[ome-users] bug in Bio-Formats Exporter for ImageJ?

Peter van Loon p.van.loon at rijkzwaan.nl
Thu Mar 13 13:01:38 GMT 2014 

Hi, 

I have problems when I use the Bio-Formats Exporter in ImageJ. I used the 
latest versions of both ImageJ and Bio-Formats (5.0.0).
I tried older versions of Bio-Formats (4.4.10) and it seemed to work but 
the next day I got the same exceptions.
I tried in the latest Fiji but with the same result.

It happens with just ordinary test files like this: RGB file (1 layer): 

This is the ImageJ Exception:

****begin*****
ImageJ 1.48s; Java 1.6.0_21 [32-bit]; Windows 7 6.1; 15MB of 640MB (2%)
 
java.lang.IllegalArgumentException: ZCT size vs image count mismatch 
(sizeZ=1, sizeC=3, sizeT=1, total=1)
        at loci.formats.FormatTools.getZCTCoords(FormatTools.java:467)
        at loci.plugins.out.Exporter.run(Exporter.java:592)
        at loci.plugins.LociExporter.run(LociExporter.java:77)
        at 
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
        at 
ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
        at ij.IJ.runUserPlugIn(IJ.java:201)
        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(Unknown Source)
****end*****
This is the log in the Bio-formats configuration:

****begin*****
Bio-Formats Plugins configuration - 2014-03-13 09:46:39

-- System properties --
java.runtime.name = Java(TM) SE Runtime Environment
sun.boot.library.path = C:\Program Files (x86)\Java\jre6\bin
java.vm.version = 17.0-b17
java.vm.vendor = Sun Microsystems Inc.
java.vendor.url = http://java.sun.com/
path.separator = ;
java.vm.name = Java HotSpot(TM) Client VM
file.encoding.pkg = sun.io
sun.java.launcher = SUN_STANDARD
user.country = NL
sun.os.patch.level = Service Pack 1
java.vm.specification.name = Java Virtual Machine Specification
user.dir = Z:\ImageJ 2014-03-08
java.runtime.version = 1.6.0_21-b07
java.awt.graphicsenv = sun.awt.Win32GraphicsEnvironment
java.endorsed.dirs = C:\Program Files (x86)\Java\jre6\lib\endorsed
os.arch = x86
java.io.tmpdir = C:\Users\pvl\AppData\Local\Temp\
line.separator = 

java.vm.specification.vendor = Sun Microsystems Inc.
user.variant = 
os.name = Windows 7
sun.jnu.encoding = Cp1252
java.library.path = C:\Program Files 
(x86)\Java\jre6\bin;.;C:\windows\Sun\Java\bin;C:\windows\system32;C:\windows;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;J:\Notes;C:\Program 
Files (x86)\Common Files\Roxio Shared\DLLShared\;C:\Program Files\jEdit
java.specification.name = Java Platform API Specification
java.class.version = 50.0
sun.management.compiler = HotSpot Client Compiler
os.version = 6.1
user.home = C:\Users\pvl
user.timezone = Europe/Berlin
java.awt.printerjob = sun.awt.windows.WPrinterJob
file.encoding = Cp1252
java.specification.version = 1.6
java.net.useSystemProxies = true
java.class.path = 
Z:\IMAGEJ~2\ij.jar;plugins\jedit.jar;plugins\ijed\jars\ij.jar
user.name = pvl
java.vm.specification.version = 1.0
java.home = C:\Program Files (x86)\Java\jre6
sun.arch.data.model = 32
user.language = nl
java.specification.vendor = Sun Microsystems Inc.
awt.toolkit = sun.awt.windows.WToolkit
java.vm.info = mixed mode, sharing
java.version = 1.6.0_21
java.ext.dirs = C:\Program Files 
(x86)\Java\jre6\lib\ext;C:\windows\Sun\Java\lib\ext
sun.boot.class.path = C:\Program Files 
(x86)\Java\jre6\lib\resources.jar;C:\Program Files 
(x86)\Java\jre6\lib\rt.jar;C:\Program Files 
(x86)\Java\jre6\lib\sunrsasign.jar;C:\Program Files 
(x86)\Java\jre6\lib\jsse.jar;C:\Program Files 
(x86)\Java\jre6\lib\jce.jar;C:\Program Files 
(x86)\Java\jre6\lib\charsets.jar;C:\Program Files (x86)\Java\jre6\classes
java.vendor = Sun Microsystems Inc.
file.separator = \
java.vendor.url.bug = http://java.sun.com/cgi-bin/bugreport.cgi
sun.io.unicode.encoding = UnicodeLittle
sun.cpu.endian = little
sun.desktop = windows
sun.cpu.isalist = pentium_pro+mmx pentium_pro pentium+mmx pentium i486 
i386 i86

-- Formats --
Successfully queried Zip reader.
Successfully queried APNG reader.
Successfully queried JPEG reader.
Successfully queried PGM reader.
Successfully queried Fits reader.
Successfully queried PCX reader.
Successfully queried GIF reader.
Successfully queried BMP reader.
Successfully queried IPLab reader.
Successfully queried Ivision reader.
Successfully queried Deltavision reader.
Successfully queried MRC reader.
Successfully queried Gatan reader.
Successfully queried GatanDM2 reader.
Successfully queried Imaris reader.
Successfully queried OpenlabRaw reader.
Successfully queried OMEXML reader.
Successfully queried LIF reader.
Successfully queried AVI reader.
Successfully queried Pict reader.
Initialized extra widgets for Pict reader.
Successfully queried SDT reader.
Initialized extra widgets for SDT reader.
Successfully queried EPS reader.
Successfully queried Slidebook reader.
Successfully queried Alicona reader.
Successfully queried MNG reader.
Successfully queried Khoros reader.
Successfully queried Visitech reader.
Successfully queried LIM reader.
Successfully queried PSD reader.
Successfully queried InCell reader.
Successfully queried L2D reader.
Successfully queried FEI reader.
Successfully queried NAF reader.
Successfully queried MINC reader.
Successfully queried QT reader.
Initialized extra widgets for QT reader.
Successfully queried MRW reader.
Successfully queried TillVision reader.
Successfully queried ARF reader.
Successfully queried Cellomics reader.
Successfully queried LiFlim reader.
Successfully queried Targa reader.
Successfully queried OxfordInstruments reader.
Successfully queried VGSAM reader.
Successfully queried HIS reader.
Successfully queried WATOP reader.
Successfully queried Seiko reader.
Successfully queried Topometrix reader.
Successfully queried UBM reader.
Successfully queried Quesant reader.
Successfully queried BioRadGel reader.
Successfully queried RHK reader.
Successfully queried MolecularImaging reader.
Successfully queried CellWorx reader.
Successfully queried Ecat7 reader.
Successfully queried VarianFDF reader.
Successfully queried AIM reader.
Successfully queried InCell3000 reader.
Successfully queried Spider reader.
Successfully queried Volocity reader.
Successfully queried Imagic reader.
Successfully queried HamamatsuVMS reader.
Successfully queried CellSens reader.
Successfully queried INR reader.
Successfully queried Kodak reader.
Successfully queried VolocityClipping reader.
Successfully queried ZeissCZI reader.
Successfully queried SIF reader.
Successfully queried NDPIS reader.
Successfully queried Povray reader.
Successfully queried IMOD reader.
Successfully queried Fake reader.
Successfully queried AFI reader.
Successfully queried Imspector reader.
Successfully queried BioRadSCN reader.
Successfully queried JEOL reader.
Successfully queried Nifti reader.
Successfully queried Analyze reader.
Successfully queried APL reader.
Successfully queried NRRD reader.
Successfully queried ICS reader.
Successfully queried PerkinElmer reader.
Successfully queried Amira reader.
Successfully queried Scanr reader.
Successfully queried BD reader.
Successfully queried Unisoku reader.
Successfully queried PDS reader.
Successfully queried Fuji reader.
Successfully queried Operetta reader.
Successfully queried Inveon reader.
Successfully queried CellVoyager reader.
Successfully queried BioRad reader.
Successfully queried FV1000 reader.
Successfully queried ZeissZVI reader.
Successfully queried IPW reader.
Successfully queried JPEG2000 reader.
Successfully queried JPX reader.
Successfully queried ND2 reader.
Initialized extra widgets for ND2 reader.
Successfully queried PCI reader.
Successfully queried ImarisHDF reader.
Successfully queried Wlz reader.
Successfully queried ZeissLSM reader.
Successfully queried SEQ reader.
Successfully queried Gel reader.
Successfully queried ImarisTiff reader.
Successfully queried Flex reader.
Error constructing widgets for Flex reader:
java.lang.RuntimeException: Unable to instantiate service for interface 
loci.formats.services.LuraWaveService
        at loci.plugins.config.FlexWidgets.<init>(FlexWidgets.java:70)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown 
Source)
        at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at java.lang.Class.newInstance0(Unknown Source)
        at java.lang.Class.newInstance(Unknown Source)
        at loci.plugins.config.FormatEntry.<init>(FormatEntry.java:79)
        at loci.plugins.config.ConfigWindow.run(ConfigWindow.java:311)
        at java.lang.Thread.run(Unknown Source)
Caused by: Unable to instantiate service for interface 
loci.formats.services.LuraWaveService
        at 
loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:173)
        at loci.plugins.config.FlexWidgets.<init>(FlexWidgets.java:67)
        ... 9 more
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown 
Source)
        at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at 
loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:171)
        ... 10 more
Caused by: java.lang.NoClassDefFoundError: com/luratech/lwf/lwfDecoder
        at 
loci.formats.services.LuraWaveServiceImpl.<init>(LuraWaveServiceImpl.java:89)
        ... 15 more
Caused by: java.lang.ClassNotFoundException: com.luratech.lwf.lwfDecoder
        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        ... 16 more
Successfully queried SVS reader.
Successfully queried Imacon reader.
Successfully queried LEO reader.
Successfully queried JPK reader.
Successfully queried NDPI reader.
Successfully queried PCORAW reader.
Successfully queried OMETiff reader.
Successfully queried PyramidTiff reader.
Successfully queried MIAS reader.
Successfully queried TCS reader.
Successfully queried Leica reader.
Successfully queried Nikon reader.
Successfully queried Fluoview reader.
Successfully queried Prairie reader.
Successfully queried Metamorph reader.
Successfully queried Micromanager reader.
Successfully queried ImprovisionTiff reader.
Successfully queried MetamorphTiff reader.
Successfully queried NikonTiff reader.
Successfully queried PhotoshopTiff reader.
Successfully queried FEITiff reader.
Successfully queried SimplePCITiff reader.
Successfully queried NikonElementsTiff reader.
Successfully queried Trestle reader.
Successfully queried SIS reader.
Successfully queried DNG reader.
Successfully queried ZeissTIFF reader.
Successfully queried LeicaSCN reader.
Successfully queried SlidebookTiff reader.
Successfully queried TiffDelegate reader.
Initialized extra widgets for TiffDelegate reader.
Successfully queried Text reader.
Successfully queried Burleigh reader.
Successfully queried Openlab reader.
Successfully queried Dicom reader.
Successfully queried SMCamera reader.
Successfully queried SBIG reader.
Successfully queried HRDGDF reader.
Successfully queried Hitachi reader.
Successfully queried Bruker reader.
Successfully queried CanonRaw reader.
Successfully queried OBF reader.

-- Libraries --
Found library Java:
    Version = 1.6.0_21 (Sun Microsystems Inc.)
    Path = C:\Program Files (x86)\Java\jre6\lib\rt.jar
Found library ImageJ:
    Path = Z:\ImageJ 2014-03-08\ij.jar
No library Java3D.
No library Jython.
No library MATLAB.
No library QuickTime for Java.
No library JAI Image I/O Tools - native codecs.
No library Nikon ND2 plugin.
Found library Bio-Formats plugins:
    Version = 12 March 2014
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
No library OME plugins.
No library Image5D.
No library View5D.
Found library Bio-Formats:
    Version = 12 March 2014
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
No library OME I/O.
No library VisBio.
No library Java Advanced Imaging.
No library JAI Image I/O Tools - Java wrapper.
Found library JAI Image I/O Tools - Java codecs:
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
Found library MDB Tools (Java port):
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
Found library NetCDF Java:
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
Found library Apache Jakarta POI (OME version):
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
Found library Simple Logging Facade for Java:
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
Found library OME-XML Java library:
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
No library OME-Java API.
No library Apache Jakarta Commons HttpClient.
No library Apache Jakarta Commons Logging.
No library Apache XML-RPC.
No library OMERO Common.
No library OMERO Client.
No library OMERO Data Model.
No library OMERO Importer.
No library Spring.
No library JBoss Client.
Found library JGoodies Forms:
    Path = Z:\IMAGEJ~2\plugins\bioformats_package.jar
No library OME Notes.
****end*****

Any Idea what's wrong?


Kind regards,
Peter


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