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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