Last active
June 30, 2022 04:59
-
-
Save guziy/8543562 to your computer and use it in GitHub Desktop.
A quick way to copy variables and metadata from one netcdf file to another using netcdf4-python
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# -*- 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Adding the four lines again works fine with NETCDF3_CLASSIC, however, when I try to use the same for NETCDF4_CLASSIC format I get the following error:
Strange is the code stops suddenly when the Fillvalue of "analysed_sst" is about to be filled and gives an error. Till then all the variable attributes are fine. Also rest of the two more variables also is not copied in the new file.