[ome-users] IllegalStateException when reading .ims file

[Melissa Linkert]

Hi Lorenz,

> when I try to read the .ims file that I've uploaded to
> https://www.openmicroscopy.org/qa2/qa/feedback/9217
> 
> with a freshly downloaded version of Fiji, I get the IllegalStateException attached.

Thank you for reporting this.  There is now a ticket for this problem on
our issue tracking system:

https://trac.openmicroscopy.org.uk/ome/ticket/12257

You have been CC'd on the ticket, and will be notified as we update the
status (if you prefer not to be notified, just let me know).

Regards,
-Melissa

On Tue, May 06, 2014 at 04:54:15PM +0200, Maier, Lorenz wrote:
> Hi,
> 
> when I try to read the .ims file that I've uploaded to
> https://www.openmicroscopy.org/qa2/qa/feedback/9217
> 
> with a freshly downloaded version of Fiji, I get the IllegalStateException attached.
> 
> 
> Best,
> Lorenz

> java.io.IOException: java.lang.IllegalStateException: 
> 	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:300)
> 	at loci.formats.services.NetCDFServiceImpl.setFile(NetCDFServiceImpl.java:103)
> 	at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:241)
> 	at loci.formats.FormatReader.setId(FormatReader.java:1315)
> 	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
> 	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
> 	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:662)
> Caused by: java.lang.IllegalStateException: 
> 	at ucar.nc2.iosp.hdf5.FractalHeap.readIndirectBlock(FractalHeap.java:456)
> 	at ucar.nc2.iosp.hdf5.FractalHeap.<init>(FractalHeap.java:186)
> 	at ucar.nc2.iosp.hdf5.H5header$DataObject.processAttributeInfoMessage(H5header.java:2344)
> 	at ucar.nc2.iosp.hdf5.H5header$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

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