[ome-devel] loci_tools.jar 1280+ series limit?
Rubén Muñoz
ruben.munoz at embl.de
Fri Jun 4 17:54:52 BST 2010
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
>>
>
>
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