<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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> <a href="http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980">http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980</a> </div><div><br></div><div>Best regards,</div><div><br></div><div>Rubén</div><br><div><div>On May 27, 2010, at 10:02 AM, Rubén Muńoz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Melissa, <div><br></div><div>Sorry but the problem seems to remain. I reproduce it as follows:</div><div><br></div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="highlightedSearchTerm">svn</span> co <a href="http://skyking.microscopy.wisc.edu/">http://skyking.microscopy.wisc.edu/</a><span class="highlightedSearchTerm">svn</span>/java/trunk my-bio-formats/trunk<span class="Apple-style-span" style="font-family: Helvetica; white-space: normal; "> </span></span></div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="Apple-style-span" style="font-family: Helvetica; white-space: normal; "><span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">cd my-bio-formats/trunk</span></span></span></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre;">ant tools</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre;">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">http://hudson.openmicroscopy.org.uk/job/LOCI/lastSuccessfulBuild/artifact/trunk/artifacts/loci_tools.jar</a>)</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre;">open /Applications/Fiji.app</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre;">Plugins->LOCI->Bioformats Importer->experiment_descriptor.xml (Use Virtual Stack)</span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre;"><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 class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.SeriesDialog.rebuildDialog(SeriesDialog.java:244)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.SeriesDialog.constructDialog(SeriesDialog.java:179)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.ImporterDialog.showDialog(ImporterDialog.java:79)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.ImporterPrompter.promptSeries(ImporterPrompter.java:138)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.ImporterPrompter.statusUpdated(ImporterPrompter.java:85)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.ImportProcess.notifyListeners(ImportProcess.java:377)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.ImportProcess.step(ImportProcess.java:618)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.Importer.showDialogs(Importer.java:124)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.in.Importer.run(Importer.java:77)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at loci.plugins.LociImporter.run(LociImporter.java:77)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.IJ.runUserPlugIn(IJ.java:183)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.IJ.runPlugIn(IJ.java:150)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.Executer.runCommand(Executer.java:145)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>at ij.Executer.run(Executer.java:76)</div><div><span class="Apple-tab-span" style="white-space:pre"> </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 class="Apple-interchange-newline"><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">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">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 <ruben.munoz@embl.de> 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></body></html>