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michaesp |
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# coding:utf-8
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"""
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Module to read and write netcdf file.
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Interface to netCDF4
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"""
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import sys
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import netCDF4
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import numpy as np
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def read_var(filename, variables, index=slice(None)):
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""" Extract variables from a netCDF
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return a list of netCDF4 array
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with time as a datetime object if possible
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index should be a slice object like np.s_[0, :, 10]
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"""
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if type(variables) is not list:
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variables = [variables]
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vararray = []
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def check_var(nvariables, variables):
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nv = set(nvariables)
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v = set(variables)
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ok = set(nv).issuperset(v)
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if not ok:
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diffvar = set(v).difference(nv)
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err = '{} not found in {}\n. Available :{}'.format(
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",".join(diffvar), filename, ",".join(nvariables))
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raise Exception(err)
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with netCDF4.MFDataset(filename) as ncfile:
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check_var(list(ncfile.variables.keys()), variables)
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for var in variables:
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if var == 'time':
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time = ncfile.variables[var]
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try:
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vardata = netCDF4.num2date(time[:], units=time.units)
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except AttributeError:
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vardata = np.array(time)
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else:
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vardata = ncfile.variables[var][index]
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vararray.append(vardata.squeeze())
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return vararray
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def read_gattributes(filename):
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""" Read global attributes from a netCDF"""
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gattributes = netCDF4.Dataset(filename).__dict__
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return gattributes
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def read_dimensions(filename):
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""" Read dimensions"""
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dimensions = netCDF4.Dataset(filename).dimensions
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return dimensions
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def read_variables(filename):
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""" Read variables"""
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variables = list(netCDF4.Dataset(filename).variables.keys())
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return variables
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def create(outname, dimensions, gattributes):
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""" create a netCDF """
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ncfile = netCDF4.Dataset(outname, 'w', format='NETCDF3_CLASSIC')
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for dim in dimensions:
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ncfile.createDimension(dim[0], dim[1])
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ncfile.setncatts(gattributes)
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return ncfile
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def addvar(ncfile, varname, vardata, dimensions):
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""" Add a variable to a netcdf"""
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var = ncfile.createVariable(varname, vardata.dtype, dimensions)
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try:
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var[:] = vardata
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except Exception as e:
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sys.stderr.write('{0} in addvar()\n'.format(e))
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sys.exit(1)
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