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"""
convert netCDF file to HDF5 using Scientific.IO.NetCDF and PyTables.
Jeff Whitaker <jeffrey.s.whitaker@noaa.gov>
Added some flags to select filters, as well as some small improvements.
Francesc Alted <faltet@pytables.com>
This requires Scientific from
http://starship.python.net/~hinsen/ScientificPython
"""
import sys, os.path, getopt, time
import tables.netcdf3
from tables.leaf import Filters
def nctoh5(ncfilename, h5filename, filters, verbose, overwritefile):
# open h5 file
if overwritefile:
h5file = tables.netcdf3.NetCDFFile(h5filename, mode = "w")
else:
h5file = tables.netcdf3.NetCDFFile(h5filename, mode = "a")
# convert to netCDF
nobjects, nbytes = h5file.nctoh5(ncfilename,filters=filters)
# ncdump-like output
if verbose:
print 'contents of hdf5 file:'
print '----------------------'
print h5file
# Close the file
h5file.close()
return nobjects, nbytes
def main():
if not tables.netcdf3.ScientificIONetCDF_imported:
sys.stderr.write(
'You need Scientific Python installed in order to use this utility.\n')
sys.exit(1)
usage = """usage: %s [-h] [-v] [-o] [--complevel=(0-9)] [--complib=lib] [--shuffle=(0|1)] [--fletcher32=(0|1)] netcdffilename hdf5filename
-h -- Print usage message.
-v -- Show more information.
-o -- Overwite destination file.
--complevel=(0-9) -- Set a compression level (0 for no compression, which
is the default).
--complib=lib -- Set the compression library to be used during the copy.
lib can be set to "zlib", "lzo" or "ucl". Defaults to "zlib".
--shuffle=(0|1) -- Activate or not the shuffling filter (default is active
if complevel>0).
--fletcher32=(0|1) -- Whether to activate or not the fletcher32 filter (not
active by default).
\n""" % os.path.basename(sys.argv[0])
try:
opts, pargs = getopt.getopt(sys.argv[1:], 'hvo',
['complevel=',
'complib=',
'shuffle=',
'fletcher32=',
])
except:
(type, value, traceback) = sys.exc_info()
print "Error parsing the options. The error was:", value
sys.stderr.write(usage)
sys.exit(0)
# default options
verbose = 0
overwritefile = 0
complevel = None
complib = None
shuffle = 0
fletcher32 = 0
# Get the options
for option in opts:
if option[0] == '-h':
sys.stderr.write(usage)
sys.exit(0)
elif option[0] == '-v':
verbose = 1
elif option[0] == '-o':
overwritefile = 1
elif option[0] == '--complevel':
complevel = int(option[1])
elif option[0] == '--complib':
complib = option[1]
elif option[0] == '--shuffle':
shuffle = int(option[1])
elif option[0] == '--fletcher32':
fletcher32 = int(option[1])
else:
print option[0], ": Unrecognized option"
sys.stderr.write(usage)
sys.exit(0)
# if we pass a number of files different from 2, abort
if len(pargs) <> 2:
print "You need to pass both source and destination!."
sys.stderr.write(usage)
sys.exit(0)
# Catch the files passed as the last arguments
ncfilename = pargs[0]
h5filename = pargs[1]
# Build the Filters instance
if complevel==None and complib==None and shuffle==0 and fletcher32==0:
filters = None
else:
if complevel is None: complevel = 0
if complib is None: complib = "zlib"
if fletcher32 is None: fletcher32 = 0
filters = Filters(complevel=complevel, complib=complib,
shuffle=shuffle, fletcher32=fletcher32)
# Some timing
t1 = time.time()
cpu1 = time.clock()
# Copy the file
if verbose:
print "+=+"*20
print "Starting conversion from %s to %s" % (ncfilename, h5filename)
if filters == None:
print "Using default filters (complevel=6,complib='zlib',shuffle=1,fletcher32=0)"
else:
print "Applying filters:", filters
print "+=+"*20
# Do the conversion
(nobjects, nbytes) = nctoh5(ncfilename, h5filename, filters, verbose, overwritefile)
# Gather some statistics
t2 = time.time()
cpu2 = time.clock()
tcopy = round(t2-t1, 3)
cpucopy = round(cpu2-cpu1, 3)
tpercent = int(round(cpucopy/tcopy, 2)*100)
if verbose:
print "Number of variables copied:", nobjects
print "KBytes copied:", round(nbytes/1024.,3)
print "Time copying: %s s (real) %s s (cpu) %s%%" % \
(tcopy, cpucopy, tpercent)
print "Copied variable/sec: ", round(nobjects / float(tcopy),1)
print "Copied KB/s :", int(nbytes / (tcopy * 1024))
|
