[ImageJ-devel] [fiji-devel] LOCI fails on current Fiji checkout (help!!)

[Curtis Rueden]

Hi Steffi,

> The same happens when I make a new clone of Fiji ...

I am doing a full build of Fiji to help diagnose.

The problem is certainly that there is a mismatch between JAR versions.

Is there a loci_tools.jar anywhere? If so, delete it. If not, the problem
must be that an old bio-formats.jar is lying around somewhere—that stack
trace indicates an old ZeissLSMReader.

I'll write back with any additional insight after some more testing.

-Curtis


On Wed, Aug 8, 2012 at 3:20 PM, Stephan Preibisch <preibisch at mpi-cbg.de>wrote:

> The same happens when I make a new clone of Fiji ...
>
> git clone ...
> git submoule init modules/imglib (without that Colocalization_Analysis and
> Fiji does not compile btw)
> git submodule update
> Build
> ImageJ
> Plugins > LOCI > Import ... choose LSM
>
> > crash
>
> Steffi
>
> On Aug 8, 2012, at 15:59 , Stephan Preibisch wrote:
>
> > Hi guys,
> >
> > during the last hour LOCI stopped working on all my machines when I try
> to open LSM files (Fiji checkout master, Build clean, Build):
> >
> > an example is here: http://fly.mpi-cbg.de/preibisch/nm/HisYFP-SPIM.zip
> >
> > preibischs-lm1:fiji preibischs$ ./ImageJ
> > SLF4J: Class path contains multiple SLF4J bindings.
> > SLF4J: Found binding in
> [jar:file:/Users/preibischs/workspace/fiji/jars/slf4j-log4j12-1.5.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> > SLF4J: Found binding in
> [jar:file:/Users/preibischs/workspace/fiji/jars/slf4j-log4j12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> > SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
> explanation.
> > [ERROR] "loci.formats.in.PovrayReader" is not valid.
> > [ERROR] "loci.formats.in.IMODReader" is not valid.
> > [ERROR] "loci.formats.in.OperettaReader" is not valid.
> > [ERROR] "loci.formats.in.ZeissTIFFReader" is not valid.
> > [ERROR] "loci.formats.in.HRDGDFReader" is not valid.
> > [ERROR] "loci.formats.in.CanonRawReader" is not valid.
> > [INFO ] Reading LSM metadata for series #0
> > java.lang.reflect.InvocationTargetException
> >       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >       at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> >       at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> >       at java.lang.reflect.Method.invoke(Method.java:597)
> >       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:680)
> > Caused by: java.lang.NoSuchMethodError:
> loci.formats.meta.MetadataStore.setImageObjectiveSettingsID(Ljava/lang/String;I)V
> >       at
> loci.formats.in.ZeissLSMReader.populateMetadataStore(ZeissLSMReader.java:1249)
> >       at
> loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:1168)
> >       at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:520)
> >       at loci.formats.FormatReader.setId(FormatReader.java:1105)
> >       at
> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> >       at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> >       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:185)
> >       at ij.IJ.runPlugIn(IJ.java:152)
> >       ... 8 more
> > [INFO ] Reading IFDs
> > [INFO ] Populating metadata
> > [INFO ] Checking comment style
> > [INFO ] Populating OME metadata
> >
> >
> > I tried replacing scifio, loci_plugins, anything that starts or includes
> loci with different versions (from the download version of Fiji and an
> older checkout where it still works) - but it will continue failing.
> >
> > I was just working on my SPIM code and suddenly it broke upon a ./Build
> where I changed nothing but my files ...
> >
> > Does anybody have a suggestion?
> >
> > Thanks a lot,
> > Steffi
> >
> > --
> > 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
>
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