damon Poburko <
[hidden email]>wrote:
> Hi All,
>
> A quick question on behalf of a colleague. He is using the LOCI Bioformats
> importer in a macro to load Zeiss ".zvi" files for analysis. Usually this
> goes smoothly, but when the LOCI importer cannot read a file, it crashes the
> macro. He would like to incorporate some kind of error handling step into
> his macro to step past the bad file and carry on to the next file. At the
> moment, he is trying to use the Bioformats Macro Extensions to find some
> parameter to use as a checkpoint, but he having problems with the syntax of
> these extensions. If anyone has elt with this problem and has any
> suggestions for how to keep the importer for stopping a macro when it can't
> open a file we'd be all ears.
>
> Many thanks,
> Damon
>
>
> --
>
> Damon Poburko, PhD
> Postdoctoral Research Fellow
> Stanford University School of Medicine
> Dept. of Molecular & Cellular Physiology
> 279 Campus Dr., Beckman B103, Stanford, CA 94305
> Ph: 650 725 7564, fax: 650 725 8021
>
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