how to read this netCDF file in python?

Question

I have this NetCDF file.

it has 2 groups in it! I want to select one group and get the desired variable. I tried this in multiple ways but I failed. I could use simply

print(ncfile.variables)

but it’s not working!

the file structure looks like this, i want to chose group /O4/ and variable ‘aerosol_optical_depth’

filename =
    'output.nc'
Source:
           C:UsersIITMDesktopworkoutput.nc
Format:
           netcdf4
Global Attributes:
           _NCProperties = 'version=2,netcdf=4.6.3,hdf5=1.10.2'
           version       = 1
Dimensions:
           DIM_SCAN_NAME  = 3
           DIM_ANGLE_NAME = 10
           DIM_LAYERS     = 20
Groups:
    /O4/
        Variables:
            vertical_column_density                                 
                   Size:       3x1
                   Dimensions: /DIM_SCAN_NAME
                   Datatype:   double
                   Attributes:
                               _FillValue  = NaN
                               description = 'o4 vertical column density'
                               units       = 'molec/cm5'
            aerosol_optical_depth                                   
                   Size:       3x1
                   Dimensions: /DIM_SCAN_NAME
                   Datatype:   single
                   Attributes:
                               _FillValue  = NaN
                               description = 'Total aerosol optical depth'
                               units       = '1'

 /TG/
        Variables:
            vertical_column_density                                  
                   Size:       3x1
                   Dimensions: /DIM_SCAN_NAME
                   Datatype:   single
                   Attributes:
                               _FillValue  = NaN
                               description = 'gas vertical column density'
                               units       = 'molec/cm2'
            vertical_column_density_error                            
                   Size:       3x1
                   Dimensions: /DIM_SCAN_NAME
                   Datatype:   single
                   Attributes:
                               _FillValue  = NaN
                               description = 'gas vertical column density error calculated from covariance smoothing error matrix, covariance measurement noise error matrix and systematic error as a fixed fraction of vcd'
                               units       = 'molec/cm2'

Asked By: Prithviraj Mali

||

Source

Answer 1

you should be able to access the variable as follows:

from netCDF4 import Dataset
file = 'C:UsersIITMDesktopworkoutput.nc'
with Dataset(file) as f:
    O4 = f.groups['O4'] # variable O4 references to group 'O4'...
    # extract everything (could also be just one variable)
    data_O4 = {}
    for attr in O4.ncattrs():
        data_O4[attr] = O4.getncattr(attr) # put everything from the group to a dict

AOD = data_O4['aerosol_optical_depth']

or more general, to import all groups/variables to a dict with nested dicts for each group:

nc_dct = {}
with Dataset(file) as f:
    for g in f.groups:
        tmp_grp = f.groups[g]
        nc_dct[g] = {}
        for attr in tmp_grp.ncattrs():
            nc_dct[g][attr] = tmp_grp.getncattr(attr)

Note: my ‘general’ solution won’t work properly if you have nested groups.

Answered By: FObersteiner

how to read this netCDF file in python?

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