[ome-users] Writing conventional TIFF through BioFormats exporter

[Curtis Rueden]

Hi Simon,

> What I still can't do is prevent the popup for the compression type.

Yeah, the issue was a bit tricky. I took a crack at it and came up with
this workaround:

https://gist.github.com/ctrueden/5805462

Hope it helps you. There is probably a simpler way but I don't have time to
investigate further.

Regards,
Curtis


On Tue, Jun 18, 2013 at 7:36 AM, simon andrews <simon.andrews at babraham.ac.uk
> wrote:

>
> On 18 Jun 2013, at 11:55, Curtis Rueden wrote:
>
> > Good point. A similar approach would be to programmatically invoke the
> Bio-Formats Exporter at the same level ImageJ would internally:
> >
> > LociExporter bfExporter = new LociExporter();
> > bfExporter.setup(arg, myImagePlus);
> > bfExporter.run(null); // ImageProcessor argument is ignored here
> >
> > Where "arg" is the same argument string passed to run.
>
> OK, I'm nearly there, but I think I might be stuck at the end.  After a
> lot of going through the source for the plugins I can now use the method
> you suggested above along with a command string such as:
>
> outfile=[d:/whatever/file.tif] splitz=[0] splitc=[0] splitt=[0]
>
> ..to get the filename set and to not prompt for the splitting options.
>  What I still can't do is prevent the popup for the compression type.
>  Looking at the Exporter.java code I don't think it's possible to do this
> as the plugin.arg value is read at the start of the run() method but only
> the outfile, splitZ, splitC and splitT values are read, then plugin.arg is
> set to null so there's no way to get anything out of there after that.  The
> compression options code also doesn't seem to have any logic to read a
> default value.
>
> If this is right then I can't see that I can do what I need through the
> plugin interface.  Am I reading this right or am I still missing something?
>
> Cheers
>
> Simon.
>
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