Due to the current gap in continued funding from the U.S. National Science Foundation (NSF), the NSF Unidata Program Center has temporarily paused most operations. See NSF Unidata Pause in Most Operations for details.

[netcdfgroup] reading gziped vlen dataset

Hi all,

I am using netcdf within the BioFormats project [1]. I am trying to read a dataset (generated with HDF5) with properties:

No. of Dimensions: 1
Dimensions Size: 663
Max dimension size: Unlimited
Data Type: String, length = variable
Chunking: 55
Compression: GZIP: level 4, Storage level allocation time: Incremental

When I want to read the data I get following error. If the same dataset is not GZIP compressed, it works...

java.lang.IllegalStateException
    at ucar.nc2.iosp.IospHelper.readData(IospHelper.java:396)
    at ucar.nc2.iosp.IospHelper.readDataFill(IospHelper.java:292)
    at ucar.nc2.iosp.hdf5.H5iosp.readData(H5iosp.java:163)
    at ucar.nc2.iosp.hdf5.H5iosp.readData(H5iosp.java:141)
    at ucar.nc2.NetcdfFile.readData(NetcdfFile.java:1957)
    at ucar.nc2.Variable.reallyRead(Variable.java:841)
    at ucar.nc2.Variable._read(Variable.java:813)
    at ucar.nc2.Variable.read(Variable.java:691)
at loci.formats.services.NetCDFServiceImpl.getArray(NetCDFServiceImpl.java:168) at loci.formats.services.NetCDFServiceImpl.getVariableValue(NetCDFServiceImpl.java:150)
    at loci.formats.in.CellH5Reader.parseROIs(CellH5Reader.java:453)

Is reading of VLen data + Compression possible with NetCDF?

Thanks a lot!

Cheers,
Christoph
[1] http://www.openmicroscopy.org/site/support/bio-formats5/developers/java-library.html



  • 2014 messages navigation, sorted by:
    1. Thread
    2. Subject
    3. Author
    4. Date
    5. ↑ Table Of Contents
  • Search the netcdfgroup archives: