I need to process a single variable in a netcdf file that actually contains many attributes and variable.
I think it is not possible to update a netcdf file (see question How to delete a variable in a Scientific.IO.NetCDF.NetCDFFile?)
My approach is the following:
get the variable to process from the original file
process the variable
copy all data from the original netcdf BUT the processed variable to the final file
copy the processed variable to the final file
My problem is to code step 3. I started with the following:
def processing(infile, variable, outfile):
data = fileH.variables[variable][:]
# do processing on data...
# and now save the result
fileH = NetCDFFile(infile, mode="r")
outfile = NetCDFFile(outfile, mode='w')
# build a list of variables without the processed variable
listOfVariables = list( itertools.ifilter( lamdba x:x!=variable , fileH.variables.keys() ) )
for ivar in listOfVariables:
# here I need to write each variable and each attribute
How can I save all data and attribute in a handfull of code without having to rebuild a whole structure of data?
解决方案
Here's what I just used and worked. @arne's answer updated for Python 3 and also to include copying variable attributes:
import netCDF4 as nc
toexclude = ['ExcludeVar1', 'ExcludeVar2']
with netCDF4.Dataset("in.nc") as src, netCDF4.Dataset("out.nc", "w") as dst:
# copy global attributes all at once via dictionary
dst.setncatts(src.__dict__)
# copy dimensions
for name, dimension in src.dimensions.items():
dst.createDimension(
name, (len(dimension) if not dimension.isunlimited() else None))
# copy all file data except for the excluded
for name, variable in src.variables.items():
if name not in toexclude:
x = dst.createVariable(name, variable.datatype, variable.dimensions)
dst[name][:] = src[name][:]
# copy variable attributes all at once via dictionary
dst[name].setncatts(src[name].__dict__)