Hi Rubén,<br><br>Sorry for the long delay in my reply. We were struggling to get Bio-Formats 4.2 out the door, as you know.<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;"><div>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. </div></div></blockquote><div><br>Sounds good.<br><br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;"><div>About
a multi-fie OME.TIF export: Have code as an ImageJ Macro. May be useful
to you just let me know.</div></div></blockquote><div><br>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.<br>
<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div style="word-wrap: break-word;"><div>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.</div></div></blockquote><div><br>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:<br>
<br><a href="http://www.loci.wisc.edu/trac/java/browser/tags/loci-tools-4.2.0/components/loci-plugins/src/loci/plugins/BF.java#L80">http://www.loci.wisc.edu/trac/java/browser/tags/loci-tools-4.2.0/components/loci-plugins/src/loci/plugins/BF.java#L80</a><br>
<br>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. :-)<br><br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;"><div>Let's keep in touch, A
new Leica format was just released as multi file OME.TIF. Do you have
example sets?</div></div></blockquote><div><br>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!<br>
<br>-Curtis<br><br></div></div><div class="gmail_quote">On Fri, Jun 4, 2010 at 11:54 AM, Rubén Muńoz <span dir="ltr"><<a href="mailto:ruben.munoz@embl.de">ruben.munoz@embl.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;">Hi Curtis, <div><br></div><div>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. </div>
<div><br></div><div>About a multi-fie OME.TIF export: Have code as an ImageJ Macro. May be useful to you just let me know.</div><div><br></div><div>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.</div>
<div><br></div><div>Let's keep in touch, A new Leica format was just released as multi file OME.TIF. Do you have example sets?</div><div><br></div><div>Regards,</div><div><br></div><font color="#888888"><div>Rubén</div>
</font><div><div></div><div class="h5"><div><br></div><div><div><div>On Jun 4, 2010, at 12:27 AM, Curtis Rueden wrote:</div><br><blockquote type="cite">Hi Rubén,<br><br>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 (<a href="https://skyking.microscopy.wisc.edu/trac/java/ticket/493" target="_blank">https://skyking.microscopy.wisc.edu/trac/java/ticket/493</a>) for more details.<br>
<br>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.<br>
<br>Regards,<br>Curtis<br><br><div class="gmail_quote">2010/6/2 Rubén Muńoz <span dir="ltr"><<a href="mailto:ruben.munoz@embl.de" target="_blank">ruben.munoz@embl.de</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;"><div>Hi Melissa, </div><div><br></div><div>Let me to get back to you regarding the series number topic. </div><div>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);</div>
<div><br></div><div>Changing the code to the Bio-Formats Macro Extensions walks around the graphical Java bug</div><div><div> <a href="http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980" target="_blank">http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980</a> </div>
<div><br></div></div><div>Best regards,</div><div><br></div><font color="#888888"><div>Rubén</div></font><div><div></div><div><br><div><div>On May 27, 2010, at 10:02 AM, Rubén Muńoz wrote:</div><br><blockquote type="cite">
<div style="word-wrap: break-word;">Hi Melissa, <div><br></div><div>Sorry but the problem seems to remain. I reproduce it as follows:</div><div><br></div><div><span style="font-family: monospace; white-space: pre-wrap;"><span>svn</span> co <a href="http://skyking.microscopy.wisc.edu/" target="_blank">http://skyking.microscopy.wisc.edu/</a><span>svn</span>/java/trunk my-bio-formats/trunk<span style="font-family: Helvetica; white-space: normal;"> </span></span></div>
<div><span style="font-family: monospace; white-space: pre-wrap;"><span style="font-family: Helvetica; white-space: normal;"><span style="font-family: monospace; white-space: pre-wrap;">cd my-bio-formats/trunk</span></span></span></div>
<div><font face="monospace"><span style="white-space: pre-wrap;">ant tools</span></font></div><div><font face="monospace"><span style="white-space: pre-wrap;">cp artifacts/loci_tools.jar /Applications/Fiji.app/plugins/ (also tried to download <a href="http://hudson.openmicroscopy.org.uk/job/LOCI/lastSuccessfulBuild/artifact/trunk/artifacts/loci_tools.jar" target="_blank">http://hudson.openmicroscopy.org.uk/job/LOCI/lastSuccessfulBuild/artifact/trunk/artifacts/loci_tools.jar</a>)</span></font></div>
<div><font face="monospace"><span style="white-space: pre-wrap;">open /Applications/Fiji.app</span></font></div><div><font face="monospace"><span style="white-space: pre-wrap;">Plugins->LOCI->Bioformats Importer->experiment_descriptor.xml (Use Virtual Stack)</span></font></div>
<div><font face="monospace"><span style="white-space: pre-wrap;"><br></span></font></div><div>Am I missing something? Seems like an ScanR specific problem.</div><div><br></div><div>I never update the plugin with the auto updater, but the exception follow up:</div>
<div><br></div><div><div>java.lang.ArrayIndexOutOfBoundsException: 1280</div><div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.SeriesDialog.rebuildDialog(SeriesDialog.java:244)</div><div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.SeriesDialog.constructDialog(SeriesDialog.java:179)</div>
<div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.ImporterDialog.showDialog(ImporterDialog.java:79)</div><div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.ImporterPrompter.promptSeries(ImporterPrompter.java:138)</div>
<div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.ImporterPrompter.statusUpdated(ImporterPrompter.java:85)</div><div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.ImportProcess.notifyListeners(ImportProcess.java:377)</div>
<div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.ImportProcess.step(ImportProcess.java:618)</div><div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)</div>
<div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.Importer.showDialogs(Importer.java:124)</div><div><span style="white-space: pre-wrap;"> </span>at loci.plugins.in.Importer.run(Importer.java:77)</div><div>
<span style="white-space: pre-wrap;"> </span>at loci.plugins.LociImporter.run(LociImporter.java:77)</div>
<div><span style="white-space: pre-wrap;"> </span>at ij.IJ.runUserPlugIn(IJ.java:183)</div><div><span style="white-space: pre-wrap;"> </span>at ij.IJ.runPlugIn(IJ.java:150)</div><div><span style="white-space: pre-wrap;"> </span>at ij.Executer.runCommand(Executer.java:145)</div>
<div><span style="white-space: pre-wrap;"> </span>at ij.Executer.run(Executer.java:76)</div><div><span style="white-space: pre-wrap;"> </span>at java.lang.Thread.run(Thread.java:637)</div><div><br></div><div>Thanks and best regards,</div>
<div><br></div><div>Rubén</div></div><div><br></div><div>On 20 May, 2010, at 5:27 PM, Melissa Linkert wrote:</div><div><div><br><blockquote type="cite"><div>Hi Rubén,<br><br><blockquote type="cite">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.<br>
</blockquote><br>Unfortunately, yes, there are some issues with opening large numbers<br>of series using the Bio-Formats plugin for ImageJ. Basically, it<br>comes down to this Java bug:<br><br><a href="http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980" target="_blank">http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980</a><br>
<br>However, we do have a work-around for this, so you should not be<br>seeing an exception. I did try to duplicate the problem using a 4000<br>series test dataset, but was able to see the series chooser window<br>without any error messages. This was with the very latest trunk build<br>
(r6348), so you may wish to try updating and see if the exception goes<br>away.<br><br>Unfortunately, even though the window displays, series beyond #456 are<br>not visible. I have filed a ticket for this problem on our Trac issue<br>
tracker. You have been CC'd on the ticket, and so will receive an<br>automated email with "LOCI Software" in the subject line when the<br>problem is fixed. In case anyone else is interested, the ticket can<br>
be viewed here:<br><br><a href="https://skyking.microscopy.wisc.edu/trac/java/ticket/493" target="_blank">https://skyking.microscopy.wisc.edu/trac/java/ticket/493</a><br><br><blockquote type="cite">I am having trouble to open an ScanR with 4000+ series with a Fiji Macro. Well... this may not be the<br>
</blockquote><blockquote type="cite">best idea but at the moment I convert to multi-file ome.tif this way.<br></blockquote><br>We're working on making the API for multi-file export more friendly,<br>so with the 4.2 release you should be able to use bfconvert to<br>
directly create a multi-file OME-TIFF dataset.<br><br>Regards,<br>-Melissa<br><br>On Wed, May 19, 2010 at 2:51 AM, Rubén Muńoz <<a href="mailto:ruben.munoz@embl.de" target="_blank">ruben.munoz@embl.de</a>> wrote:<br>
<blockquote type="cite">Hi Melissa,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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.<br>
</blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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.<br>
</blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Please note that the set is converting with bfconvert. I could provide the set to to you on demand only because is really big.<br></blockquote>
<blockquote type="cite"><br></blockquote><blockquote type="cite">java.lang.ArrayIndexOutOfBoundsException: 1280<br></blockquote><blockquote type="cite"> at loci.plugins.in.SeriesDialog.rebuildDialog(SeriesDialog.java:244)<br>
</blockquote><blockquote type="cite"> at loci.plugins.in.SeriesDialog.constructDialog(SeriesDialog.java:179)<br></blockquote><blockquote type="cite"> at loci.plugins.in.ImporterDialog.showDialog(ImporterDialog.java:79)<br>
</blockquote><blockquote type="cite"> at loci.plugins.in.ImporterPrompter.promptSeries(ImporterPrompter.java:138)<br></blockquote><blockquote type="cite"> at loci.plugins.in.ImporterPrompter.statusUpdated(ImporterPrompter.java:85)<br>
</blockquote><blockquote type="cite"> at loci.plugins.in.ImportProcess.notifyListeners(ImportProcess.java:377)<br></blockquote><blockquote type="cite"> at loci.plugins.in.ImportProcess.step(ImportProcess.java:618)<br>
</blockquote><blockquote type="cite"> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)<br></blockquote><blockquote type="cite"> at loci.plugins.in.Importer.showDialogs(Importer.java:124)<br></blockquote>
<blockquote type="cite"> at loci.plugins.in.Importer.run(Importer.java:77)<br></blockquote><blockquote type="cite"> at loci.plugins.LociImporter.run(LociImporter.java:77)<br></blockquote><blockquote type="cite">
at ij.IJ.runUserPlugIn(IJ.java:189)<br></blockquote><blockquote type="cite"> at ij.IJ.runPlugIn(IJ.java:155)<br></blockquote><blockquote type="cite"> at ij.Executer.runCommand(Executer.java:147)<br></blockquote>
<blockquote type="cite"> at ij.Executer.run(Executer.java:78)<br></blockquote><blockquote type="cite"> at java.lang.Thread.run(Thread.java:637)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">
Best wishes,<br></blockquote><blockquote type="cite">Ruben<br></blockquote></div></blockquote></div><br></div></div></blockquote></div><br></div></div></div><br>_______________________________________________<br>
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