Hi Jonas, > I uploaded a sample image (seq1615.jp2) anyway for testing
Thanks, I tested on my system. It prints a warning "Expected positive value for PhysicalSizeZ; got 0.0" but the image window opens. Other Bio-Formats devs: can you reproduce? > (but where did it go?) Files uploaded using that mechanism are placed on the Fiji web server ( fiji.sc) in a private folder; we assume you do not want your data shared publicly unless you say otherwise. Regards, Curtis On Fri, Dec 14, 2012 at 4:49 AM, Jonas Øgaard <[email protected]> wrote: > 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 >>> >> >> > -- > Please avoid top-posting, and please make sure to reply-to-all! > > Mailing list web interface: http://groups.google.com/group/fiji-devel >
_______________________________________________ ImageJ-devel mailing list [email protected] http://imagej.net/mailman/listinfo/imagej-devel
