def _add_available_aux_coords(self, cube, filenames):
from iris.aux_factory import HybridPressureFactory
from iris.coords import AuxCoord
from iris.exceptions import CoordinateNotFoundError
import iris
if cube.coords('hybrid A coefficient at layer midpoints'):
# First convert the hybrid coefficients to hPa, so that air pressure will be in hPa
cube.coord('hybrid A coefficient at layer midpoints').convert_units('hPa')
try:
surface_pressure = cube.coord('surface pressure')
except iris.exceptions.CoordinateNotFoundError as e:
# If there isn't a surface pressure coordinate we can try and pull out the lowest pressure level
with demote_warnings():
surface_pressure_cubes = iris.load(filenames, 'atmospheric pressure at interfaces',
callback=self.load_multiple_files_callback)
surface_pressure_cube = surface_pressure_cubes.concatenate_cube()[:, -1, :, :]
surface_pressure = AuxCoord(points=surface_pressure_cube.data, long_name='surface pressure', units='Pa')
cube.add_aux_coord(surface_pressure, (0, 2, 3))
surface_pressure.convert_units('hPa')
if len(cube.coords(long_name='hybrid level at layer midpoints')) > 0:
cube.add_aux_factory(HybridPressureFactory(delta=cube.coord('hybrid A coefficient at layer midpoints'),
sigma=cube.coord('hybrid B coefficient at layer midpoints'),
surface_air_pressure=surface_pressure))
def test_preserves_lazy(self):
test_bounds = np.array([[[11.0, 12.0], [12.0, 13.0], [13.0, 14.0]],
[[21.0, 22.0], [22.0, 23.0], [23.0, 24.0]]])
test_points = np.array([[11.1, 12.2, 13.3], [21.4, 22.5, 23.6]])
lazy_points = as_lazy_data(test_points)
lazy_bounds = as_lazy_data(test_bounds)
coord = AuxCoord(points=lazy_points, bounds=lazy_bounds, units='m')
coord.convert_units('ft')
self.assertTrue(coord.has_lazy_points())
self.assertTrue(coord.has_lazy_bounds())
test_points_ft = Unit('m').convert(test_points, 'ft')
test_bounds_ft = Unit('m').convert(test_bounds, 'ft')
self.assertArrayAllClose(coord.points, test_points_ft)
self.assertArrayAllClose(coord.bounds, test_bounds_ft)
def _add_available_aux_coords(self, cube, filenames):
import iris
from iris.aux_factory import HybridPressureFactory
from iris.coords import AuxCoord
from iris.exceptions import CoordinateNotFoundError
# Only do this for fields with a vertical component - this check is a bit hacky though (doesn't consider 3D with no time...)
if cube.ndim == 4:
# Only read the first file for these coefficients as they are time-independant and iris won't merge them
hybrid_a = _get_cubes(filenames, 'hybrid A coefficient at layer midpoints')
hybrid_b = _get_cubes(filenames, 'hybrid B coefficient at layer midpoints')
hybrid_a_coord = AuxCoord(points=hybrid_a[0].data, long_name='hybrid A coefficient at layer midpoints', units='Pa')
hybrid_b_coord = AuxCoord(points=hybrid_b[0].data, long_name='hybrid B coefficient at layer midpoints', units='1')
if cube.coords('surface pressure'):
surface_pressure = cube.coord('surface pressure')
else:
try:
# If there isn't a surface pressure coordinate we can try and pull out the lowest pressure level
surface_pressure_cubes = _get_cubes(filenames, 'atmospheric pressure at interfaces',
callback=self.load_multiple_files_callback)
surface_pressure_cube = surface_pressure_cubes.concatenate_cube()[:,-1,:,:]
surface_pressure = AuxCoord(points=surface_pressure_cube.data, long_name='surface pressure', units='Pa')
cube.add_aux_coord(surface_pressure, (0, 2, 3))
except ValueError:
# Try and get it from the vphysc stream
v_files = ['_'.join(f.split('_')[:-1]) + '_vphysc.nc' for f in filenames]
try:
surface_pressure_cubes = _get_cubes(v_files, 'atmospheric pressure at interfaces',
callback=self.load_multiple_files_callback)
except:
# If we can't do that then just exit - there must be a cleaner way to do this...
return
surface_pressure_cube = surface_pressure_cubes.concatenate_cube()[:,-1,:,:]
surface_pressure = AuxCoord(points=surface_pressure_cube.data, long_name='surface pressure', units='Pa')
cube.add_aux_coord(surface_pressure, (0, 2, 3))
# First convert the hybrid coefficients to hPa, so that air pressure will be in hPa
hybrid_a_coord.convert_units('hPa')
surface_pressure.convert_units('hPa')
cube.add_aux_coord(hybrid_a_coord, (1,))
cube.add_aux_coord(hybrid_b_coord, (1,))
if len(cube.coords(long_name='hybrid level at layer midpoints')) > 0:
cube.add_aux_factory(HybridPressureFactory(delta=hybrid_a_coord, sigma=hybrid_b_coord,
surface_air_pressure=surface_pressure))
def _add_available_aux_coords(self, cube, filenames):
from iris.aux_factory import HybridPressureFactory
from iris.coords import AuxCoord
from cis.data_io.netcdf import read
ps_filenames = [
f.replace('concbc', 'ps_TL95L80_192x48NH_3hr') for f in filenames
]
# These will be the same for all files
hybrid_a = read(ps_filenames[0], 'a')['a']
hybrid_b = read(ps_filenames[0], 'b')['b']
hybrid_a_coord = AuxCoord(
points=hybrid_a[:],
long_name='vertical coordinate formula term: a(k)',
units='Pa')
hybrid_b_coord = AuxCoord(
points=hybrid_b[:],
long_name='vertical coordinate formula term: b(k)',
units='1')
# This needs to be from each file and then merged
surface_pressure_cube = _get_cubes(
ps_filenames, 'ps',
callback=self.load_multiple_files_callback).concatenate_cube()
surface_pressure = AuxCoord(points=surface_pressure_cube.data,
standard_name='surface_air_pressure',
long_name='surface pressure',
units='Pa')
# First convert the hybrid coefficients to hPa, so that air pressure will be in hPa
hybrid_a_coord.convert_units('hPa')
surface_pressure.convert_units('hPa')
cube.add_aux_coord(surface_pressure, (0, 2, 3))
cube.add_aux_coord(hybrid_a_coord, (1, ))
cube.add_aux_coord(hybrid_b_coord, (1, ))
cube.add_aux_factory(
HybridPressureFactory(delta=hybrid_a_coord,
sigma=hybrid_b_coord,
surface_air_pressure=surface_pressure))
def _add_available_aux_coords(self, cube, filenames):
import iris
from iris.aux_factory import HybridPressureFactory
from iris.coords import AuxCoord
from iris.exceptions import CoordinateNotFoundError
# Only do this for fields with a vertical component - this check is a bit hacky though (doesn't consider 3D with no time...)
if cube.ndim == 4:
# Only read the first file for these coefficients as they are time-independant and iris won't merge them
hybrid_a = _get_cubes(filenames,
'hybrid A coefficient at layer midpoints')
hybrid_b = _get_cubes(filenames,
'hybrid B coefficient at layer midpoints')
hybrid_a_coord = AuxCoord(
points=hybrid_a[0].data,
long_name='hybrid A coefficient at layer midpoints',
units='Pa',
var_name='hyam')
hybrid_b_coord = AuxCoord(
points=hybrid_b[0].data,
long_name='hybrid B coefficient at layer midpoints',
units='1',
var_name='hybm')
if cube.coords('surface pressure'):
surface_pressure = cube.coord('surface pressure')
elif cube.coords('surface_air_pressure'):
surface_pressure = cube.coord('surface_air_pressure')
else:
try:
# If there isn't a surface pressure coordinate we can try loading it manually
surface_pressure_cube = _get_cubes(
filenames,
'surface_air_pressure',
callback=self.load_multiple_files_callback
).concatenate_cube()
surface_pressure = AuxCoord(
points=surface_pressure_cube.data,
standard_name='surface_air_pressure',
long_name='surface pressure',
units='Pa')
cube.add_aux_coord(surface_pressure, (0, 2, 3))
except ValueError:
try:
# If there isn't a surface pressure coordinate we can try and pull out the lowest pressure level
surface_pressure_cubes = _get_cubes(
filenames,
'atmospheric pressure at interfaces',
callback=self.load_multiple_files_callback)
surface_pressure_cube = surface_pressure_cubes.concatenate_cube(
)[:, -1, :, :]
surface_pressure = AuxCoord(
points=surface_pressure_cube.data,
long_name='surface pressure',
units='Pa')
cube.add_aux_coord(surface_pressure, (0, 2, 3))
except ValueError:
# Try and get it from the vphysc stream
v_files = [
'_'.join(f.split('_')[:-1]) + '_vphyscm.nc'
for f in filenames
]
try:
surface_pressure_cubes = _get_cubes(
v_files,
'atmospheric pressure at interfaces',
callback=self.load_multiple_files_callback)
except:
# If we can't do that then just exit - there must be a cleaner way to do this...
return
surface_pressure_cube = surface_pressure_cubes.concatenate_cube(
)[:, -1, :, :]
surface_pressure = AuxCoord(
points=surface_pressure_cube.data,
long_name='surface pressure',
units='Pa')
cube.add_aux_coord(surface_pressure, (0, 2, 3))
# First convert the hybrid coefficients to hPa, so that air pressure will be in hPa
hybrid_a_coord.convert_units('hPa')
surface_pressure.convert_units('hPa')
cube.add_aux_coord(hybrid_a_coord, (1, ))
cube.add_aux_coord(hybrid_b_coord, (1, ))
if len(cube.coords(
long_name='hybrid level at layer midpoints')) > 0:
cube.add_aux_factory(
HybridPressureFactory(
delta=hybrid_a_coord,
sigma=hybrid_b_coord,
surface_air_pressure=surface_pressure))
def create_data_object(self, filenames, variable):
logging.debug("Creating data object for variable " + variable)
variables = [("ER2_IMU/Longitude", "x"), ("ER2_IMU/Latitude", "y"),
("ER2_IMU/gps_time", "t"), ("State/Pressure", "p"),
("DataProducts/Altitude", "z"), ("header/date", ""),
(variable, '')]
logging.info("Listing coordinates: " + str(variables))
var_data = read_many_files_individually(filenames,
[v[0] for v in variables])
date_times = []
for times, date in zip(var_data['ER2_IMU/gps_time'],
var_data['header/date']):
# Date is stored as an array (of length 92??) of floats with format: yyyymmdd
date_str = str(int(date[0]))
t_unit = Unit('hours since {}-{}-{} 00:00:00'.format(
date_str[0:4], date_str[4:6], date_str[6:8]))
date_times.append(
t_unit.convert(get_data(times), cis_standard_time_unit))
# time_data = utils.concatenate([get_data(i) for i in var_data['ER2_IMU/gps_time']])
# date_str = str(int(var_data['header/date'][0][0]))
# Flatten the data by taking the 0th column of the transpose
time_coord = DimCoord(utils.concatenate(date_times).T[0],
standard_name='time',
units=cis_standard_time_unit)
# TODO This won't work for multiple files since the altitude bins are different for each flight...
alt_data = utils.concatenate(
[get_data(i) for i in var_data["DataProducts/Altitude"]])
alt_coord = DimCoord(alt_data[0], standard_name='altitude', units='m')
pres_data = utils.concatenate(
[get_data(i) for i in var_data["State/Pressure"]])
pres_coord = AuxCoord(pres_data,
standard_name='air_pressure',
units='atm')
# Fix the air-pressure units
pres_coord.convert_units('hPa')
lat_data = utils.concatenate(
[get_data(i) for i in var_data['ER2_IMU/Latitude']])
lat_coord = AuxCoord(lat_data.T[0], standard_name='latitude')
lon_data = utils.concatenate(
[get_data(i) for i in var_data['ER2_IMU/Longitude']])
lon_coord = AuxCoord(lon_data.T[0], standard_name='longitude')
data = utils.concatenate([get_data(i) for i in var_data[variable]])
metadata = get_metadata(var_data[variable][0])
cube = Cube(np.ma.masked_invalid(data),
long_name=metadata.misc['Description'],
units=self.clean_units(metadata.units),
dim_coords_and_dims=[(alt_coord, 1), (time_coord, 0)],
aux_coords_and_dims=[(lat_coord, (0, )),
(lon_coord, (0, )),
(pres_coord, (0, 1))])
gd = GriddedData.make_from_cube(cube)
return gd
