[ome-users] I/O problem during file import using Bio-Formats Importer in Fiji
Sebastien Besson (Staff)
s.besson at dundee.ac.uk
Thu May 26 09:59:24 BST 2016
Hi Robert,
Many thanks for the detailed report, the file sharing and the investigation. We could indeed reproduce
the issue you described.
So far the netcdf dependency upgrade has been blocked by Java 6 which we will drop for
Bio-Formats 5.2.0. We will be looking into upgrading this HDF library as well as part of the next
release.
Also, is it possible for us to use your attached .ims file as a public sample?
Best,
Sebastien
On 24 May 2016, at 16:34, CHODKOWSKI Robert <r.chodkowski at andor.com<mailto:r.chodkowski at andor.com>> wrote:
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
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Error details:
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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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