[ImageJ-devel] [fiji-devel] LOCI crashes with current Fiji build on runtime

[Melissa Linkert]

Hi Steffi,

> running the SPIM registration I run into the problem that it is not possible to open images anymore because of a java.lang.NoSuchMethodError (see full exception below): ome.xml.model.Experimenter.setDisplayName(Ljava/lang/String;)V
> 
> A similar error (setAcquiredDate instead of setDisplayName) can be reproduced using the Script editor with beanshell and the mitosis.tif (ImageJ example image):
*snip*
> 
> Does anyone know why this happens (was fine some days ago)...

As far as I can tell, this is because when you build Fiji you now get
two different versions of Bio-Formats in the 'jars' and 'plugins'
directories.  plugins/loci_tools.jar is a specific version from April
2012, where plugins/loci_plugins.jar and jars/bio-formats.jar (and
jars/loci-common.jar etc.) are the latest 4.4-SNAPSHOT version from
Maven.  4.4-SNAPSHOT had some subtle API changes a couple of weeks ago,
which would cause this error if older and newer JARs were mixed on the
CLASSPATH.

I would guess that this is somewhat related to this thread:

https://groups.google.com/forum/?fromgroups#!topic/fiji-devel/r1JOg4C8_68

...but I could easily be wrong.

Regards,
-Melissa

On Thu, Jul 19, 2012 at 12:02:36PM -0400, Stephan Preibisch wrote:
> Hi,
> 
> running the SPIM registration I run into the problem that it is not possible to open images anymore because of a java.lang.NoSuchMethodError (see full exception below): ome.xml.model.Experimenter.setDisplayName(Ljava/lang/String;)V
> 
> A similar error (setAcquiredDate instead of setDisplayName) can be reproduced using the Script editor with beanshell and the mitosis.tif (ImageJ example image):
> 
>    import loci.formats.ChannelSeparator;
>    import loci.formats.MetadataTools;
>    import loci.formats.meta.IMetadata;
>    import loci.formats.IFormatReader;
> 
>    final IFormatReader r = new ChannelSeparator();
> 
>    final IMetadata omexmlMeta = MetadataTools.createOMEXMLMetadata();
>    r.setMetadataStore( omexmlMeta );
>    r.setId( "/Users/preibischs/Desktop/mitosis.tif" );
> 
> -> Target exception: java.lang.NoSuchMethodError: ome.xml.model.Image.setAcquiredDate(Ljava/lang/String;)V
> 
> Does anyone know why this happens (was fine some days ago)...
> 
> Thanks a lot, 
> Steffi
> 
> 
> 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: ome.xml.model.Experimenter.setDisplayName(Ljava/lang/String;)V
> 	at loci.formats.ome.OMEXMLMetadataImpl.setExperimenterDisplayName(OMEXMLMetadataImpl.java:7386)
> 	at loci.formats.meta.FilterMetadata.setExperimenterDisplayName(FilterMetadata.java:889)
> 	at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:1192)
> 	at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:520)
> 	at loci.formats.FormatReader.setId(FormatReader.java:1091)
> 	at loci.formats.ImageReader.setId(ImageReader.java:682)
> 	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
> 	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:261)
> 	at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:638)
> 	at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:583)
> 	at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:573)
> 	at mpicbg.imglib.io.LOCI.openLOCIFloatType(LOCI.java:568)
> 	at fiji.plugin.Bead_Registration.getInteractiveDoGParameters(Bead_Registration.java:673)
> 	at fiji.plugin.Bead_Registration.getConfiguration(Bead_Registration.java:320)
> 	at fiji.plugin.Bead_Registration.access$100(Bead_Registration.java:40)
> 	at fiji.plugin.Bead_Registration$1.dialogItemChanged(Bead_Registration.java:208)
> 	at ij.gui.GenericDialog.showDialog(GenericDialog.java:1052)
> 	at fiji.plugin.Bead_Registration.singleChannel(Bead_Registration.java:265)
> 	at fiji.plugin.Bead_Registration.run(Bead_Registration.java:75)
> 	at ij.IJ.runUserPlugIn(IJ.java:185)
> 	at ij.IJ.runPlugIn(IJ.java:152)
> 
> -- 
> Please avoid top-posting, and please make sure to reply-to-all!
> 
> Mailing list web interface: http://groups.google.com/group/fiji-devel