def _add_available_aux_coords(self, cube, filenames):
"""
Add any altitude or pressure Auxiliary coordinates that IRIS does not load by default.
:type cube: data_io.gridded_data.GriddedData
:type filenames: list
:return:
"""
from iris.coords import AuxCoord
def _make_aux_coord_and_dims_from_geopotential(g_cube):
from scipy.constants import g
points = g_cube.data / g
dims = list(range(len(g_cube.shape)))
coord = AuxCoord(
points=points,
standard_name='altitude',
long_name='Geopotential height at layer midpoints',
var_name='altitude',
units='meter',
attributes={'positive': 'up'})
return coord, dims
def _make_aux_coord_and_dims_from_geopotential_height(g_ht_cube):
dims = list(range(len(g_ht_cube.shape)))
coord = AuxCoord(
points=g_ht_cube.data,
standard_name='altitude',
long_name='Geopotential height at layer midpoints',
var_name='altitude',
units='meter',
attributes={'positive': 'up'})
return coord, dims
def _make_aux_coord_and_dims_from_air_pressure(aps_cube):
dims = list(range(len(aps_cube.shape)))
coord = AuxCoord(points=aps_cube.data,
standard_name='air_pressure',
long_name='Air Pressure',
var_name='air_pressure',
units='Pa')
return coord, dims
aux_coord_creation_functions = {
'geopotential': _make_aux_coord_and_dims_from_geopotential,
'geopotential_height':
_make_aux_coord_and_dims_from_geopotential_height,
'air_pressure': _make_aux_coord_and_dims_from_air_pressure
}
for standard_name, make_aux_coord in list(
aux_coord_creation_functions.items()):
constraint = DisplayConstraint(
cube_func=lambda c: c.standard_name == standard_name,
display=standard_name)
try:
aux_cube = gridded_data.load_cube(filenames, constraint)
aux_coord, dims = make_aux_coord(aux_cube)
cube.add_aux_coord(aux_coord, dims)
except ValueError:
pass # The field doesn't exist; that's OK we just won't add it.
def _create_cube(self, filenames, variable):
"""Creates a cube for the specified variable.
:param filenames: List of filenames to read coordinates from
:param variable: Optional variable to read while we're reading the coordinates, can be a string or a
VariableConstraint object
:return: If variable was specified this will return an UngriddedData object, otherwise a CoordList
"""
import six
from cis.exceptions import InvalidVariableError
from cis.data_io.products.gridded_NetCDF import DisplayConstraint
from cis.data_io.gridded_data import load_cube
from iris.exceptions import CoordinateNotFoundError
# Check if the files given actually exist.
for filename in filenames:
with open(filename) as f:
pass
variable_constraint = variable
if isinstance(variable, six.string_types):
# noinspection PyPep8
variable_constraint = DisplayConstraint(
cube_func=(lambda c: c.var_name == variable or c.standard_name
== variable or c.long_name == variable),
display=variable)
if len(filenames) == 1:
callback_function = self.load_single_file_callback
else:
callback_function = self.load_multiple_files_callback
try:
cube = load_cube(filenames,
variable_constraint,
callback=callback_function)
except ValueError as e:
if variable is None:
message = "File contains more than one cube variable name must be specified"
elif e.args[0] == "No cubes found":
message = "Variable not found: {} \nTo see a list of variables run: cis info {}" \
.format(str(variable), filenames[0])
else:
message = e.args[0]
raise InvalidVariableError(message)
try:
hybrid_ht = cube.coord(name_or_coord='Hybrid height')
hybrid_ht.attributes[
'formula'] = 'z(k,j,i) = a(k) + b(k)*orog(j,i)'
hybrid_ht.convert_units('m')
except CoordinateNotFoundError as e:
pass
try:
cube.coord(long_name='t').standard_name = 'time'
except CoordinateNotFoundError as e:
pass
self._add_available_aux_coords(cube, filenames)
return cube
def _create_cube(self, filenames, variable):
"""Creates a cube for the specified variable.
:param filenames: List of filenames to read coordinates from
:param variable: Optional variable to read while we're reading the coordinates, can be a string or a
VariableConstraint object
:return: If variable was specified this will return an UngriddedData object, otherwise a CoordList
"""
from cis.exceptions import InvalidVariableError
from cis.data_io.products.gridded_NetCDF import DisplayConstraint
from cis.data_io.gridded_data import load_cube
from iris.exceptions import ConstraintMismatchError, CoordinateNotFoundError
# Check if the files given actually exist.
for filename in filenames:
with open(filename) as f:
pass
variable_constraint = variable
if isinstance(variable, basestring):
# noinspection PyPep8
variable_constraint = DisplayConstraint(cube_func=(lambda c: c.var_name == variable or
c.standard_name == variable or
c.long_name == variable), display=variable)
if len(filenames) == 1:
callback_function = self.load_single_file_callback
else:
callback_function = self.load_multiple_files_callback
try:
cube = load_cube(filenames, variable_constraint, callback=callback_function)
except ConstraintMismatchError as e:
if variable is None:
message = "File contains more than one cube variable name must be specified"
elif e.message == "no cubes found":
message = "Variable not found: {} \nTo see a list of variables run: cis info {}" \
.format(str(variable), filenames[0])
else:
message = e.message
raise InvalidVariableError(message)
except ValueError as e:
raise IOError(str(e))
try:
hybrid_ht = cube.coord(name_or_coord='Hybrid height')
hybrid_ht.attributes['formula'] = 'z(k,j,i) = a(k) + b(k)*orog(j,i)'
hybrid_ht.convert_units('m')
except CoordinateNotFoundError as e:
pass
try:
cube.coord(long_name='t').standard_name = 'time'
except CoordinateNotFoundError as e:
pass
self._add_available_aux_coords(cube, filenames)
return cube
def _add_available_aux_coords(self, cube, filenames):
"""
Add any altitude or pressure Auxiliary coordinates that IRIS does not load by default.
:type cube: data_io.gridded_data.GriddedData
:type filenames: list
:return:
"""
from iris.coords import AuxCoord
def _make_aux_coord_and_dims_from_geopotential(g_cube):
from scipy.constants import g
points = g_cube.data / g
dims = list(range(len(g_cube.shape)))
coord = AuxCoord(points=points,
standard_name='altitude',
long_name='Geopotential height at layer midpoints',
var_name='altitude',
units='meter',
attributes={'positive': 'up'})
return coord, dims
def _make_aux_coord_and_dims_from_geopotential_height(g_ht_cube):
dims = list(range(len(g_ht_cube.shape)))
coord = AuxCoord(points=g_ht_cube.data,
standard_name='altitude',
long_name='Geopotential height at layer midpoints',
var_name='altitude',
units='meter',
attributes={'positive': 'up'})
return coord, dims
def _make_aux_coord_and_dims_from_air_pressure(aps_cube):
dims = list(range(len(aps_cube.shape)))
coord = AuxCoord(points=aps_cube.data,
standard_name='air_pressure',
long_name='Air Pressure',
var_name='air_pressure',
units='Pa')
return coord, dims
aux_coord_creation_functions = {'geopotential': _make_aux_coord_and_dims_from_geopotential,
'geopotential_height': _make_aux_coord_and_dims_from_geopotential_height,
'air_pressure': _make_aux_coord_and_dims_from_air_pressure}
for standard_name, make_aux_coord in list(aux_coord_creation_functions.items()):
constraint = DisplayConstraint(cube_func=lambda c: c.standard_name == standard_name,
display=standard_name)
try:
aux_cube = gridded_data.load_cube(filenames, constraint)
aux_coord, dims = make_aux_coord(aux_cube)
cube.add_aux_coord(aux_coord, dims)
except iris.exceptions.ConstraintMismatchError:
pass # The field doesn't exist; that's OK we just won't add it.
def _create_cube(self, filenames, variable):
"""Creates a cube for the specified variable.
:param filenames: List of filenames to read coordinates from
:param variable: Optional variable to read while we're reading the coordinates, can be a string or a
VariableConstraint object
:return: If variable was specified this will return an UngriddedData object, otherwise a CoordList
"""
from cis.exceptions import InvalidVariableError
from cis.data_io import gridded_data
import iris
# Check if the files given actually exist.
for filename in filenames:
with open(filename) as f:
pass
variable_constraint = variable
if isinstance(variable, str):
variable_constraint = DisplayConstraint(cube_func=(lambda c: c.var_name == variable or
c.standard_name == variable or
c.long_name == variable), display=variable,
coord_values={'hybrid level at layer midpoints':
(lambda lev: lev == 31)})
if len(filenames) == 1:
callback_function = self.load_single_file_callback
else:
callback_function = self.load_multiple_files_callback
try:
cube = gridded_data.load_cube(filenames, variable_constraint, callback=callback_function)
except iris.exceptions.ConstraintMismatchError as e:
if variable is None:
message = "File contains more than one cube variable name must be specified"
elif e.message == "no cubes found":
message = "Variable not found: {} \nTo see a list of variables run: cis info {}" \
.format(str(variable), filenames[0])
else:
message = e.message
raise InvalidVariableError(message)
except ValueError as e:
raise IOError(str(e))
self._add_available_aux_coords(cube, filenames)
return cube
