Hi Melissa, Jonas & everyone,<div><br></div><div><div>> As long as Jonas is able to see the image in Fiji and there is truly</div><div>> no physical pixel size, this is not a bug.</div><div><br></div><div>I agree, but what I meant was that from his prior message, it sounded like he was getting an exception:</div>
<div><br></div><div><div>> java.lang.IllegalArgumentException: 0 must not be null and positive.</div></div><div><br></div></div><div>So by my vague question "can you reproduce?" I actually meant "can you reproduce the IllegalArgumentException". Apologies for being unclear.</div>
<div><br></div><div>From your mail, it sounds like you see the same behavior as me: a relatively harmless warning, rather than exception that prevents the image window from appearing.</div><div><br></div><div>Jonas: Did you double check that your Fiji is 100% up to date? Help > Update Fiji, no "locally modified" or "local-only" files at all? And if so, do you still receive an exception?</div>
<div><br></div><div>Thanks,</div><div>Curtis</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Dec 14, 2012 at 3:04 PM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<div><br>
> > I uploaded a sample image (seq1615.jp2) anyway for testing<br>
><br>
> Thanks, I tested on my system. It prints a warning "Expected positive value<br>
> for PhysicalSizeZ; got 0.0" but the image window opens.<br>
><br>
> Other Bio-Formats devs: can you reproduce?<br>
<br>
</div>Yes, and that is the correct behavior. So far as I can see from opening<br>
the file in Nikon's Elements software, this file contains no physical<br>
size/calibration information. Bio-Formats is simply warning that a<br>
physical pixel size of 0 was found, which means that it will not be<br>
preserved if you were to convert the file to some other format (only<br>
values greater than 0 are preserved).<br>
<br>
As long as Jonas is able to see the image in Fiji and there is truly no<br>
physical pixel size, this is not a bug.<br>
<br>
Regards,<br>
-Melissa<br>
<div><div><br>
On Fri, Dec 14, 2012 at 02:06:41PM -0600, Curtis Rueden wrote:<br>
> Hi Jonas,<br>
><br>
> > I uploaded a sample image (seq1615.jp2) anyway for testing<br>
><br>
> Thanks, I tested on my system. It prints a warning "Expected positive value<br>
> for PhysicalSizeZ; got 0.0" but the image window opens.<br>
><br>
> Other Bio-Formats devs: can you reproduce?<br>
><br>
> > (but where did it go?)<br>
><br>
> Files uploaded using that mechanism are placed on the Fiji web server (<br>
> <a href="http://fiji.sc" target="_blank">fiji.sc</a>) in a private folder; we assume you do not want your data shared<br>
> publicly unless you say otherwise.<br>
><br>
> Regards,<br>
> Curtis<br>
><br>
><br>
> On Fri, Dec 14, 2012 at 4:49 AM, Jonas Øgaard <<a href="mailto:jonas@ogaard.no" target="_blank">jonas@ogaard.no</a>> wrote:<br>
><br>
> > Hi,<br>
> ><br>
> > Now all is good!<br>
> > Thanks a ton and more.<br>
> ><br>
> > I uploaded a sample image (seq1615.jp2) anyway for testing (but where did<br>
> > it go?)<br>
> ><br>
> > Sincerely,<br>
> > JonasD<br>
> ><br>
> ><br>
> > On Thu, Dec 13, 2012 at 5:11 PM, Jonas D. S. Øgaard <<br>
> > <a href="mailto:jonas.ogaard@gmail.com" target="_blank">jonas.ogaard@gmail.com</a>> wrote:<br>
> ><br>
> >> Essentially any (Nikon NIS) JPEG2000 formatted images fails. Will sen one<br>
> >> when home.<br>
> >><br>
> >> //JonasD<br>
> >><br>
> >> Den 13. des. 2012 kl. 17:08 skrev Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>>:<br>
> >><br>
> >> Hi Jonas,<br>
> >><br>
> >> > java.lang.IllegalArgumentException: 0 must not be null and positive.<br>
> >><br>
> >> That is actually great news. It means we fixed the problem with the<br>
> >> update site. Now there is most likely a bona fide bug in Bio-Formats.<br>
> >><br>
> >> Would you be willing to send us a problematic dataset, so that we can<br>
> >> address the issue? You can use Fiji's Help > Upload Sample Image feature to<br>
> >> send it if is smaller than ~250MB.<br>
> >><br>
> >> But first, just to be sure: please run Help > Update Fiji and make sure<br>
> >> it says your Fiji is fully up to date, with no locally modified files.<br>
> >><br>
> >> Thanks,<br>
> >> Curtis<br>
> >><br>
> >><br>
> >> On Thu, Dec 13, 2012 at 6:42 AM, Jonas Øgaard <<a href="mailto:jonas@ogaard.no" target="_blank">jonas@ogaard.no</a>> wrote:<br>
> >><br>
> >>> OK, back at work today. Here is trace log after attempting to import<br>
> >>> using LOCI:<br>
> >>><br>
> >>> java.lang.reflect.InvocationTargetException<br>
> >>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
> >>> at<br>
> >>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br>
> >>> at<br>
> >>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br>
> >>> at java.lang.reflect.Method.invoke(Method.java:601)<br>
> >>> at ij.Command.runPlugIn(Command.java:146)<br>
> >>> at ij.Command.runCommand(Command.java:95)<br>
> >>> at ij.Executer.run(Executer.java:64)<br>
> >>> at java.lang.Thread.run(Thread.java:722)<br>
> >>> Caused by: java.lang.IllegalArgumentException: 0 must not be null and<br>
> >>> positive.<br>
> >>> at<br>
> >>> ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56)<br>
> >>> at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:272)<br>
> >>> at<br>
> >>> loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:246)<br>
> >>> at loci.formats.ChannelFiller.setId(ChannelFiller.java:267)<br>
> >>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)<br>
> >>> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)<br>
> >>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)<br>
> >>> at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:285)<br>
> >>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)<br>
> >>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)<br>
> >>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)<br>
> >>> at loci.plugins.in.ImportProcess.setId(ImportProcess.java:682)<br>
> >>> at<br>
> >>> loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:519)<br>
> >>> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:150)<br>
> >>> at loci.plugins.in.Importer.showDialogs(Importer.java:141)<br>
> >>> at loci.plugins.in.Importer.run(Importer.java:79)<br>
> >>> at loci.plugins.LociImporter.run(LociImporter.java:81)<br>
> >>> at ij.IJ.runUserPlugIn(IJ.java:184)<br>
> >>> at ij.IJ.runPlugIn(IJ.java:151)<br>
> >>> ... 8 more<br>
> >>><br>
> >>> Sincerely,<br>
> >>> Jonas Ogaard<br>
> >>><br>
> >>><br>
> >>> On Tue, Dec 11, 2012 at 11:17 PM, Jonas Øgaard <<a href="mailto:jonas@ogaard.no" target="_blank">jonas@ogaard.no</a>> wrote:<br>
> >>><br>
> >>>> Hi again, Curtis!<br>
> >>>><br>
> >>>> > I sat at work all day today pulling my hair - I could not make it<br>
> >>>>> > work.<br>
> >>>>><br>
> >>>>> My sincerest apologies for the pain. It is almost certainly due to<br>
> >>>>> problems on the update site, not your configuration.<br>
> >>>>><br>
> >>>><br>
> >>>> Please don't apologize for providing me with tools for science (;<br>
> >>>> I will try it out first thing tomorrow. Pretty much done with<br>
> >>>> developing, now it's time for analysis (:<br>
> >>>><br>
> >>>> Besides, I like a challenge - although I have to admit this time I was<br>
> >>>> in over my head.<br>
> >>>><br>
> >>>> Oh, by the way, I'm not sure if the Maven dependencies are all sorted<br>
> >>>> with regards to a certain Jama package... It looks for version 1.0.2<br>
> >>>> whereas the latest release is 1.0.3 so it cannot be found... I managed to<br>
> >>>> get it working through manually installing 1.0.2. It also works by changing<br>
> >>>> the pom files of VIB-lib, VIB_ and 3D_viewer making them up to date. Having<br>
> >>>> said that I only have a faintest clue of the infrastructure of Maven<br>
> >>>> repositories...<br>
> >>>><br>
> >>>> Anyway, it didn't help me with my loci (;<br>
> >>>><br>
> >>>> Sincerely,<br>
> >>>> Jonas<br>
> >>>><br>
> >>>><br>
> >>>>><br>
> >>>>> I have updated the Bio-Formats installation in Fiji to the absolute<br>
> >>>>> latest available, and hopefully ironed out these problems. Can you please<br>
> >>>>> run Help > Update Fiji to install all the updates, and let me know if<br>
> >>>>> Bio-Formats becomes functional for you?<br>
> >>>>><br>
> >>>>> Thanks,<br>
> >>>>> Curtis<br>
> >>>>><br>
> >>>>><br>
> >>>>> On Tue, Dec 11, 2012 at 10:55 AM, Jonas Øgaard <<a href="mailto:jonas@ogaard.no" target="_blank">jonas@ogaard.no</a>>wrote:<br>
> >>>>><br>
> >>>>>> Hi there,<br>
> >>>>>><br>
> >>>>>> I have a working version of Fiji running at home (where I'm at now)<br>
> >>>>>> and don't dare to break it, but I sat at work all day today pulling my hair<br>
> >>>>>> - I could not make it work.<br>
> >>>>>><br>
> >>>>>> I tried fresh downloads (fiji with and without jre), I tried removing<br>
> >>>>>> one LOCI-jar, then the other, then both. I tried updating both fiji and<br>
> >>>>>> imagej in two seperate clean setups, and also tried repeating updates to<br>
> >>>>>> make sure no more components where awaiting updates.<br>
> >>>>>><br>
> >>>>>> It could be that the java-install is not entirely stable/up-to-date -<br>
> >>>>>> it's running JRE6. Haven't tried 7.<br>
> >>>>>><br>
> >>>>>> I have no clue. Working from home tomorrow where it's safe & stable!<br>
> >>>>>><br>
> >>>>>> Sincerely,<br>
> >>>>>> Jonas<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>> On Tue, Dec 11, 2012 at 5:47 PM, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>>wrote:<br>
> >>>>>><br>
> >>>>>>> Hi Jonas,<br>
> >>>>>>><br>
> >>>>>>> > I am unable to import files with LOCI, no matter which loci-jar is<br>
> >>>>>>> > deleted or not...<br>
> >>>>>>><br>
> >>>>>>> I updated Fiji with the 4.4.5 release of Bio-Formats last night, so<br>
> >>>>>>> these errors are almost certainly my fault.<br>
> >>>>>>><br>
> >>>>>>> Unfortunately, I am unable to replicate the problem. I tried<br>
> >>>>>>> updating an existing Fiji on another workstation, and all worked fine<br>
> >>>>>>> (though I did have to click "break the dependency" in response to one<br>
> >>>>>>> prompt). I also tried with a fresh continuous release downloaded from<br>
> >>>>>>> <a href="http://fiji.sc" target="_blank">fiji.sc</a> just now, and it also worked.<br>
> >>>>>>><br>
> >>>>>>> If you run Help > Update Fiji, click on Advanced mode, what do you<br>
> >>>>>>> see for "Locally modified files" and "Uninstalled files only"? A fully<br>
> >>>>>>> up-to-date Fiji should not have any entries.<br>
> >>>>>>><br>
> >>>>>>> -Curtis<br>
> >>>>>>><br>
> >>>>>>><br>
> >>>>>>> On Tue, Dec 11, 2012 at 6:31 AM, <<a href="mailto:jonas.ogaard@gmail.com" target="_blank">jonas.ogaard@gmail.com</a>> wrote:<br>
> >>>>>>><br>
> >>>>>>>> Hi!<br>
> >>>>>>>><br>
> >>>>>>>> I am still having difficulties with the latest Fiji (both w/w/out<br>
> >>>>>>>> jre) and LOCI. Receiving same errors as described above.<br>
> >>>>>>>><br>
> >>>>>>>> As of now I am unable to import files with LOCI, no matter which<br>
> >>>>>>>> loci-jar is deleted or not...<br>
> >>>>>>>><br>
> >>>>>>>> Have I magically jinxed my Fiji folder (again) or is this a problem<br>
> >>>>>>>> shared by others?<br>
> >>>>>>>><br>
> >>>>>>>> Awesome work btw, Johannes (:<br>
> >>>>>>>><br>
> >>>>>>>> //Jonas<br>
> >>>>>>>><br>
> >>>>>>>> On Wednesday, August 1, 2012 7:37:26 PM UTC+2, Johannes Schindelin<br>
> >>>>>>>> wrote:<br>
> >>>>>>>><br>
> >>>>>>>>> Hi Sebi,<br>
> >>>>>>>>><br>
> >>>>>>>>> On Wed, 1 Aug 2012, <a href="mailto:sebr...@gmail.com" target="_blank">sebr...@gmail.com</a> wrote:<br>
> >>>>>>>>><br>
> >>>>>>>>> > I tried to download the most up-to-date version (<br>
</div></div>> >>>>>>>>> > <a href="http://jenkins.imagej.net/job/**Stable-Fiji/**" target="_blank">http://jenkins.imagej.net/job/**Stable-Fiji/**</a><br>
> >>>>>>>>> lastSuccessfulBuild/artifact/**fiji-nojre.zip<<a href="http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip" target="_blank">http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip</a>>)<br>
<div><div>> >>>>>>>>><br>
> >>>>>>>>> ><br>
> >>>>>>>>> ><br>
> >>>>>>>>> > This contains the loci_tools.jar as well as the the individual<br>
> >>>>>>>>> jars. So<br>
> >>>>>>>>> > should i just delete which files? This issues is quite critical<br>
> >>>>>>>>> for us,<br>
> >>>>>>>>> > since the Loci Bio-Format import is cruicial for us (and<br>
> >>>>>>>>> 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<br>
> >>>>>>>>> enabling<br>
> >>>>>>>>> multiple update sites introduced the bug that removing files from<br>
> >>>>>>>>> update<br>
> >>>>>>>>> sites does not mark them as obsolete if you updated the files<br>
> >>>>>>>>> successfully<br>
> >>>>>>>>> before. We just did not hit that bug because we did not remove<br>
> >>>>>>>>> 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<br>
> >>>>>>>>> version (for<br>
> >>>>>>>>> which I need to be comfortable with the current state first,<br>
> >>>>>>>>> though ;-).<br>
> >>>>>>>>> Should be happening within the hour.<br>
> >>>>>>>>><br>
> >>>>>>>>> Ciao,<br>
> >>>>>>>>> Dscho<br>
> >>>>>>>>><br>
> >>>>>>>><br>
> >>>>>>>> _______________________________________________<br>
> >>>>>>>> ImageJ-devel mailing list<br>
> >>>>>>>> <a href="mailto:ImageJ-devel@imagej.net" target="_blank">ImageJ-devel@imagej.net</a><br>
> >>>>>>>> <a href="http://imagej.net/mailman/listinfo/imagej-devel" target="_blank">http://imagej.net/mailman/listinfo/imagej-devel</a><br>
> >>>>>>>><br>
> >>>>>>>><br>
> >>>>>>><br>
> >>>>>><br>
> >>>>><br>
> >>>><br>
> >>> --<br>
> >>> Please avoid top-posting, and please make sure to reply-to-all!<br>
> >>><br>
> >>> Mailing list web interface: <a href="http://groups.google.com/group/fiji-devel" target="_blank">http://groups.google.com/group/fiji-devel</a><br>
> >>><br>
> >><br>
> >><br>
> > --<br>
> > Please avoid top-posting, and please make sure to reply-to-all!<br>
> ><br>
> > Mailing list web interface: <a href="http://groups.google.com/group/fiji-devel" target="_blank">http://groups.google.com/group/fiji-devel</a><br>
> ><br>
><br>
> --<br>
> Please avoid top-posting, and please make sure to reply-to-all!<br>
><br>
> Mailing list web interface: <a href="http://groups.google.com/group/fiji-devel" target="_blank">http://groups.google.com/group/fiji-devel</a><br>
<br>
--<br>
Please avoid top-posting, and please make sure to reply-to-all!<br>
<br>
Mailing list web interface: <a href="http://groups.google.com/group/fiji-devel" target="_blank">http://groups.google.com/group/fiji-devel</a><br>
</div></div></blockquote></div><br></div>