NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 715 - BioFormats import module fails with exception on OME-TIFF, others, following 3/8 Fiji update
BioFormats import module fails with exception on OME-TIFF, others, following ...
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
Macintosh Mac OS
: P5 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-03-08 18:48 CST by Jonathan Barchi
Modified: 2014-03-09 05:10 CDT
1 user (show)

See Also:


Attachments
Full system/java information (37.56 KB, text/plain)
2014-03-08 18:48 CST, Jonathan Barchi

Description Jonathan Barchi 2014-03-08 18:48:49 CST
Created attachment 135
Full system/java information

Hello,

After accepting an update to Fiji that was published today, I'm finding that the BioFormats import module fails in the process of loading OME-TIFF, at least. A quick google search turned up at least one other mention of this problem, in that case while importing .czi files.

An exception is thrown during the actual import process, after BioFormats scans the file and prompts you with a window of import options. After clicking OK to start the import, a NoSuchMethodError is thrown for org.joda.time.Instant.parse:

Full java/system information can be found here: 
http://pastebin.com/9mFaBX6C

And here is the full trace:

There was a problem with the class org.joda.time.Instant which can be found here:
/Applications/Fiji.app/jars/jruby-1.6.7.2.jar
/Applications/Fiji.app/jars/joda-time-2.2.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: org.joda.time.Instant.parse(Ljava/lang/String;Lorg/joda/time/format/DateTimeFormatter;)Lorg/joda/time/Instant;
at ome.xml.model.primitives.Timestamp.(Timestamp.java:82)
at loci.formats.MetadataTools.setDefaultCreationDate(MetadataTools.java:404)
at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:234)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:138)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:101)
at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:587)
at loci.formats.FormatReader.setId(FormatReader.java:1319)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:711)
at loci.formats.FormatReader.setId(FormatReader.java:1319)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:479)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
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:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:695)
Comment 1 Curtis Rueden 2014-03-09 05:10:52 CDT
I uploaded a fix. Please update your Fiji and try again!