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 >>>>> >>>>> >>>> >>> >> >
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