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

Thu Jun 3 23:27:06 BST 2010

Hi Rubén,

FYI, this problem with large numbers of series should be fixed in the latest
trunk. There are still problems with the series chooser dialog box beyond
~1200 on Linux, or ~3000 or so on Mac OS X, but since you are calling from a
macro, it will hopefully work. This bugfix will be incorporated into the 4.2
release later this month. See ticket #493 (
https://skyking.microscopy.wisc.edu/trac/java/ticket/493) for more details.

In general, please note that the Bio-Formats Importer plugin has been going
through many changes lately, but we're nearing the end—I'll be sending
another email to the OME and ImageJ lists with more details early next week.

Regards,
Curtis

2010/6/2 Rubén Muñoz <ruben.munoz at embl.de>

> Hi Melissa,
>
> Let me to get back to you regarding the series number topic.
> You probably already know, but for those people that may face the same
> problem in the future, it only arises when using:  run("Bio-Formats
> Importer",op);
>
> Changing the code to the Bio-Formats Macro Extensions walks around the
> graphical Java bug
>  http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980
>
> Best regards,
>
> Rubén
>
> On May 27, 2010, at 10:02 AM, Rubén Muñoz wrote:
>
> Hi Melissa,
>
> Sorry but the problem seems to remain. I reproduce it as follows:
>
> svn co http://skyking.microscopy.wisc.edu/svn/java/trunk
> my-bio-formats/trunk
> cd my-bio-formats/trunk
> ant tools
> cp artifacts/loci_tools.jar /Applications/Fiji.app/plugins/ (also tried to
> download
> http://hudson.openmicroscopy.org.uk/job/LOCI/lastSuccessfulBuild/artifact/trunk/artifacts/loci_tools.jar
> )
> open /Applications/Fiji.app
> Plugins->LOCI->Bioformats Importer->experiment_descriptor.xml (Use Virtual
> Stack)
>
> Am I missing something? Seems like an ScanR specific problem.
>
> I never update the plugin with the auto updater, but the exception follow
> up:
>
> 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:183)
> at ij.IJ.runPlugIn(IJ.java:150)
> at ij.Executer.runCommand(Executer.java:145)
>  at ij.Executer.run(Executer.java:76)
> at java.lang.Thread.run(Thread.java:637)
>
> Thanks and best regards,
>
> Rubén
>
> On 20 May, 2010, at 5:27 PM, Melissa Linkert wrote:
>
> 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
>
>
>
>
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>
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