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 <[email protected]>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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