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
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