[Pytables-users] nctoh5

[Jeff W. <jef...@no...>]

Hi:

I just wrote a script to convert a netcdf datasets to hdf5.  It's posted 
below, in case others might find it useful (you can try it on the files 
at ftp://ftp.cdc.noaa.gov/Datasets/ncep.reanalysis).   I have a question 
regarding EArrays - I see how to append values and to write the entire 
array at once, but is there a way to update an array record without 
re-writing the whole thing?  

Here's the nctoh5 script (requires Scientific from 
http://starship.python.net/~hinsen/ScientificPython).

"""
convert netCDF file to HDF5 using Scientific.IO.NetCDF and PyTables.
Jeff Whitaker <jef...@no...>
"""
import Scientific.IO.NetCDF as NetCDF
import tables, sys
# open netCDF file
ncfile = NetCDF.NetCDFFile(sys.argv[1],mode = "r")
# open h5 file.
h5file = tables.openFile(sys.argv[2], mode = "w")
# loop over variables in netCDF file.
for varname in ncfile.variables.keys():
    var = ncfile.variables[varname]
    vardims = list(var.dimensions)
    vardimsizes = [ncfile.dimensions[vardim] for vardim in vardims]
    # use long_name for title.
    if hasattr(var,'long_name'):
       title = var.long_name
    else: # or, just use some bogus title.
       title = varname + ' array'
    # if variable has unlimited dimension or has rank>1,
    # make it enlargeable (with zlib compression).
    if vardimsizes[0] == None or len(vardimsizes) > 1:
        vardimsizes[0] = 0
        vardata = h5file.createEArray(h5file.root, varname,
        tables.Atom(shape=tuple(vardimsizes),dtype=var.typecode(),),
        title,filters=tables.Filters(complevel=6,complib='zlib'))
    # write data to enlargeable array on record at a time.
    # (so the whole array doesn't have to be kept in memory).
        for n in range(var.shape[0]):
            vardata.append(var[n:n+1])
    # or else, create regular array write data to it all at once.
    else:
        vardata=h5file.createArray(h5file.root,varname,var[:],title)
    # set variable attributes.
    for key,val in var.__dict__.iteritems():
        setattr(vardata.attrs,key,val)
    setattr(vardata.attrs,'dimensions',tuple(vardims))
# set global (file) attributes.
for key,val in ncfile.__dict__.iteritems():
    setattr(h5file.root._v_attrs,key,val)
# Close the file
h5file.close()

-Jeff



-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/CDC1        FAX   : (303)497-6449
325 Broadway                Web   : http://www.cdc.noaa.gov/~jsw
Boulder, CO, USA 80305-3328 Office: Skaggs Research Cntr 1D-124