Basic Tutorial

Let’t open some netCDF file with netCDF4. We will use test.nc located in tests directory

In [1]: from netCDF4 import Dataset
In [2]: fl = Dataset('./tests/test.nc')

And create ncfile instance:

In [3]: from fixnc import ncfile
In [4]: nc = ncfile(fl)

Here is how the header of the netCDF file will look like:

In [5]: nc
Out[5]:
File format: NETCDF4
Dimentions: X(10), Y(10), T(5)
variables:
         float32 T(T)
           unuts: hours since 2001-01-01 00:00:00
         float32 mytemp(T, X, Y)
           longname: Temperature
           shortname: temp

We would like to rename dimentions, update variable names and add some attributes. The netCDF header is represented as set of Ordered dictionaries. For example here are our dimentions:

In [6]: nc.dims
Out[6]:
OrderedDict([(u'X',
              OrderedDict([('name', u'X'),
                           ('size', 10),
                           ('isunlimited', False)])),
             (u'Y',
              OrderedDict([('name', u'Y'),
                           ('size', 10),
                           ('isunlimited', False)])),
             (u'T',
              OrderedDict([('name', u'T'),
                           ('size', 5),
                           ('isunlimited', True)]))])

We can change the names of dimentions with rename_dim method:

In [7]: nc.rename_dim('X','lon')
   ...: nc.rename_dim('Y','lat')
   ...: nc.rename_dim('T','time',)
   ...: nc
   ...:
Out[7]:
File format: NETCDF4
Dimentions: lon(10), lat(10), time(5)
variables:
         float32 T(time)
           unuts: hours since 2001-01-01 00:00:00
         float32 mytemp(time, lon, lat)
           longname: Temperature
           shortname: temp

Note, that names of the dimentions in the description of the variables are also changed. You can change this behaviour by setting renameall=False.

Now rename variables:

In [8]: nc.rename_var('T','time')
   ...: nc.rename_var('mytemp', 'temp')
   ...: nc
   ...:
Out[8]:
File format: NETCDF4
Dimentions: lon(10), lat(10), time(5)
variables:
         float32 time(time)
           unuts: hours since 2001-01-01 00:00:00
         float32 temp(time, lon, lat)
           longname: Temperature
           shortname: temp

Note that unit attribute for time is wrong, let’s fix it:

In [9]: nc.rename_attr('time','unuts','units')
   ...: nc
   ...:
Out[9]:
File format: NETCDF4
Dimentions: lon(10), lat(10), time(5)
variables:
         float32 time(time)
           units: hours since 2001-01-01 00:00:00
         float32 temp(time, lon, lat)
           longname: Temperature
           shortname: temp

Add a bit more information about time by providing additional attributes:

In [10]: nc.add_attr('time','standard_name', 'time')
    ...: nc.add_attr('time','calendar','proleptic_gregorian')
    ...: nc
    ...:
Out[10]:
File format: NETCDF4
Dimentions: lon(10), lat(10), time(5)
variables:
         float32 time(time)
           units: hours since 2001-01-01 00:00:00
           standard_name: time
           calendar: proleptic_gregorian
         float32 temp(time, lon, lat)
           longname: Temperature
           shortname: temp

And add some global attribute as well:

In [11]: nc.add_gattr('history','fixed with fixnc')
    ...: nc
    ...:
Out[11]:
File format: NETCDF4
Dimentions: lon(10), lat(10), time(5)
variables:
         float32 time(time)
           units: hours since 2001-01-01 00:00:00
           standard_name: time
           calendar: proleptic_gregorian
         float32 temp(time, lon, lat)
           longname: Temperature
           shortname: temp

         history:fixed with fixnc

Now we can save the result:

In [12]: nc.save('out.nc')

And compare once again the original and the resulting files:

In [14]: !ncdump -h ./tests/test.nc
netcdf test {
dimensions:
        X = 10 ;
        Y = 10 ;
        T = UNLIMITED ; // (5 currently)
variables:
        float T(T) ;
                T:unuts = "hours since 2001-01-01 00:00:00" ;
        float mytemp(T, X, Y) ;
                mytemp:longname = "Temperature" ;
                mytemp:shortname = "temp" ;
}

In [15]: !ncdump -h ./out.nc
netcdf out {
dimensions:
        lon = 10 ;
        lat = 10 ;
        time = UNLIMITED ; // (5 currently)
variables:
        float time(time) ;
                time:units = "hours since 2001-01-01 00:00:00" ;
                time:standard_name = "time" ;
                time:calendar = "proleptic_gregorian" ;
        float temp(time, lon, lat) ;
                temp:longname = "Temperature" ;
                temp:shortname = "temp" ;

// global attributes:
                :history = "fixed with fixnc" ;
}