Hi Jonas,<div><br></div><div><div>> java.lang.IllegalArgumentException: 0 must not be null and positive.</div></div><div><br></div><div>That is actually great news. It means we fixed the problem with the update site. Now there is most likely a bona fide bug in Bio-Formats.</div>
<div><br></div><div>Would you be willing to send us a problematic dataset, so that we can address the issue? You can use Fiji's Help > Upload Sample Image feature to send it if is smaller than ~250MB.</div><div><br>
</div><div>But first, just to be sure: please run Help > Update Fiji and make sure it says your Fiji is fully up to date, with no locally modified files.</div><div><br></div><div>Thanks,</div><div>Curtis</div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Thu, Dec 13, 2012 at 6:42 AM, Jonas Øgaard <span dir="ltr"><<a href="mailto:jonas@ogaard.no" target="_blank">jonas@ogaard.no</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
OK, back at work today. Here is trace log after attempting to import using LOCI:<div><br></div><div><div><font face="courier new, monospace">java.lang.reflect.InvocationTargetException</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at java.lang.reflect.Method.invoke(Method.java:601)</font></div><div class="im"><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at ij.Command.runPlugIn(Command.java:146)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at ij.Command.runCommand(Command.java:95)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at ij.Executer.run(Executer.java:64)</font></div>
</div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at java.lang.Thread.run(Thread.java:722)</font></div><div><font face="courier new, monospace">Caused by: java.lang.IllegalArgumentException: 0 must not be null and positive.</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:272)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:246)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.ChannelFiller.setId(ChannelFiller.java:267)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:285)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImportProcess.setId(ImportProcess.java:682)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:519)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:150)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.plugins.in.Importer.showDialogs(Importer.java:141)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.plugins.in.Importer.run(Importer.java:79)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at loci.plugins.LociImporter.run(LociImporter.java:81)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at ij.IJ.runUserPlugIn(IJ.java:184)</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>at ij.IJ.runPlugIn(IJ.java:151)</font></div><div><font face="courier new, monospace"><span style="white-space:pre-wrap"> </span>... 8 more</font></div>
</div><div><br></div><div>Sincerely,</div><div>Jonas Ogaard</div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Dec 11, 2012 at 11:17 PM, Jonas Øgaard <span dir="ltr"><<a href="mailto:jonas@ogaard.no" target="_blank">jonas@ogaard.no</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi again, Curtis!<div><br><div class="gmail_extra"><div class="gmail_quote"><div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div><div>> I sat at work all day today pulling my hair - I could not make it</div>
<div>> work.</div></div><div><br></div></div><div>My sincerest apologies for the pain. It is almost certainly due to problems on the update site, not your configuration.</div></blockquote><div><br></div></div><div>Please don't apologize for providing me with tools for science (;</div>
<div>I will try it out first thing tomorrow. Pretty much done with developing, now it's time for analysis (:</div><div><br></div><div>Besides, I like a challenge - although I have to admit this time I was in over my head.</div>
<div><br></div><div>Oh, by the way, I'm not sure if the Maven dependencies are all sorted with regards to a certain Jama package... It looks for version 1.0.2 whereas the latest release is 1.0.3 so it cannot be found... I managed to get it working through manually installing 1.0.2. It also works by changing the pom files of VIB-lib, VIB_ and 3D_viewer making them up to date. Having said that I only have a faintest clue of the infrastructure of Maven repositories...</div>
<div><br></div><div>Anyway, it didn't help me with my loci (;<br></div><div><br></div><div>Sincerely,</div><div>Jonas</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br></div><div>I have updated the Bio-Formats installation in Fiji to the absolute latest available, and hopefully ironed out these problems. Can you please run Help > Update Fiji to install all the updates, and let me know if Bio-Formats becomes functional for you?</div>
<div><br></div><div>Thanks,</div>
<div>Curtis<br></div><div><div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Dec 11, 2012 at 10:55 AM, Jonas Øgaard <span dir="ltr"><<a href="mailto:jonas@ogaard.no" target="_blank">jonas@ogaard.no</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Hi there,</div><div><br></div>I have a working version of Fiji running at home (where I'm at now) and don't dare to break it, but I sat at work all day today pulling my hair - I could not make it work.<div><br>
</div><div>I tried fresh downloads (fiji with and without jre), I tried removing one LOCI-jar, then the other, then both. I tried updating both fiji and imagej in two seperate clean setups, and also tried repeating updates to make sure no more components where awaiting updates.</div>
<div><br></div><div>It could be that the java-install is not entirely stable/up-to-date - it's running JRE6. Haven't tried 7.</div><div><br></div><div>I have no clue. Working from home tomorrow where it's safe & stable!</div>
<div><br></div><div>Sincerely,</div><div>Jonas</div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Dec 11, 2012 at 5:47 PM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Jonas,<div><br></div><div><div>> I am unable to import files with LOCI, no matter which loci-jar is</div><div>> deleted or not...</div>
</div><div><br></div><div>I updated Fiji with the 4.4.5 release of Bio-Formats last night, so these errors are almost certainly my fault.</div>
<div><br></div><div>Unfortunately, I am unable to replicate the problem. I tried updating an existing Fiji on another workstation, and all worked fine (though I did have to click "break the dependency" in response to one prompt). I also tried with a fresh continuous release downloaded from <a href="http://fiji.sc" target="_blank">fiji.sc</a> just now, and it also worked.</div>
<div><br></div><div>If you run Help > Update Fiji, click on Advanced mode, what do you see for "Locally modified files" and "Uninstalled files only"? A fully up-to-date Fiji should not have any entries.</div>
<div><br></div><div>-Curtis</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Dec 11, 2012 at 6:31 AM, <span dir="ltr"><<a href="mailto:jonas.ogaard@gmail.com" target="_blank">jonas.ogaard@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div>Hi!</div><div><br></div>I am still having difficulties with the latest Fiji (both w/w/out jre) and LOCI. Receiving same errors as described above.<div>
<br></div><div>As of now I am unable to import files with LOCI, no matter which loci-jar is deleted or not...</div><div><br></div><div>Have I magically jinxed my Fiji folder (again) or is this a problem shared by others?</div>
<div><br></div><div>Awesome work btw, Johannes (:</div><div><br></div><div>//Jonas</div><div><div><br>On Wednesday, August 1, 2012 7:37:26 PM UTC+2, Johannes Schindelin wrote:</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi Sebi,
<br><div>
<br>On Wed, 1 Aug 2012, <a>sebr...@gmail.com</a> wrote:
<br>
<br>> I tried to download the most up-to-date version (
<br>> <a href="http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip" target="_blank">http://jenkins.imagej.net/job/<u></u>Stable-Fiji/<u></u>lastSuccessfulBuild/artifact/<u></u>fiji-nojre.zip</a>)
<br>>
<br>>
<br>> This contains the loci_tools.jar as well as the the individual jars. So
<br>> should i just delete which files? This issues is quite critical for us,
<br>> since the Loci Bio-Format import is cruicial for us (and customer) to
<br>> import the OME-TIFF data produced by our imaging software.
<br>
<br>Yes, it is safe to delete loci_tools.jar. My work last year on enabling
<br>multiple update sites introduced the bug that removing files from update
<br>sites does not mark them as obsolete if you updated the files successfully
<br>before. We just did not hit that bug because we did not remove files in a
<br>long time ;-)
<br>
<br>> Do you still have an idea when this problem might get solved?
<br>
<br>It is fixed in the source code, I just have to upload a new version (for
<br>which I need to be comfortable with the current state first, though ;-).
<br>Should be happening within the hour.
<br>
<br>Ciao,
<br>Dscho
<br></div></blockquote></div>
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