[ome-users] Bioformats Exporter plugin in Fiji

[Roger Leigh]

Dear Lorenz,

I can reproduce your problem with the macro recorder.  I have created a
ticket for this:  http://trac.openmicroscopy.org.uk/ome/ticket/12123

Regarding the options, I'm afraid I'll have to defer to others more
expert here regarding the imagej plugin internals.  I can't see anything
but the "save" option being actively set by the plugin, so I'm unsure
from where the "write" and "compression" parts of the string are set
(and even the use of "save" is odd given that "outfile" is preferred,
though this is likely a separate point).  It's unclear to me the
distinction between Macro.getOptions and plugin.arg, and why only "save"
is obtained from Macro.getOptions, and not the other options.  Can
anyone clarify this?

If invoked via Java, the split values are set in the run() method, and
the initial values are set from splitZ/splitC/splitT values obtained
from Macro.getValue().  So long as you can arrange for the values to be
set prior to invocation, this should work.  However, if this is where
the bug lies, it will still fail of course.  While you can call the java
interface directly, the only entry point is the run() method, which
still limits the argument passing to the LociExporter arg string when
you construct it.


Kind regards,
Roger

On 23/03/14 14:08, Maier, Lorenz wrote:
> Dear all,
>
> am I right that the only way to use the splitting options of the
> Bioformats Expporter with the ImageJ macro interface is checking the
> Macro.getOptions()?
>
> Would there be any way to circumvent this, maybe by calling the Java
> interface of the Exporter directly?
[...]
>
> is there a reason why the bioformats exporter checks only at plugin.arg
> if splitting C,Z,T is requested? In my eyes, the code should also check
> Macro.getOptions(). The code in question starts at
>   bioformats/components/bio-formats-plugins/src/loci/plugins/out/Exporter.java, line 127.
>
> The selection of these options is neither recorded correctly using the
> macro recorder. It inserts “write write write” in the options and shows
> a warning that this is probably wrong.


--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096