CODEWITHSUNDEEP
pythonnetcdfpython-xarray
user12938030
user12938030

Reputation: 117

edit an existing NetCDF / write a netcdf to the same name

I am trying to edit netcdf datasets and save them back to the same filename (e.g. to change the attributes or change variable names in a dataset). e.g.:

import xarray as xr
import numpy as np

data = xr.DataArray(np.random.randn(2, 3), coords={'x': ['a', 'b']}, dims=('x', 'y'))
data.to_netcdf('test.nc')

test_open=xr.open_dataset('test.nc')
test_open=test_open.rename({'__xarray_dataarray_variable__':'var'})
test_open.to_netcdf('test.nc')

This gives a 'permission denied' error "PermissionError: [Errno 13] Permission denied"

Reading https://github.com/pydata/xarray/issues/2887, it seems it's to do with the file being open, and I've also tried:

with xr.open_dataset('test.nc') as test_open:
    test_open=test_open.rename({'__xarray_dataarray_variable__':'var'})
    test_open.to_netcdf('test.nc')

or

with xr.open_dataset('test.nc') as test_open:
    test_open=test_open.rename({'__xarray_dataarray_variable__':'var'})
test_open.to_netcdf('test.nc')

I often need to do this with large datasets so would rather not load the dataset into memory, although even if I do I sometimes get 'HDF5' errors.

I don't fully understand what is causing the problem here, can anyone explain? It seems like it must be a common problem to change metadata on a dataset without having to load or rename the dataset. I'm using the latest version of xarray, 0.16.1.

Upvotes: 4

Views: 2942

Answers (1)

Eric Bridger
Eric Bridger

Reputation: 3794

From: https://xarray.pydata.org/en/stable/user-guide/io.html

"It is possible to append or overwrite netCDF variables using the mode='a' argument. When using this option, all variables in the dataset will be written to the original netCDF file, regardless if they exist in the original dataset."

In the python NetCDF library I use:

netCDF4.Dataset(file,'r+',clobber=True).

to edit attributes and variables in place. Perhaps clobber could be passed to xarray's **kwargs which get passed to the underlying NetCDF4 engine.

Upvotes: 1

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