Hi Steffi,<br><br>> The same happens when I make a new clone of Fiji ...<br><div class="gmail_quote"><br></div><div class="gmail_quote">I am doing a full build of Fiji to help diagnose.</div><div class="gmail_quote"><br>
</div><div class="gmail_quote">The problem is certainly that there is a mismatch between JAR versions.</div><div class="gmail_quote"><br></div><div class="gmail_quote">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.</div>
<div class="gmail_quote"><br></div><div class="gmail_quote">I'll write back with any additional insight after some more testing.</div><div class="gmail_quote"><br></div><div class="gmail_quote">-Curtis</div><div class="gmail_quote">
<br></div><div class="gmail_quote"><br></div><div class="gmail_quote">On Wed, Aug 8, 2012 at 3:20 PM, Stephan Preibisch <span dir="ltr"><<a href="mailto:preibisch@mpi-cbg.de" target="_blank">preibisch@mpi-cbg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">The same happens when I make a new clone of Fiji ...<br>
<br>
git clone ...<br>
git submoule init modules/imglib (without that Colocalization_Analysis and Fiji does not compile btw)<br>
git submodule update<br>
Build<br>
ImageJ<br>
Plugins > LOCI > Import ... choose LSM<br>
<br>
> crash<br>
<br>
Steffi<br>
<div class="HOEnZb"><div class="h5"><br>
On Aug 8, 2012, at 15:59 , Stephan Preibisch wrote:<br>
<br>
> Hi guys,<br>
><br>
> during the last hour LOCI stopped working on all my machines when I try to open LSM files (Fiji checkout master, Build clean, Build):<br>
><br>
> an example is here: <a href="http://fly.mpi-cbg.de/preibisch/nm/HisYFP-SPIM.zip" target="_blank">http://fly.mpi-cbg.de/preibisch/nm/HisYFP-SPIM.zip</a><br>
><br>
> preibischs-lm1:fiji preibischs$ ./ImageJ<br>
> SLF4J: Class path contains multiple SLF4J bindings.<br>
> SLF4J: Found binding in [jar:file:/Users/preibischs/workspace/fiji/jars/slf4j-log4j12-1.5.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]<br>
> SLF4J: Found binding in [jar:file:/Users/preibischs/workspace/fiji/jars/slf4j-log4j12.jar!/org/slf4j/impl/StaticLoggerBinder.class]<br>
> SLF4J: See <a href="http://www.slf4j.org/codes.html#multiple_bindings" target="_blank">http://www.slf4j.org/codes.html#multiple_bindings</a> for an explanation.<br>
> [ERROR] "loci.formats.in.PovrayReader" is not valid.<br>
> [ERROR] "loci.formats.in.IMODReader" is not valid.<br>
> [ERROR] "loci.formats.in.OperettaReader" is not valid.<br>
> [ERROR] "loci.formats.in.ZeissTIFFReader" is not valid.<br>
> [ERROR] "loci.formats.in.HRDGDFReader" is not valid.<br>
> [ERROR] "loci.formats.in.CanonRawReader" is not valid.<br>
> [INFO ] Reading LSM metadata for series #0<br>
> java.lang.reflect.InvocationTargetException<br>
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)<br>
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br>
> at java.lang.reflect.Method.invoke(Method.java:597)<br>
> at ij.Command.runPlugIn(Command.java:146)<br>
> at ij.Command.runCommand(Command.java:95)<br>
> at ij.Executer.run(Executer.java:64)<br>
> at java.lang.Thread.run(Thread.java:680)<br>
> Caused by: java.lang.NoSuchMethodError: loci.formats.meta.MetadataStore.setImageObjectiveSettingsID(Ljava/lang/String;I)V<br>
> at loci.formats.in.ZeissLSMReader.populateMetadataStore(ZeissLSMReader.java:1249)<br>
> at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:1168)<br>
> at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:520)<br>
> at loci.formats.FormatReader.setId(FormatReader.java:1105)<br>
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)<br>
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br>
> at loci.plugins.in.Importer.showDialogs(Importer.java:141)<br>
> at loci.plugins.in.Importer.run(Importer.java:79)<br>
> at loci.plugins.LociImporter.run(LociImporter.java:81)<br>
> at ij.IJ.runUserPlugIn(IJ.java:185)<br>
> at ij.IJ.runPlugIn(IJ.java:152)<br>
> ... 8 more<br>
> [INFO ] Reading IFDs<br>
> [INFO ] Populating metadata<br>
> [INFO ] Checking comment style<br>
> [INFO ] Populating OME metadata<br>
><br>
><br>
> 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.<br>
><br>
> I was just working on my SPIM code and suddenly it broke upon a ./Build where I changed nothing but my files ...<br>
><br>
> Does anybody have a suggestion?<br>
><br>
> Thanks a lot,<br>
> Steffi<br>
><br>
> --<br>
> Please avoid top-posting, and please make sure to reply-to-all!<br>
><br>
> Mailing list web interface: <a href="http://groups.google.com/group/fiji-devel" target="_blank">http://groups.google.com/group/fiji-devel</a><br>
<br>
--<br>
Please avoid top-posting, and please make sure to reply-to-all!<br>
<br>
Mailing list web interface: <a href="http://groups.google.com/group/fiji-devel" target="_blank">http://groups.google.com/group/fiji-devel</a><br>
</div></div></blockquote></div><br>