def extract(core_netcdf):
"""
Extracts all CO and O3 data from a FAAM core netCDF.
"""
ncfilename = os.path.join(core_netcdf.path, core_netcdf.filename)
ds = FAAM_Dataset(ncfilename)
_ds_index = ds.index.ravel()
units = 'seconds since %s 00:00:00 +0000' % str(_ds_index[0])[:10]
timestamp = netCDF4.num2date(ds.variables['Time'][:].ravel(), units)
n = timestamp.size
if 'CO_AERO' in ds.variables.keys():
co_aero = ds.variables['CO_AERO'][:]
co_aero_flag = ds.variables['CO_AERO_FLAG'][:]
co_aero[co_aero_flag != 0] = -9999.0
else:
co_aero = np.zeros(n)-9999.0
if 'O3_TECO' in ds.variables.keys():
o3_teco = ds.variables['O3_TECO'][:]
o3_teco_flag = ds.variables['O3_TECO_FLAG'][:]
o3_teco[o3_teco_flag != 0] = -9999.0
else:
o3_teco = np.zeros(n)-9999.0
# Old FAAM files didn't have the GIN instrument fitted
if 'LAT_GIN' in ds.variables.keys():
lon_var_name = 'LON_GIN'
lat_var_name = 'LAT_GIN'
alt_var_name = 'ALT_GIN'
elif 'LAT_GPS' in ds.variables.keys():
lon_var_name = 'LON_GPS'
lat_var_name = 'LAT_GPS'
alt_var_name = 'GPS_ALT'
if len(ds.variables[lon_var_name][:].shape) > 1:
x = ds.variables[lon_var_name][:, 0].ravel()
y = ds.variables[lat_var_name][:, 0].ravel()
z = ds.variables[alt_var_name][:, 0].ravel()
else:
x = ds.variables[lon_var_name][:].ravel()
y = ds.variables[lat_var_name][:].ravel()
z = ds.variables[alt_var_name][:].ravel()
wow = ds.variables['WOW_IND'][:].ravel()
timestamp_string = [t.strftime('%Y-%m-%dT%H:%M:%S') for t in timestamp]
fid = [core_netcdf.fid,]*n
result = zip(list(np.array(timestamp_string)[wow == 0]),
list(np.array(fid)[wow == 0]),
list(x[wow == 0]),
list(y[wow == 0]),
list(z[wow == 0]),
list(co_aero[wow == 0]),
list(o3_teco[wow == 0]))
return result
# open the output file and write the column labels out
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