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

[Stephan Preibisch]

No, I can only see

jars/
MD5 (scifio.jar) = 9e101ed5cd590534f74d0001b98c1918
MD5 (loci-common.jar) = 10d372b14b99965ec8c8f809d5973853

plugins/
MD5 (loci_plugins.jar) = 9b4a563016f5c2e9e1347a2c969bba05

For some files I get a different error:
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

Beanshell reports for: 
print( loci.formats.meta.MetadataStore.class.getResource( "/loci/formats/meta/MetadataStore.class" ));
jar:file:/Users/preibischs/workspace/fiji/jars/scifio.jar!/loci/formats/meta/MetadataStore.class

Thanks for looking into it, 
Steffi

On Aug 8, 2012, at 16:22 , Curtis Rueden wrote:

> 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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