def _create_coord_list(self, filename):
import numpy as np
coords = CoordList()
time_data = read(filename, 'time')['time']
try:
alt_data = read(filename, 'altitude')['altitude']
except InvalidVariableError:
alt_data = read(filename, 'range')['range']
len_y = alt_data.shape[1]
time_arr = utils.expand_1d_to_2d_array(time_data[:], len_y, axis=1)
t_coord = Coord(time_arr, get_metadata(time_data), axis='x')
t_coord.convert_to_std_time()
coords.append(t_coord)
#alt_arr = utils.expand_1d_to_2d_array(alt_data[:], len_x, axis=0)
alt_arr = alt_data[:, :, 0] #eliminate "angle" axis
#alt_arr = alt_data #eliminate "angle" axis
coords.append(Coord(alt_arr, get_metadata(alt_data), axis='y'))
lat_data = read(filename, 'latitude')['latitude']
lat_arr = np.ones(alt_arr.shape) * lat_data[:]
coords.append(Coord(lat_arr, get_metadata(lat_data)))
lon_data = read(filename, 'longitude')['longitude']
lon_arr = np.ones(alt_arr.shape) * lon_data[:]
coords.append(Coord(lon_arr, get_metadata(lon_data)))
return coords
def _create_coord_list(self, filename):
import numpy as np
coords = CoordList()
time_data = read(filename, 'time')['time']
len_x = time_data.shape[0]
try:
alt_data = read(filename, 'altitude')['altitude']
except InvalidVariableError:
alt_data = read(filename, 'range')['range']
len_y = alt_data.shape[0]
time_arr = utils.expand_1d_to_2d_array(time_data[:], len_y, axis=1)
t_coord = Coord(time_arr, get_metadata(time_data), axis='x')
t_coord.convert_to_std_time()
coords.append(t_coord)
alt_arr = utils.expand_1d_to_2d_array(alt_data[:], len_x, axis=0)
coords.append(Coord(alt_arr, get_metadata(alt_data), axis='y'))
lat_data = read(filename, 'latitude')['latitude']
lat_arr = np.ones(alt_arr.shape) * lat_data[:]
coords.append(Coord(lat_arr, get_metadata(lat_data)))
lon_data = read(filename, 'longitude')['longitude']
lon_arr = np.ones(alt_arr.shape) * lon_data[:]
coords.append(Coord(lon_arr, get_metadata(lon_data)))
return coords
def _add_aux_coordinate(dim_coords, filename, aux_coord_name, length):
"""
Add an auxiliary coordinate to a list of (reshaped) dimension coordinates
:param dim_coords: CoordList of one-dimensional coordinates representing physical dimensions
:param filename: The data file containing the aux coord
:param aux_coord_name: The name of the aux coord to add to the coord list
:param length: The length of the data dimensions which this auxiliary coordinate should span
:return: A CoordList of reshaped (2D) physical coordinates plus the 2D auxiliary coordinate
"""
from cis.data_io.Coord import Coord
from cis.utils import expand_1d_to_2d_array
from cis.data_io.netcdf import read
# We assume that the auxilliary coordinate is the same shape across files
d = read(filename, [aux_coord_name])[aux_coord_name]
# Reshape to the length given
aux_data = expand_1d_to_2d_array(d[:], length, axis=0)
# Get the length of the auxiliary coordinate
len_y = d[:].size
for dim_coord in dim_coords:
dim_coord.data = expand_1d_to_2d_array(dim_coord.data, len_y, axis=1)
all_coords = dim_coords + [Coord(aux_data, get_metadata(d))]
return all_coords
def create_coords(self, filenames, variable=None):
"""
Reads the coordinates and data if required from the files
:param filenames: List of filenames to read coordinates from
:param variable: load a variable for the data
:return: Coordinates
"""
from iris.cube import Cube
from iris.coords import DimCoord
from cis.data_io.netcdf import read
from cis.utils import concatenate
data_variables, variable_selector = self._load_data(filenames, variable)
aux_coords = self._create_coordinates_list(data_variables, variable_selector)
dim_coords = [(DimCoord(np.arange(len(aux_coords[0].points)), var_name='obs'), (0,))]
if variable is None:
raise ValueError("Must specify variable")
aux_coord_name = variable_selector.find_auxiliary_coordinate(variable)
if aux_coord_name is not None:
# We assume that the auxilliary coordinate is the same shape across files
v = read(filenames[0], [aux_coord_name])[aux_coord_name]
aux_meta = get_metadata(v)
# We have to assume the shape here...
dim_coords.append((DimCoord(v[:], var_name=aux_coord_name, units=aux_meta.units,
long_name=aux_meta.long_name), (1,)))
cube_meta = get_metadata(data_variables[variable][0])
return Cube(concatenate([d[:] for d in data_variables[variable]]),
units=cube_meta.units, var_name=variable, long_name=cube_meta.long_name,
dim_coords_and_dims=dim_coords, aux_coords_and_dims=[(c, (0,)) for c in aux_coords])
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 create_coords(self, filenames, variable=None):
"""
Reads the coordinates and data if required from the files
:param filenames: List of filenames to read coordinates from
:param variable: load a variable for the data
:return: Coordinates
"""
from iris.cube import Cube
from iris.coords import DimCoord
from cis.data_io.netcdf import read
from cis.utils import concatenate
data_variables, variable_selector = self._load_data(
filenames, variable)
aux_coords = self._create_coordinates_list(data_variables,
variable_selector)
dim_coords = [(DimCoord(np.arange(len(aux_coords[0].points)),
var_name='obs'), (0, ))]
if variable is None:
raise ValueError("Must specify variable")
aux_coord_name = variable_selector.find_auxiliary_coordinate(variable)
if aux_coord_name is not None:
# We assume that the auxilliary coordinate is the same shape across files
v = read(filenames[0], [aux_coord_name])[aux_coord_name]
aux_meta = get_metadata(v)
# We have to assume the shape here...
dim_coords.append((DimCoord(v[:],
var_name=aux_coord_name,
units=aux_meta.units,
long_name=aux_meta.long_name), (1, )))
cube_meta = get_metadata(data_variables[variable][0])
return Cube(concatenate([d[:] for d in data_variables[variable]]),
units=cube_meta.units,
var_name=variable,
long_name=cube_meta.long_name,
dim_coords_and_dims=dim_coords,
aux_coords_and_dims=[(c, (0, )) for c in aux_coords])