[ome-users] I/O problem during file import using Bio-Formats Importer in Fiji
CHODKOWSKI Robert
r.chodkowski at andor.com
Tue May 24 16:34:25 BST 2016
Hi,
My name is Robert and I'm a senior software engineer working in Andor Technology. I was trying to use Bio-Formats importer in Fiji to open files (Files->Import->Bio Formats) created in Imaris format (*.ims) and I was getting I/O error when trying to open multi-channel image. It seems to be a problem with metadata block being too big to open by NetcdfFile.open() method. I use the latest Bio-Formats plugin (v5.1.10) which uses netcdf-4.3.19.jar to open Imaris files. When I updated the netcdf library in Fiji\jars folder to the latest version (netcdfAll-4.6.5.jar) the problem with opening the Imaris files seems to be fixed. Would be possible to update netcdf library in the next Fiji release to fix this problem?
I also attached the ims file that causing the I/O error in Fiji.
Many Thanks,
Robert Chodkowski
Senior Software Engineer
Andor Technology
Springvale Business Park
7 Millennium Way,
Belfast,
Co. Antrim
BT12 7AL
Tel: +44 (0)28 9023 7126
mailto:r.chodkowski at andor.com
skype: andor.r.chodkowski
[Andor Bitplane]
[Oxford]
Error details:
[cid:image001.png at 01D1B5D8.D76F3D10]
Stack trace log:
java.io.IOException: java.lang.IllegalStateException: MessageDataspace: unknown version= 117
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:425)
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:392)
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:379)
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:367)
at loci.formats.services.NetCDFServiceImpl.init(NetCDFServiceImpl.java:307)
at loci.formats.services.NetCDFServiceImpl.setFile(NetCDFServiceImpl.java:100)
at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:247)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:216)
at ij.IJ.runPlugIn(IJ.java:180)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: MessageDataspace: unknown version= 117
at ucar.nc2.iosp.hdf5.H5header$MessageDataspace.read(H5header.java:2826)
at ucar.nc2.iosp.hdf5.H5header$MessageAttribute.read(H5header.java:3683)
at ucar.nc2.iosp.hdf5.H5header$DataObject.processAttributeInfoMessage(H5header.java:2364)
at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2332)
at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:2180)
at ucar.nc2.iosp.hdf5.H5header.getDataObject(H5header.java:2027)
at ucar.nc2.iosp.hdf5.H5header.access$600(H5header.java:70)
at ucar.nc2.iosp.hdf5.H5header$DataObjectFacade.<init>(H5header.java:2073)
at ucar.nc2.iosp.hdf5.H5header.readGroupNew(H5header.java:3911)
at ucar.nc2.iosp.hdf5.H5header.access$900(H5header.java:70)
at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2153)
at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:2118)
at ucar.nc2.iosp.hdf5.H5header.makeNetcdfGroup(H5header.java:472)
at ucar.nc2.iosp.hdf5.H5header.read(H5header.java:215)
at ucar.nc2.iosp.hdf5.H5iosp.open(H5iosp.java:128)
at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1521)
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:813)
at ucar.nc2.NetcdfFile.open(NetcdfFile.java:422)
... 17 more
Information about your version of Java:
os.arch => amd64
os.name => Windows 7
os.version => 6.1
java.version => 1.8.0_66
java.vendor => Oracle Corporation
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.8.0_66-b18
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 25.66-b18
java.vm.vendor => Oracle Corporation
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.8
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: C:\Tools\Fiji.app/java/win64/jdk1.8.0_66//jre
imagej.dir => C:\Tools\Fiji.app
Information about the version of each plugin:
Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160504193521)
Fiji: http://update.fiji.sc/ (last check:20160509090721)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160518185210)
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