Python netCDF4 - adding a new variable to existing file with change in shape

Question

I have two netCDF files: file1.nc and file2.nc The only difference is that file1.nc contains one variable 'rho' which I want to append to file2.nc but by modifying the variables. The original file2.nc does not contain 'rho' in it. I am using Python module netCDF4.

import netCDF4 as ncd  
file1data=ncd.Dataset('file1.nc')

file1data.variables['rho']

<class 'netCDF4._netCDF4.Variable'> float64 rho(ocean_time, s_rho, eta_rho, xi_rho)
    long_name: density anomaly
    units: kilogram meter-3
    time: ocean_time
    grid: grid
    location: face
    coordinates: lon_rho lat_rho s_rho ocean_time
    field: density, scalar, series
    _FillValue: 1e+37 
unlimited dimensions: ocean_time 
current shape = (2, 15, 1100, 1000) 
filling on

So rho has shape of [2,15,1100,1000] but while adding to file2.nc, I only want to add rho[1,15,1100,1000] i.e. only the data of the second time step. This will result in 'rho' in file2.nc being of shape [15,1100,1000]. But I have been unable to do so.

I have been trying code like this:

file1data=ncd.Dataset('file1.nc')
rho2=file1data.variables['rho']
file2data=ncd.Dataset('file2.nc','r+') # I also tried with 'w' option; it does not work
file2data.createVariable('rho','float64')
file2data.variables['rho']=rho2  # to copy rho2's attributes
file2data.variables['rho'][:]=rho2[-1,15,1100,1000] # to modify rho's shape in file2.nc
file2data.close()

What am I missing here?

sorry I meant: So rho has shape of [2,15,1100,1000] but while adding to file2.nc, I only want to add rho[1, :, :, :] i.e. only the data of the second time step. — insane_oceanographer
– insane_oceanographer, Commented Jan 14, 2019 at 22:48
What are the variables and dimensions in the second file? Are they the same with file1? If in file2, you have array shaped [15,1100,1000], you should squeeze (use module NumPy) the dimensions i.e import numpy as np;file2data.variables['rho'][:]=np.squeeze(rho2[-1,15,1100,1000]) — msi_gerva
– msi_gerva, Commented Jan 15, 2019 at 10:30

msi_gerva · Accepted Answer · 2019-01-15 14:15:09Z

1

You have not specified the size of variable rho in your second netCDF file.

What you are doing is:

file2data.createVariable('rho','float64')

while it is supposed to be

file2data.createVariable('rho','float64',('ocean_time', 's_rho', 'eta_rho', 'xi_rho'))

answered Jan 15, 2019 at 14:15

msi_gerva

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