[ome-devel] loci_tools.jar 1280+ series limit?

[Melissa Linkert]

Hi Rubén,

> Before going into debugging, I would like to ask you if you are concerned about a maximum number of > series that the LOCI plugin of Fiji will handle.

Unfortunately, yes, there are some issues with opening large numbers
of series using the Bio-Formats plugin for ImageJ.  Basically, it
comes down to this Java bug:

http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980

However, we do have a work-around for this, so you should not be
seeing an exception.  I did try to duplicate the problem using a 4000
series test dataset, but was able to see the series chooser window
without any error messages.  This was with the very latest trunk build
(r6348), so you may wish to try updating and see if the exception goes
away.

Unfortunately, even though the window displays, series beyond #456 are
not visible.  I have filed a ticket for this problem on our Trac issue
tracker.  You have been CC'd on the ticket, and so will receive an
automated email with "LOCI Software" in the subject line when the
problem is fixed.  In case anyone else is interested, the ticket can
be viewed here:

https://skyking.microscopy.wisc.edu/trac/java/ticket/493

> I am having trouble to open an ScanR with 4000+ series with a Fiji Macro. Well... this may not be the
> best idea but at the moment I convert to multi-file ome.tif this way.

We're working on making the API for multi-file export more friendly,
so with the 4.2 release you should be able to use bfconvert to
directly create a multi-file OME-TIFF dataset.

Regards,
-Melissa

On Wed, May 19, 2010 at 2:51 AM, Rubén Muñoz <ruben.munoz at embl.de> wrote:
> Hi Melissa,
>
> Before going into debugging, I would like to ask you if you are concerned about a maximum number of series that the LOCI plugin of Fiji will handle.
>
> I am having trouble to open an ScanR with 4000+ series with a Fiji Macro. Well... this may not be the best idea but at the moment I convert to multi-file ome.tif this way. Any idea would be appreciated.
>
> Please note that the set is converting with bfconvert. I could provide the set to to you on demand only because is really big.
>
> java.lang.ArrayIndexOutOfBoundsException: 1280
>        at loci.plugins.in.SeriesDialog.rebuildDialog(SeriesDialog.java:244)
>        at loci.plugins.in.SeriesDialog.constructDialog(SeriesDialog.java:179)
>        at loci.plugins.in.ImporterDialog.showDialog(ImporterDialog.java:79)
>        at loci.plugins.in.ImporterPrompter.promptSeries(ImporterPrompter.java:138)
>        at loci.plugins.in.ImporterPrompter.statusUpdated(ImporterPrompter.java:85)
>        at loci.plugins.in.ImportProcess.notifyListeners(ImportProcess.java:377)
>        at loci.plugins.in.ImportProcess.step(ImportProcess.java:618)
>        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
>        at loci.plugins.in.Importer.showDialogs(Importer.java:124)
>        at loci.plugins.in.Importer.run(Importer.java:77)
>        at loci.plugins.LociImporter.run(LociImporter.java:77)
>        at ij.IJ.runUserPlugIn(IJ.java:189)
>        at ij.IJ.runPlugIn(IJ.java:155)
>        at ij.Executer.runCommand(Executer.java:147)
>        at ij.Executer.run(Executer.java:78)
>        at java.lang.Thread.run(Thread.java:637)
>
> Best wishes,
> Ruben