The problem: CF compliant readers cannot read HOPS dataset directly. The solution: read with the netCDF4-python raw interface and create a CF object from the data.

NOTE: Ideally this should be a nco script that could be run as a CLI script and fix the files. Here I am using Python+iris. That works and could be written as a CLI script too. The main advantage is that it takes care of the CF boilerplate. However, this approach is to "heavy-weight" to be applied in many variables and files.



In [1]:

    
from netCDF4 import Dataset

url = ('http://geoport.whoi.edu/thredds/dodsC/usgs/data2/rsignell/gdrive/'
       'nsf-alpha/Data/MIT_MSEAS/MSEAS_Tides_20160317/mseas_tides_2015071612_2015081612_01h.nc')

nc = Dataset(url)

Extract lon, lat variables from vgrid2 and u, v variables from vbaro. The goal is to split the joint variables into individual CF compliant phenomena.



In [2]:

    
vtime = nc['time']
coords = nc['vgrid2']
vbaro = nc['vbaro']

Using iris to create the CF object.

NOTE: ideally lon, lat should be DimCoord like time and not AuxCoord, but iris refuses to create 2D DimCoord. Not sure if CF enforces that though.

First the Coordinates.

FIXME: change to a full time slice later!



In [3]:

    
itime = -1



In [4]:

    
import iris
iris.FUTURE.netcdf_no_unlimited = True

time = iris.coords.DimCoord(vtime[itime],
                            var_name='time',
                            long_name=vtime.long_name,
                            standard_name='longitude',
                            units=vtime.units)

longitude = iris.coords.AuxCoord(coords[:, :, 0],
                                 var_name='vlat',
                                 standard_name='longitude',
                                 units='degrees')

latitude = iris.coords.AuxCoord(coords[:, :, 1],
                                var_name='vlon',
                                standard_name='latitude',
                                units='degrees')

Now the phenomena.

NOTE: You don't need the broadcast_to trick if saving more than 1 time step. Here I just wanted the single time snapshot to have the time dimension to create a full example.



In [5]:

    
import numpy as np

u = vbaro[itime, :, :, 0]
u_cube = iris.cube.Cube(np.broadcast_to(u, (1,) + u.shape),
                        units=vbaro.units,
                        long_name=vbaro.long_name,
                        var_name='u',
                        standard_name='barotropic_eastward_sea_water_velocity',
                        dim_coords_and_dims=[(time, 0)],
                        aux_coords_and_dims=[(latitude, (1, 2)),
                                             (longitude, (1, 2))])

v = vbaro[itime, :, :, 1]
v_cube = iris.cube.Cube(np.broadcast_to(v, (1,) + v.shape),
                        units=vbaro.units,
                        long_name=vbaro.long_name,
                        var_name='v',
                        standard_name='barotropic_northward_sea_water_velocity',
                        dim_coords_and_dims=[(time, 0)],
                        aux_coords_and_dims=[(latitude, (1, 2)),
                                             (longitude, (1, 2))])

Join the individual CF phenomena into one dataset.



In [6]:

    
cubes = iris.cube.CubeList([u_cube, v_cube])

Save the CF-compliant file!



In [7]:

    
iris.save(cubes, 'hops.nc')



In [8]:

    
nc2 = netCDF4.Dataset('hops.nc','r+')
nc2









    



ncdump: /home/usgs/miniconda/envs/ioos/bin/../lib/./libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)
ncdump: /home/usgs/miniconda/envs/ioos/bin/../lib/./libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)
ncdump: /home/usgs/miniconda/envs/ioos/bin/../lib/./libcrypto.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)
netcdf hops {
dimensions:
	time = 1 ;
	dim1 = 866 ;
	dim2 = 1032 ;
variables:
	float u(time, dim1, dim2) ;
		u:standard_name = "barotropic_eastward_sea_water_velocity" ;
		string u:long_name = "barotropic velocity" ;
		u:units = "centimeter second-1" ;
		u:coordinates = "vlat vlon" ;
	float time(time) ;
		time:axis = "X" ;
		time:units = "seconds since 2015-07-16 12:00:00 0:00" ;
		time:standard_name = "longitude" ;
		string time:long_name = "time since initialization" ;
		time:calendar = "gregorian" ;
	float vlon(dim1, dim2) ;
		vlon:units = "degrees" ;
		vlon:standard_name = "latitude" ;
	float vlat(dim1, dim2) ;
		vlat:units = "degrees" ;
		vlat:standard_name = "longitude" ;
	float v(time, dim1, dim2) ;
		v:standard_name = "barotropic_northward_sea_water_velocity" ;
		string v:long_name = "barotropic velocity" ;
		v:units = "centimeter second-1" ;
		v:coordinates = "vlat vlon" ;

// global attributes:
		:Conventions = "CF-1.5" ;
}