A quick way to copy variables and metadata from one netcdf file to another using netcdf4-python

Converter.py

# -*- coding: utf-8 -*-
from netCDF4 import Dataset

#input file
dsin = Dataset("crop.nc")

#output file
dsout = Dataset("crop.nc3", "w", format="NETCDF3_CLASSIC")

#Copy dimensions
for dname, the_dim in dsin.dimensions.iteritems():
    print dname, len(the_dim)
    dsout.createDimension(dname, len(the_dim) if not the_dim.isunlimited() else None)


# Copy variables
for v_name, varin in dsin.variables.iteritems():
    outVar = dsout.createVariable(v_name, varin.datatype, varin.dimensions)
    print varin.datatype
    
    # Copy variable attributes
    outVar.setncatts({k: varin.getncattr(k) for k in varin.ncattrs()})
    
    outVar[:] = varin[:]
# close the output file
dsout.close()

I have just tested a python3 version of the script on a file I have:

https://github.com/guziy/PyNotebooks/blob/master/netcdf/test_copy.ipynb

Is it possible for you to share the problematic file? Just a small part of it that causes the error.

The input files I am using can be found here: ftp://ftp.nodc.noaa.gov/pub/data.nodc/ghrsst/GDS2/L4/GLOB/NCEI/AVHRR_OI/v2/2020/085/20200325120000-NCEI-L4_GHRSST-SSTblend-AVHRR_OI-GLOB-v02.0-fv02.0.nc

I have updated the example, by adding a special treatment for the _FillValue attribute.

https://github.com/guziy/PyNotebooks/blob/master/netcdf/test_copy.ipynb

I wanted to point out that there is maybe a more elegant way of doing it now with xarray:

with xarray.open_dataset("test.nc") as ds:
       # do things with ds1 = f(ds)
       ds1.to_netcdf("copy_test.nc")

Thanks That worked for me.
Cheers