[ome-devel] loci_tools.jar 1280+ series limit?
Curtis Rueden
ctrueden at wisc.edu
Mon Jul 19 22:49:02 BST 2010
Hi Rubén,
Sorry for the long delay in my reply. We were struggling to get Bio-Formats
4.2 out the door, as you know.
Nice to hear from you. We currently find bio-formats more useful and our
> next goal is to collaborate with Leica and use Bio-Formats to make their
> latest OME.TIF incorporate SPW features. There are special interests in
> that.
>
Sounds good.
About a multi-fie OME.TIF export: Have code as an ImageJ Macro. May be
> useful to you just let me know.
>
If your macro is working for you, great. The eventual goal is to update the
Bio-Formats Exporter plugin to support multi-file OME-TIFF export, but it is
not an urgent priority for us.
I understand that the bug "#493 Series beyond 456 do not appear in ImageJ
> plugin" should go, but the SeriesDialog is only useful for smaller sets.
> Could one type the series manually? When using run("Bio-Formats Importer",
> "... series_1"); it still instantiates a SeriesDialog but doesn't show it
> before the exception.
>
Right. At the moment, the BF.openImagePlus call plow through all the ImageJ
GenericDialog instantiations—sorry to hear that causes a problem for you. In
theory, it is unnecessary to do so; see this note in the code:
http://www.loci.wisc.edu/trac/java/browser/tags/loci-tools-4.2.0/components/loci-plugins/src/loci/plugins/BF.java#L80
However, it has not been well tested to comment out the use of
ImporterPrompter. But feel free to give it a shot with your many-series data
and let us know how it goes. :-)
Let's keep in touch, A new Leica format was just released as multi file
> OME.TIF. Do you have example sets?
>
Hmm, not to my knowledge. We have some in the old "LOME" format, but looking
through our samples, nothing in this new Leica OME-TIFF-based format that I
could see. If you have a sample dataset you are willing to pass along to
Melissa, we would highly appreciate it!
-Curtis
On Fri, Jun 4, 2010 at 11:54 AM, Rubén Muñoz <ruben.munoz at embl.de> wrote:
> Hi Curtis,
>
> Nice to hear from you. We currently find bio-formats more useful and our
> next goal is to collaborate with Leica and use Bio-Formats to make their
> latest OME.TIF incorporate SPW features. There are special interests in
> that.
>
> About a multi-fie OME.TIF export: Have code as an ImageJ Macro. May be
> useful to you just let me know.
>
> I understand that the bug "#493 Series beyond 456 do not appear in ImageJ
> plugin" should go, but the SeriesDialog is only useful for smaller sets.
> Could one type the series manually? When using run("Bio-Formats Importer",
> "... series_1"); it still instantiates a SeriesDialog but doesn't show it
> before the exception.
>
> Let's keep in touch, A new Leica format was just released as multi file
> OME.TIF. Do you have example sets?
>
> Regards,
>
> Rubén
>
> On Jun 4, 2010, at 12:27 AM, Curtis Rueden wrote:
>
> 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
>>
>>
>>
>>
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>>
>
>
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