Hi, Now all is good! Thanks a ton and more.
I uploaded a sample image (seq1615.jp2) anyway for testing (but where did it go?) Sincerely, JonasD On Thu, Dec 13, 2012 at 5:11 PM, Jonas D. S. Øgaard <[email protected]>wrote: > Essentially any (Nikon NIS) JPEG2000 formatted images fails. Will sen one > when home. > > //JonasD > > Den 13. des. 2012 kl. 17:08 skrev Curtis Rueden <[email protected]>: > > Hi Jonas, > > > java.lang.IllegalArgumentException: 0 must not be null and positive. > > 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. > > 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. > > 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. > > Thanks, > Curtis > > > On Thu, Dec 13, 2012 at 6:42 AM, Jonas Øgaard <[email protected]> wrote: > >> OK, back at work today. Here is trace log after attempting to import >> using LOCI: >> >> java.lang.reflect.InvocationTargetException >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) >> at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >> at java.lang.reflect.Method.invoke(Method.java:601) >> at ij.Command.runPlugIn(Command.java:146) >> at ij.Command.runCommand(Command.java:95) >> at ij.Executer.run(Executer.java:64) >> at java.lang.Thread.run(Thread.java:722) >> Caused by: java.lang.IllegalArgumentException: 0 must not be null and >> positive. >> at >> ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56) >> at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:272) >> at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:246) >> at loci.formats.ChannelFiller.setId(ChannelFiller.java:267) >> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552) >> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) >> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552) >> at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:285) >> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552) >> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552) >> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552) >> at loci.plugins.in.ImportProcess.setId(ImportProcess.java:682) >> at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:519) >> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:150) >> at loci.plugins.in.Importer.showDialogs(Importer.java:141) >> at loci.plugins.in.Importer.run(Importer.java:79) >> at loci.plugins.LociImporter.run(LociImporter.java:81) >> at ij.IJ.runUserPlugIn(IJ.java:184) >> at ij.IJ.runPlugIn(IJ.java:151) >> ... 8 more >> >> Sincerely, >> Jonas Ogaard >> >> >> On Tue, Dec 11, 2012 at 11:17 PM, Jonas Øgaard <[email protected]> wrote: >> >>> Hi again, Curtis! >>> >>> > I sat at work all day today pulling my hair - I could not make it >>>> > work. >>>> >>>> My sincerest apologies for the pain. It is almost certainly due to >>>> problems on the update site, not your configuration. >>>> >>> >>> Please don't apologize for providing me with tools for science (; >>> I will try it out first thing tomorrow. Pretty much done with >>> developing, now it's time for analysis (: >>> >>> Besides, I like a challenge - although I have to admit this time I was >>> in over my head. >>> >>> 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... >>> >>> Anyway, it didn't help me with my loci (; >>> >>> Sincerely, >>> Jonas >>> >>> >>>> >>>> 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? >>>> >>>> Thanks, >>>> Curtis >>>> >>>> >>>> On Tue, Dec 11, 2012 at 10:55 AM, Jonas Øgaard <[email protected]> wrote: >>>> >>>>> Hi there, >>>>> >>>>> 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. >>>>> >>>>> 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. >>>>> >>>>> It could be that the java-install is not entirely stable/up-to-date - >>>>> it's running JRE6. Haven't tried 7. >>>>> >>>>> I have no clue. Working from home tomorrow where it's safe & stable! >>>>> >>>>> Sincerely, >>>>> Jonas >>>>> >>>>> >>>>> On Tue, Dec 11, 2012 at 5:47 PM, Curtis Rueden <[email protected]>wrote: >>>>> >>>>>> Hi Jonas, >>>>>> >>>>>> > I am unable to import files with LOCI, no matter which loci-jar is >>>>>> > deleted or not... >>>>>> >>>>>> I updated Fiji with the 4.4.5 release of Bio-Formats last night, so >>>>>> these errors are almost certainly my fault. >>>>>> >>>>>> 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 fiji.sc just >>>>>> now, and it also worked. >>>>>> >>>>>> 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. >>>>>> >>>>>> -Curtis >>>>>> >>>>>> >>>>>> On Tue, Dec 11, 2012 at 6:31 AM, <[email protected]> wrote: >>>>>> >>>>>>> Hi! >>>>>>> >>>>>>> I am still having difficulties with the latest Fiji (both w/w/out >>>>>>> jre) and LOCI. Receiving same errors as described above. >>>>>>> >>>>>>> As of now I am unable to import files with LOCI, no matter which >>>>>>> loci-jar is deleted or not... >>>>>>> >>>>>>> Have I magically jinxed my Fiji folder (again) or is this a problem >>>>>>> shared by others? >>>>>>> >>>>>>> Awesome work btw, Johannes (: >>>>>>> >>>>>>> //Jonas >>>>>>> >>>>>>> On Wednesday, August 1, 2012 7:37:26 PM UTC+2, Johannes Schindelin >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Sebi, >>>>>>>> >>>>>>>> On Wed, 1 Aug 2012, [email protected] wrote: >>>>>>>> >>>>>>>> > I tried to download the most up-to-date version ( >>>>>>>> > http://jenkins.imagej.net/job/**Stable-Fiji/** >>>>>>>> lastSuccessfulBuild/artifact/**fiji-nojre.zip<http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip>) >>>>>>>> >>>>>>>> > >>>>>>>> > >>>>>>>> > This contains the loci_tools.jar as well as the the individual >>>>>>>> jars. So >>>>>>>> > should i just delete which files? This issues is quite critical >>>>>>>> for us, >>>>>>>> > since the Loci Bio-Format import is cruicial for us (and >>>>>>>> customer) to >>>>>>>> > import the OME-TIFF data produced by our imaging software. >>>>>>>> >>>>>>>> Yes, it is safe to delete loci_tools.jar. My work last year on >>>>>>>> enabling >>>>>>>> multiple update sites introduced the bug that removing files from >>>>>>>> update >>>>>>>> sites does not mark them as obsolete if you updated the files >>>>>>>> successfully >>>>>>>> before. We just did not hit that bug because we did not remove >>>>>>>> files in a >>>>>>>> long time ;-) >>>>>>>> >>>>>>>> > Do you still have an idea when this problem might get solved? >>>>>>>> >>>>>>>> It is fixed in the source code, I just have to upload a new version >>>>>>>> (for >>>>>>>> which I need to be comfortable with the current state first, though >>>>>>>> ;-). >>>>>>>> Should be happening within the hour. >>>>>>>> >>>>>>>> Ciao, >>>>>>>> Dscho >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> ImageJ-devel mailing list >>>>>>> [email protected] >>>>>>> http://imagej.net/mailman/listinfo/imagej-devel >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> -- >> Please avoid top-posting, and please make sure to reply-to-all! >> >> Mailing list web interface: http://groups.google.com/group/fiji-devel >> > >
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