[ome-users] Bioformats Exporter plugin in Fiji

[Melissa Linkert]

Hi Jan,

> >I can reproduce your problem with the macro recorder.  I have created a
> >ticket for this:  http://trac.openmicroscopy.org.uk/ome/ticket/12123
> 
> This should be fixed with the pull request:
> https://github.com/openmicroscopy/bioformats/pull/986

Thank you very much for submitting a pull request.  We are reviewing it
now, and will follow up there with any questions or comments.

Barring any (unlikely!) major issues, I would expect this fix to be included
in the upcoming 5.0.1 release.

Regards,
-Melissa

On Mon, Mar 24, 2014 at 07:29:09PM +0100, Jan Eglinger wrote:
> Dear all,
> 
> On 24.03.2014, 5:08 PM, Roger Leigh wrote:
> >I can reproduce your problem with the macro recorder.  I have created a
> >ticket for this:  http://trac.openmicroscopy.org.uk/ome/ticket/12123
> 
> This should be fixed with the pull request:
> https://github.com/openmicroscopy/bioformats/pull/986
> 
> >
> >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?
> >
> 
> The macro parameters are recorded via three instances of
> ij.gui.GenericDialog shown in sequence. The second dialog is the one
> to blame, because all three parameters started with "write" followed
> by a space. The macro recorder records boolean options by taking the
> checkbox label up to the first space as a parameter, so all three
> options result in a simple "write". Adding underscores changes will
> make the macro code look like:
> 
> run("Bio-Formats Exporter", "save=/tmp/4.ome.tif
> write_each_z_section write_each_timepoint write_each_channel
> compression=Uncompressed");
> 
> (The "compression" parameter is recorded by the third dialog.)
> 
> Hope that helps,
> 
> Jan
> (Fiji user, and contributor once in a while : )
> 
> 
> >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.
> >
> 
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