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

[Rubén Muñoz]

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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