def test_simple_intersect(self):
cube = iris.cube.Cube(np.array([[1,2,3,4,5],
[2,3,4,5,6],
[3,4,5,6,7],
[4,5,6,7,8],
[5,6,7,8,9]], dtype=np.int32))
lonlat_cs = iris.coord_systems.RotatedGeogCS(10, 20)
cube.add_dim_coord(iris.coords.DimCoord(np.arange(5, dtype=np.float32) * 90 - 180, 'longitude', units='degrees', coord_system=lonlat_cs), 1)
cube.add_dim_coord(iris.coords.DimCoord(np.arange(5, dtype=np.float32) * 45 - 90, 'latitude', units='degrees', coord_system=lonlat_cs), 0)
cube.add_aux_coord(iris.coords.DimCoord(points=np.int32(11), long_name='pressure', units='Pa'))
cube.rename("temperature")
cube.units = "K"
cube2 = iris.cube.Cube(np.array([[1,2,3,4,5],
[2,3,4,5,6],
[3,4,5,6,7],
[4,5,6,7,8],
[5,6,7,8,50]], dtype=np.int32))
lonlat_cs = iris.coord_systems.RotatedGeogCS(10, 20)
cube2.add_dim_coord(iris.coords.DimCoord(np.arange(5, dtype=np.float32) * 90, 'longitude', units='degrees', coord_system=lonlat_cs), 1)
cube2.add_dim_coord(iris.coords.DimCoord(np.arange(5, dtype=np.float32) * 45 - 90, 'latitude', units='degrees', coord_system=lonlat_cs), 0)
cube2.add_aux_coord(iris.coords.DimCoord(points=np.int32(11), long_name='pressure', units='Pa'))
cube2.rename("")
r = iris.analysis.maths.intersection_of_cubes(cube, cube2)
self.assertCML(r, ('cdm', 'test_simple_cube_intersection.cml'))
def _make_cube(field, converter):
# Convert the field to a Cube.
(factories, references, standard_name, long_name, units, attributes,
cell_methods, dim_coords_and_dims, aux_coords_and_dims) = converter(field)
try:
data = field._data
except AttributeError:
data = field.data
cube = iris.cube.Cube(data,
attributes=attributes,
cell_methods=cell_methods,
dim_coords_and_dims=dim_coords_and_dims,
aux_coords_and_dims=aux_coords_and_dims)
# Temporary code to deal with invalid standard names in the
# translation table.
if standard_name is not None:
cube.rename(standard_name)
if long_name is not None:
cube.long_name = long_name
if units is not None:
# Temporary code to deal with invalid units in the translation
# table.
try:
cube.units = units
except ValueError:
msg = 'Ignoring PP invalid units {!r}'.format(units)
warnings.warn(msg)
cube.attributes['invalid_units'] = units
cube.units = iris.unit._UNKNOWN_UNIT_STRING
return cube, factories, references
def _sanitise_metadata(cube, unit):
"""
As part of the maths metadata contract, clear the necessary or
unsupported metadata from the resultant cube of the maths operation.
"""
# Clear the cube names.
cube.rename(None)
# Clear the cube cell methods.
cube.cell_methods = None
# Clear the cell measures.
for cm in cube.cell_measures():
cube.remove_cell_measure(cm)
# Clear the ancillary variables.
for av in cube.ancillary_variables():
cube.remove_ancillary_variable(av)
# Clear the STASH attribute, if present.
if "STASH" in cube.attributes:
del cube.attributes["STASH"]
# Set the cube units.
cube.units = unit
def _make_cube(field, converter):
# Convert the field to a Cube.
metadata = converter(field)
cube_data = field.core_data()
cube = iris.cube.Cube(cube_data,
attributes=metadata.attributes,
cell_methods=metadata.cell_methods,
dim_coords_and_dims=metadata.dim_coords_and_dims,
aux_coords_and_dims=metadata.aux_coords_and_dims)
# Temporary code to deal with invalid standard names in the
# translation table.
if metadata.standard_name is not None:
cube.rename(metadata.standard_name)
if metadata.long_name is not None:
cube.long_name = metadata.long_name
if metadata.units is not None:
# Temporary code to deal with invalid units in the translation
# table.
try:
cube.units = metadata.units
except ValueError:
msg = 'Ignoring PP invalid units {!r}'.format(metadata.units)
warnings.warn(msg)
cube.attributes['invalid_units'] = metadata.units
cube.units = cf_units._UNKNOWN_UNIT_STRING
return cube, metadata.factories, metadata.references
def _make_cube(field, converter):
# Convert the field to a Cube.
metadata = converter(field)
cube_data = field.core_data()
cube = iris.cube.Cube(cube_data,
attributes=metadata.attributes,
cell_methods=metadata.cell_methods,
dim_coords_and_dims=metadata.dim_coords_and_dims,
aux_coords_and_dims=metadata.aux_coords_and_dims)
# Temporary code to deal with invalid standard names in the
# translation table.
if metadata.standard_name is not None:
cube.rename(metadata.standard_name)
if metadata.long_name is not None:
cube.long_name = metadata.long_name
if metadata.units is not None:
# Temporary code to deal with invalid units in the translation
# table.
try:
cube.units = metadata.units
except ValueError:
msg = 'Ignoring PP invalid units {!r}'.format(metadata.units)
warnings.warn(msg)
cube.attributes['invalid_units'] = metadata.units
cube.units = cf_units._UNKNOWN_UNIT_STRING
return cube, metadata.factories, metadata.references
def _make_cube(field, converter):
# Convert the field to a Cube.
(factories, references, standard_name, long_name, units, attributes,
cell_methods, dim_coords_and_dims, aux_coords_and_dims) = converter(field)
try:
data = field._data
except AttributeError:
data = field.data
cube = iris.cube.Cube(data,
attributes=attributes,
cell_methods=cell_methods,
dim_coords_and_dims=dim_coords_and_dims,
aux_coords_and_dims=aux_coords_and_dims)
# Temporary code to deal with invalid standard names in the
# translation table.
if standard_name is not None:
cube.rename(standard_name)
if long_name is not None:
cube.long_name = long_name
if units is not None:
# Temporary code to deal with invalid units in the translation
# table.
try:
cube.units = units
except ValueError:
msg = 'Ignoring PP invalid units {!r}'.format(units)
warnings.warn(msg)
cube.attributes['invalid_units'] = units
cube.units = iris.unit._UNKNOWN_UNIT_STRING
return cube, factories, references
def _process_action_result(self, obj, cube):
"""Process the result of an action."""
factory = None
# NB. The names such as 'CoordAndDims' and 'CellMethod' are defined by
# the "deferred import" performed by Rule.run_actions() above.
if isinstance(obj, CoordAndDims):
obj.add_coord(cube)
#cell methods - not yet implemented
elif isinstance(obj, CellMethod):
cube.add_cell_method(obj)
elif isinstance(obj, CMAttribute):
# Temporary code to deal with invalid standard names from the translation table.
# TODO: when name is "standard_name" force the value to be a real standard name
if obj.name == 'standard_name' and obj.value is not None:
cube.rename(obj.value)
elif obj.name == 'units':
# Graceful loading of units.
try:
setattr(cube, obj.name, obj.value)
except ValueError:
msg = 'Ignoring PP invalid units {!r}'.format(obj.value)
warnings.warn(msg)
cube.attributes['invalid_units'] = obj.value
cube.units = cf_units._UNKNOWN_UNIT_STRING
else:
setattr(cube, obj.name, obj.value)
elif isinstance(obj, CMCustomAttribute):
cube.attributes[obj.name] = obj.value
elif isinstance(obj, Factory):
factory = obj
elif isinstance(obj, DebugString):
print(obj)
# The function returned nothing, like the pp save actions, "lbft = 3"
elif obj is None:
pass
else:
raise Exception(
"Object could not be added to cube. Unknown type: " +
obj.__class__.__name__)
return factory
def _process_action_result(self, obj, cube):
"""Process the result of an action."""
factory = None
# NB. The names such as 'CoordAndDims' and 'CellMethod' are defined by
# the "deferred import" performed by Rule.run_actions() above.
if isinstance(obj, CoordAndDims):
obj.add_coord(cube)
#cell methods - not yet implemented
elif isinstance(obj, CellMethod):
cube.add_cell_method(obj)
elif isinstance(obj, CMAttribute):
# Temporary code to deal with invalid standard names from the translation table.
# TODO: when name is "standard_name" force the value to be a real standard name
if obj.name == 'standard_name' and obj.value is not None:
cube.rename(obj.value)
elif obj.name == 'units':
# Graceful loading of units.
try:
setattr(cube, obj.name, obj.value)
except ValueError:
msg = 'Ignoring PP invalid units {!r}'.format(obj.value)
warnings.warn(msg)
cube.attributes['invalid_units'] = obj.value
cube.units = iris.unit._UNKNOWN_UNIT_STRING
else:
setattr(cube, obj.name, obj.value)
elif isinstance(obj, CMCustomAttribute):
cube.attributes[obj.name] = obj.value
elif isinstance(obj, Factory):
factory = obj
elif isinstance(obj, DebugString):
print obj
# The function returned nothing, like the pp save actions, "lbft = 3"
elif obj is None:
pass
else:
raise Exception("Object could not be added to cube. Unknown type: " + obj.__class__.__name__)
return factory
def _process_action_result(self, obj, cube):
"""Process the result of an action."""
factory = None
# NB. The names such as 'Coord' and 'CellMethod' are defined by
# the "deferred import" performed by Rule.run_actions() above.
if isinstance(obj, Coord):
cube.add_coord(obj)
elif isinstance(obj, CoordAndDims):
obj.add_coord(cube)
elif isinstance(obj, Factory):
factory = obj
#cell methods - not yet implemented
elif isinstance(obj, CellMethod):
cube.add_cell_method(obj)
elif isinstance(obj, DebugString):
print obj
elif isinstance(obj, CMAttribute):
# Temporary code to deal with invalid standard names from the translation table.
# TODO: when name is "standard_name" force the value to be a real standard name
if obj.name == 'standard_name' and obj.value is not None:
cube.rename(obj.value)
else:
setattr(cube, obj.name, obj.value)
elif isinstance(obj, CMCustomAttribute):
cube.attributes[obj.name] = obj.value
# The function returned nothing, like the pp save actions, "lbft = 3"
elif obj is None:
pass
else:
raise Exception("Object could not be added to cube. Unknown type: " + obj.__class__.__name__)
return factory
def calculate(name, cubelist):
"""Calculates any variable available from the cubelist
Args:
name (string): The CF standard name of the variable to be calculated
cubelist (iris.cube.CubeList): A cubelist containing either the
requested variable or the variables required to calculate the
requested variable
Returns:
iris.cube.Cube: The variable requested
Raises:
ValueError: If the requested variable is not available or there are
multiple matching cubes in the input `cubelist`.
"""
# If the cube is in the cubelist simply extract and return it
newcubelist = cubelist.extract(name)
if len(newcubelist) == 1:
return newcubelist[0].copy()
elif len(newcubelist) > 1:
raise ValueError('Multiple cubes found matching ' + name +
' not sure which to use')
# If an equation is present for the requested variable the try to derive the
# variable from existing cube in the input cubelist
elif name in available:
# Calculate all required variables
args = [calc(var, cubelist) for var in available[name]['required']]
# Call the function to calculate the requested variable
cube = available[name]['function'](*args)
cube.rename(name)
return cube
else:
raise ValueError('Can not get ' + name + ' from cubelist.')
def curl(i_cube, j_cube, k_cube=None, ignore=None):
r'''
Calculate the 3d curl of the given vector of cubes.
Args:
* i_cube
The i cube of the vector to operate on
* j_cube
The j cube of the vector to operate on
Kwargs:
* k_cube
The k cube of the vector to operate on
Return (i_cmpt_curl_cube, j_cmpt_curl_cube, k_cmpt_curl_cube)
The calculation of curl is dependent on the type of
:func:`iris.coord_systems.CoordSystem` in the cube:
Cartesian curl
The Cartesian curl is defined as:
.. math::
\nabla\times \vec u =
(\frac{\delta w}{\delta y} - \frac{\delta v}{\delta z})\vec a_i
-
(\frac{\delta w}{\delta x} - \frac{\delta u}{\delta z})\vec a_j
+
(\frac{\delta v}{\delta x} - \frac{\delta u}{\delta y})\vec a_k
Spherical curl
When spherical calculus is used, i_cube is the phi vector
component (e.g. eastward), j_cube is the theta component
(e.g. northward) and k_cube is the radial component.
The spherical curl is defined as:
.. math::
\nabla\times \vec A = \frac{1}{r cos \theta}
(\frac{\delta}{\delta \theta}
(\vec A_\phi cos \theta) -
\frac{\delta \vec A_\theta}{\delta \phi}) \vec r +
\frac{1}{r}(\frac{1}{cos \theta}
\frac{\delta \vec A_r}{\delta \phi} -
\frac{\delta}{\delta r} (r \vec A_\phi))\vec \theta +
\frac{1}{r}
(\frac{\delta}{\delta r}(r \vec A_\theta) -
\frac{\delta \vec A_r}{\delta \theta}) \vec \phi
where phi is longitude, theta is latitude.
'''
if ignore is not None:
ignore = None
warnings.warn('The ignore keyword to iris.analysis.calculus.curl '
'is deprecated, ignoring is now done automatically.')
# Get the vector quantity names.
# (i.e. ['easterly', 'northerly', 'vertical'])
vector_quantity_names, phenomenon_name = \
spatial_vectors_with_phenom_name(i_cube, j_cube, k_cube)
cubes = filter(None, [i_cube, j_cube, k_cube])
# get the names of all coords binned into useful comparison groups
coord_comparison = iris.analysis.coord_comparison(*cubes)
bad_coords = coord_comparison['ungroupable_and_dimensioned']
if bad_coords:
raise ValueError("Coordinates found in one cube that describe "
"a data dimension which weren't in the other "
"cube ({}), try removing this coordinate.".format(
', '.join(group.name() for group in bad_coords)))
bad_coords = coord_comparison['resamplable']
if bad_coords:
raise ValueError('Some coordinates are different ({}), consider '
'resampling.'.format(
', '.join(group.name() for group in bad_coords)))
ignore_string = ''
if coord_comparison['ignorable']:
ignore_string = ' (ignoring {})'.format(
', '.join(group.name() for group in bad_coords))
# Get the dim_coord, or None if none exist, for the xyz dimensions
x_coord = i_cube.coord(axis='X')
y_coord = i_cube.coord(axis='Y')
z_coord = i_cube.coord(axis='Z')
y_dim = i_cube.coord_dims(y_coord)[0]
horiz_cs = i_cube.coord_system('CoordSystem')
# Planar (non spherical) coords?
ellipsoidal = isinstance(horiz_cs, (iris.coord_systems.GeogCS,
iris.coord_systems.RotatedGeogCS))
if not ellipsoidal:
# TODO Implement some mechanism for conforming to a common grid
dj_dx = _curl_differentiate(j_cube, x_coord)
prototype_diff = dj_dx
# i curl component (dk_dy - dj_dz)
dk_dy = _curl_differentiate(k_cube, y_coord)
dk_dy = _curl_regrid(dk_dy, prototype_diff)
dj_dz = _curl_differentiate(j_cube, z_coord)
dj_dz = _curl_regrid(dj_dz, prototype_diff)
# TODO Implement resampling in the vertical (which regridding
# does not support).
if dj_dz is not None and dj_dz.data.shape != prototype_diff.data.shape:
dj_dz = _curl_change_z(dj_dz, z_coord, prototype_diff)
i_cmpt = _curl_subtract(dk_dy, dj_dz)
dj_dz = dk_dy = None
# j curl component (di_dz - dk_dx)
di_dz = _curl_differentiate(i_cube, z_coord)
di_dz = _curl_regrid(di_dz, prototype_diff)
# TODO Implement resampling in the vertical (which regridding
# does not support).
if di_dz is not None and di_dz.data.shape != prototype_diff.data.shape:
di_dz = _curl_change_z(di_dz, z_coord, prototype_diff)
dk_dx = _curl_differentiate(k_cube, x_coord)
dk_dx = _curl_regrid(dk_dx, prototype_diff)
j_cmpt = _curl_subtract(di_dz, dk_dx)
di_dz = dk_dx = None
# k curl component ( dj_dx - di_dy)
di_dy = _curl_differentiate(i_cube, y_coord)
di_dy = _curl_regrid(di_dy, prototype_diff)
# Since prototype_diff == dj_dx we don't need to recalculate dj_dx
# dj_dx = _curl_differentiate(j_cube, x_coord)
# dj_dx = _curl_regrid(dj_dx, prototype_diff)
k_cmpt = _curl_subtract(dj_dx, di_dy)
di_dy = dj_dx = None
result = [i_cmpt, j_cmpt, k_cmpt]
# Spherical coords (GeogCS or RotatedGeogCS).
else:
# A_\phi = i ; A_\theta = j ; A_\r = k
# theta = lat ; phi = long ;
# r_cmpt = 1 / (r * cos(lat)) *
# (d/dtheta (i_cube * sin(lat)) - d_j_cube_dphi)
# phi_cmpt = 1/r * ( d/dr (r * j_cube) - d_k_cube_dtheta)
# theta_cmpt = 1/r * ( 1/cos(lat) * d_k_cube_dphi - d/dr (r * i_cube)
if y_coord.name() != 'latitude' or x_coord.name() != 'longitude':
raise ValueError('Expecting latitude as the y coord and '
'longitude as the x coord for spherical curl.')
# Get the radius of the earth - and check for sphericity
ellipsoid = horiz_cs
if isinstance(horiz_cs, iris.coord_systems.RotatedGeogCS):
ellipsoid = horiz_cs.ellipsoid
if ellipsoid:
# TODO: Add a test for this
r = ellipsoid.semi_major_axis
r_unit = iris.unit.Unit("m")
spherical = (ellipsoid.inverse_flattening == 0.0)
else:
r = DEFAULT_SPHERICAL_EARTH_RADIUS
r_unit = DEFAULT_SPHERICAL_EARTH_RADIUS_UNIT
spherical = True
if not spherical:
raise ValueError('Cannot take the curl over a non-spherical '
'ellipsoid.')
lon_coord = x_coord.copy()
lat_coord = y_coord.copy()
lon_coord.convert_units('radians')
lat_coord.convert_units('radians')
lat_cos_coord = _coord_cos(lat_coord)
# TODO Implement some mechanism for conforming to a common grid
temp = iris.analysis.maths.multiply(i_cube, lat_cos_coord, y_dim)
dicos_dtheta = _curl_differentiate(temp, lat_coord)
prototype_diff = dicos_dtheta
# r curl component: 1 / (r * cos(lat)) * (dicos_dtheta - d_j_cube_dphi)
# Since prototype_diff == dicos_dtheta we don't need to
# recalculate dicos_dtheta.
d_j_cube_dphi = _curl_differentiate(j_cube, lon_coord)
d_j_cube_dphi = _curl_regrid(d_j_cube_dphi, prototype_diff)
new_lat_coord = d_j_cube_dphi.coord('latitude')
new_lat_cos_coord = _coord_cos(new_lat_coord)
lat_dim = d_j_cube_dphi.coord_dims(new_lat_coord)[0]
r_cmpt = iris.analysis.maths.divide(_curl_subtract(dicos_dtheta,
d_j_cube_dphi),
r * new_lat_cos_coord, dim=lat_dim)
r_cmpt.units = r_cmpt.units / r_unit
d_j_cube_dphi = dicos_dtheta = None
# phi curl component: 1/r * ( drj_dr - d_k_cube_dtheta)
drj_dr = _curl_differentiate(r * j_cube, z_coord)
if drj_dr is not None:
drj_dr.units = drj_dr.units * r_unit
drj_dr = _curl_regrid(drj_dr, prototype_diff)
d_k_cube_dtheta = _curl_differentiate(k_cube, lat_coord)
d_k_cube_dtheta = _curl_regrid(d_k_cube_dtheta, prototype_diff)
if drj_dr is None and d_k_cube_dtheta is None:
phi_cmpt = None
else:
phi_cmpt = 1/r * _curl_subtract(drj_dr, d_k_cube_dtheta)
phi_cmpt.units = phi_cmpt.units / r_unit
drj_dr = d_k_cube_dtheta = None
# theta curl component: 1/r * ( 1/cos(lat) * d_k_cube_dphi - dri_dr )
d_k_cube_dphi = _curl_differentiate(k_cube, lon_coord)
d_k_cube_dphi = _curl_regrid(d_k_cube_dphi, prototype_diff)
if d_k_cube_dphi is not None:
d_k_cube_dphi = iris.analysis.maths.divide(d_k_cube_dphi,
lat_cos_coord)
dri_dr = _curl_differentiate(r * i_cube, z_coord)
if dri_dr is not None:
dri_dr.units = dri_dr.units * r_unit
dri_dr = _curl_regrid(dri_dr, prototype_diff)
if d_k_cube_dphi is None and dri_dr is None:
theta_cmpt = None
else:
theta_cmpt = 1/r * _curl_subtract(d_k_cube_dphi, dri_dr)
theta_cmpt.units = theta_cmpt.units / r_unit
d_k_cube_dphi = dri_dr = None
result = [phi_cmpt, theta_cmpt, r_cmpt]
for direction, cube in zip(vector_quantity_names, result):
if cube is not None:
cube.rename('%s curl of %s' % (direction, phenomenon_name))
return result
def load_NAMEIII_trajectory(filename):
"""
Load a NAME III trajectory file returning a
generator of :class:`iris.cube.Cube` instances.
Args:
* filename (string):
Name of file to load.
Returns:
A generator :class:`iris.cube.Cube` instances.
"""
time_unit = cf_units.Unit('hours since epoch',
calendar=cf_units.CALENDAR_GREGORIAN)
with open(filename, 'r') as infile:
header = read_header(infile)
# read the column headings
for line in infile:
if line.startswith(" "):
break
headings = [heading.strip() for heading in line.split(",")]
# read the columns
columns = [[] for i in range(len(headings))]
for line in infile:
values = [v.strip() for v in line.split(",")]
for c, v in enumerate(values):
if "UTC" in v:
v = v.replace(":00 ", " ") # Strip out milliseconds.
v = datetime.datetime.strptime(v, NAMEIII_DATETIME_FORMAT)
else:
try:
v = float(v)
except ValueError:
pass
columns[c].append(v)
# Where's the Z column?
z_column = None
for i, heading in enumerate(headings):
if heading.startswith("Z "):
z_column = i
break
if z_column is None:
raise TranslationError("Expected a Z column")
# Every column up to Z becomes a coordinate.
coords = []
for name, values in zip(headings[:z_column+1], columns[:z_column+1]):
values = np.array(values)
if np.all(np.array(values) == values[0]):
values = [values[0]]
standard_name = long_name = units = None
if isinstance(values[0], datetime.datetime):
values = time_unit.date2num(values)
units = time_unit
if name == "Time":
name = "time"
elif " (Lat-Long)" in name:
if name.startswith("X"):
name = "longitude"
elif name.startswith("Y"):
name = "latitude"
units = "degrees"
elif name == "Z (m asl)":
name = "altitude"
units = "m"
long_name = "altitude above sea level"
elif name == "Z (m agl)":
name = 'height'
units = "m"
long_name = "height above ground level"
elif name == "Z (FL)":
name = "flight_level"
long_name = name
try:
coord = DimCoord(values, units=units)
except ValueError:
coord = AuxCoord(values, units=units)
coord.rename(name)
if coord.long_name is None and long_name is not None:
coord.long_name = long_name
coords.append(coord)
# Every numerical column after the Z becomes a cube.
for name, values in zip(headings[z_column+1:], columns[z_column+1:]):
try:
float(values[0])
except ValueError:
continue
# units embedded in column heading?
name, units = _split_name_and_units(name)
cube = iris.cube.Cube(values, units=units)
cube.rename(name)
for coord in coords:
dim = 0 if len(coord.points) > 1 else None
if isinstance(coord, DimCoord) and coord.name() == "time":
cube.add_dim_coord(coord.copy(), dim)
else:
cube.add_aux_coord(coord.copy(), dim)
yield cube
def _generate_cubes(header, column_headings, coords, data_arrays,
cell_methods=None):
"""
Yield :class:`iris.cube.Cube` instances given
the headers, column headings, coords and data_arrays extracted
from a NAME file.
"""
for i, data_array in enumerate(data_arrays):
# Turn the dictionary of column headings with a list of header
# information for each field into a dictionary of headings for
# just this field.
field_headings = {k: v[i] for k, v in six.iteritems(column_headings)}
# Make a cube.
cube = iris.cube.Cube(data_array)
# Determine the name and units.
name = '{} {}'.format(field_headings['Species'],
field_headings['Quantity'])
name = name.upper().replace(' ', '_')
cube.rename(name)
# Some units are not in SI units, are missing spaces or typed
# in the wrong case. _parse_units returns units that are
# recognised by Iris.
cube.units = _parse_units(field_headings['Unit'])
# Define and add the singular coordinates of the field (flight
# level, time etc.)
z_coord = _cf_height_from_name(field_headings['Z'])
cube.add_aux_coord(z_coord)
# Define the time unit and use it to serialise the datetime for
# the time coordinate.
time_unit = cf_units.Unit(
'hours since epoch', calendar=cf_units.CALENDAR_GREGORIAN)
# Build time, latitude and longitude coordinates.
for coord in coords:
pts = coord.values
coord_sys = None
if coord.name == 'latitude' or coord.name == 'longitude':
coord_units = 'degrees'
coord_sys = iris.coord_systems.GeogCS(EARTH_RADIUS)
if coord.name == 'time':
coord_units = time_unit
pts = time_unit.date2num(coord.values)
if coord.dimension is not None:
if coord.name == 'longitude':
circular = iris.util._is_circular(pts, 360.0)
else:
circular = False
icoord = DimCoord(points=pts,
standard_name=coord.name,
units=coord_units,
coord_system=coord_sys,
circular=circular)
if coord.name == 'time' and 'Av or Int period' in \
field_headings:
dt = coord.values - \
field_headings['Av or Int period']
bnds = time_unit.date2num(
np.vstack((dt, coord.values)).T)
icoord.bounds = bnds
else:
icoord.guess_bounds()
cube.add_dim_coord(icoord, coord.dimension)
else:
icoord = AuxCoord(points=pts[i],
standard_name=coord.name,
coord_system=coord_sys,
units=coord_units)
if coord.name == 'time' and 'Av or Int period' in \
field_headings:
dt = coord.values - \
field_headings['Av or Int period']
bnds = time_unit.date2num(
np.vstack((dt, coord.values)).T)
icoord.bounds = bnds[i, :]
cube.add_aux_coord(icoord)
# Headings/column headings which are encoded elsewhere.
headings = ['X', 'Y', 'Z', 'Time', 'Unit', 'Av or Int period',
'X grid origin', 'Y grid origin',
'X grid size', 'Y grid size',
'X grid resolution', 'Y grid resolution', ]
# Add the Main Headings as attributes.
for key, value in six.iteritems(header):
if value is not None and value != '' and \
key not in headings:
cube.attributes[key] = value
# Add the Column Headings as attributes
for key, value in six.iteritems(field_headings):
if value is not None and value != '' and \
key not in headings:
cube.attributes[key] = value
if cell_methods is not None:
cube.add_cell_method(cell_methods[i])
yield cube
def _generate_cubes(header,
column_headings,
coords,
data_arrays,
cell_methods=None):
"""
Yield :class:`iris.cube.Cube` instances given
the headers, column headings, coords and data_arrays extracted
from a NAME file.
"""
for i, data_array in enumerate(data_arrays):
# Turn the dictionary of column headings with a list of header
# information for each field into a dictionary of headings for
# just this field.
field_headings = {k: v[i] for k, v in column_headings.items()}
# Make a cube.
cube = iris.cube.Cube(data_array)
# Determine the name and units.
name = "{} {}".format(field_headings["Species"],
field_headings["Quantity"])
name = name.upper().replace(" ", "_")
cube.rename(name)
# Some units are not in SI units, are missing spaces or typed
# in the wrong case. _parse_units returns units that are
# recognised by Iris.
cube.units = _parse_units(field_headings["Units"])
# Define and add the singular coordinates of the field (flight
# level, time etc.)
if "Z" in field_headings:
(upper_bound, ) = [
field_headings["... to [Z]"]
if "... to [Z]" in field_headings else None
]
(lower_bound, ) = [
field_headings["... from [Z]"]
if "... from [Z]" in field_headings else None
]
z_coord = _cf_height_from_name(
field_headings["Z"],
upper_bound=upper_bound,
lower_bound=lower_bound,
)
cube.add_aux_coord(z_coord)
# Define the time unit and use it to serialise the datetime for
# the time coordinate.
time_unit = cf_units.Unit("hours since epoch",
calendar=cf_units.CALENDAR_GREGORIAN)
# Build time, height, latitude and longitude coordinates.
for coord in coords:
pts = coord.values
coord_sys = None
if coord.name == "latitude" or coord.name == "longitude":
coord_units = "degrees"
coord_sys = iris.coord_systems.GeogCS(EARTH_RADIUS)
if (coord.name == "projection_x_coordinate"
or coord.name == "projection_y_coordinate"):
coord_units = "m"
coord_sys = iris.coord_systems.OSGB()
if coord.name == "height":
coord_units = "m"
long_name = "height above ground level"
pts = coord.values
if coord.name == "altitude":
coord_units = "m"
long_name = "altitude above sea level"
pts = coord.values
if coord.name == "air_pressure":
coord_units = "Pa"
pts = coord.values
if coord.name == "flight_level":
pts = coord.values
long_name = "flight_level"
coord_units = _parse_units("FL")
if coord.name == "time":
coord_units = time_unit
pts = time_unit.date2num(coord.values).astype(float)
if coord.dimension is not None:
if coord.name == "longitude":
circular = iris.util._is_circular(pts, 360.0)
else:
circular = False
if coord.name == "flight_level":
icoord = DimCoord(points=pts,
units=coord_units,
long_name=long_name)
else:
icoord = DimCoord(
points=pts,
standard_name=coord.name,
units=coord_units,
coord_system=coord_sys,
circular=circular,
)
if coord.name == "height" or coord.name == "altitude":
icoord.long_name = long_name
if (coord.name == "time"
and "Av or Int period" in field_headings):
dt = coord.values - field_headings["Av or Int period"]
bnds = time_unit.date2num(np.vstack((dt, coord.values)).T)
icoord.bounds = bnds.astype(float)
else:
icoord.guess_bounds()
cube.add_dim_coord(icoord, coord.dimension)
else:
icoord = AuxCoord(
points=pts[i],
standard_name=coord.name,
coord_system=coord_sys,
units=coord_units,
)
if (coord.name == "time"
and "Av or Int period" in field_headings):
dt = coord.values - field_headings["Av or Int period"]
bnds = time_unit.date2num(np.vstack((dt, coord.values)).T)
icoord.bounds = bnds[i, :].astype(float)
cube.add_aux_coord(icoord)
# Headings/column headings which are encoded elsewhere.
headings = [
"X",
"Y",
"Z",
"Time",
"T",
"Units",
"Av or Int period",
"... from [Z]",
"... to [Z]",
"X grid origin",
"Y grid origin",
"X grid size",
"Y grid size",
"X grid resolution",
"Y grid resolution",
"Number of field cols",
"Number of preliminary cols",
"Number of fields",
"Number of series",
"Output format",
]
# Add the Main Headings as attributes.
for key, value in header.items():
if value is not None and value != "" and key not in headings:
cube.attributes[key] = value
# Add the Column Headings as attributes
for key, value in field_headings.items():
if value is not None and value != "" and key not in headings:
cube.attributes[key] = value
if cell_methods is not None:
cube.add_cell_method(cell_methods[i])
yield cube
def load_NAMEIII_trajectory(filename):
"""
Load a NAME III trajectory file returning a
generator of :class:`iris.cube.Cube` instances.
Args:
* filename (string):
Name of file to load.
Returns:
A generator :class:`iris.cube.Cube` instances.
"""
time_unit = cf_units.Unit("hours since epoch",
calendar=cf_units.CALENDAR_GREGORIAN)
with open(filename, "r") as infile:
header = read_header(infile)
# read the column headings
for line in infile:
if line.startswith(" "):
break
headings = [heading.strip() for heading in line.split(",")]
# read the columns
columns = [[] for i in range(len(headings))]
for line in infile:
values = [v.strip() for v in line.split(",")]
for c, v in enumerate(values):
if "UTC" in v:
v = datetime.datetime.strptime(v, NAMETRAJ_DATETIME_FORMAT)
else:
try:
v = float(v)
except ValueError:
pass
columns[c].append(v)
# Sort columns according to PP Index
columns_t = list(map(list, zip(*columns)))
columns_t.sort(key=itemgetter(1))
columns = list(map(list, zip(*columns_t)))
# Where's the Z column?
z_column = None
for i, heading in enumerate(headings):
if heading.startswith("Z "):
z_column = i
break
if z_column is None:
raise TranslationError("Expected a Z column")
# Every column up to Z becomes a coordinate.
coords = []
for name, values in zip(headings[:z_column + 1], columns[:z_column + 1]):
values = np.array(values)
if np.all(np.array(values) == values[0]):
values = [values[0]]
long_name = units = None
if isinstance(values[0], datetime.datetime):
values = time_unit.date2num(values).astype(float)
units = time_unit
if name == "Time":
name = "time"
elif " (Lat-Long)" in name:
if name.startswith("X"):
name = "longitude"
elif name.startswith("Y"):
name = "latitude"
units = "degrees"
elif name == "Z (m asl)":
name = "altitude"
units = "m"
long_name = "altitude above sea level"
elif name == "Z (m agl)":
name = "height"
units = "m"
long_name = "height above ground level"
elif name == "Z (FL)":
name = "flight_level"
long_name = name
try:
coord = DimCoord(values, units=units)
except ValueError:
coord = AuxCoord(values, units=units)
coord.rename(name)
if coord.long_name is None and long_name is not None:
coord.long_name = long_name
coords.append(coord)
# Every numerical column after the Z becomes a cube.
for name, values in zip(headings[z_column + 1:], columns[z_column + 1:]):
try:
float(values[0])
except ValueError:
continue
# units embedded in column heading?
name, units = _split_name_and_units(name)
cube = iris.cube.Cube(values, units=units)
cube.rename(name)
# Add the Main Headings as attributes.
for key, value in header.items():
if value is not None and value != "" and key not in headings:
cube.attributes[key] = value
# Add coordinates
for coord in coords:
dim = 0 if len(coord.points) > 1 else None
if dim == 0 and coord.name() == "time":
cube.add_dim_coord(coord.copy(), dim)
elif dim == 0 and coord.name() == "PP Index":
cube.add_dim_coord(coord.copy(), dim)
else:
cube.add_aux_coord(coord.copy(), dim)
yield cube
def curl(i_cube, j_cube, k_cube=None, ignore=None, update_history=True):
r'''
Calculate the 3d curl of the given vector of cubes.
Args:
* i_cube
The i cube of the vector to operate on
* j_cube
The j cube of the vector to operate on
Kwargs:
* k_cube
The k cube of the vector to operate on
Return (i_cmpt_curl_cube, j_cmpt_curl_cube, k_cmpt_curl_cube)
The calculation of curl is dependent on the type of :func:`iris.coord_systems.HorizontalCS` in the cube:
Cartesian curl
The Cartesian curl is defined as:
.. math::
\nabla\times \vec u = (\frac{\delta w}{\delta y} - \frac{\delta v}{\delta z}) \vec a_i - (\frac{\delta w}{\delta x} - \frac{\delta u}{\delta z})\vec a_j + (\frac{\delta v}{\delta x} - \frac{\delta u}{\delta y})\vec a_k
Spherical curl
When spherical calculus is used, i_cube is the phi vector component (e.g. eastward), j_cube is the theta component
(e.g. northward) and k_cube is the radial component.
The spherical curl is defined as:
.. math::
\nabla\times \vec A = \frac{1}{r cos \theta}(\frac{\delta}{\delta \theta}(\vec A_\phi cos \theta) - \frac{\delta \vec A_\theta}{\delta \phi}) \vec r + \frac{1}{r}(\frac{1}{cos \theta} \frac{\delta \vec A_r}{\delta \phi} - \frac{\delta}{\delta r} (r \vec A_\phi))\vec \theta + \frac{1}{r}(\frac{\delta}{\delta r}(r \vec A_\theta) - \frac{\delta \vec A_r}{\delta \theta}) \vec \phi
where phi is longitude, theta is latitude.
'''
if ignore is not None:
ignore = None
warnings.warn('The ignore keyword to iris.analysis.calculus.curl is deprecated, ignoring is now done automatically.')
# get the radius of the earth
latlon_cs = i_cube.coord_system(iris.coord_systems.LatLonCS)
if latlon_cs and latlon_cs.datum.is_spherical():
r = latlon_cs.datum.semi_major_axis
r_unit = latlon_cs.datum.units
else:
r = iris.analysis.cartography.DEFAULT_SPHERICAL_EARTH_RADIUS
r_unit = iris.analysis.cartography.DEFAULT_SPHERICAL_EARTH_RADIUS_UNIT
# Get the vector quantity names (i.e. ['easterly', 'northerly', 'vertical'])
vector_quantity_names, phenomenon_name = spatial_vectors_with_phenom_name(i_cube, j_cube, k_cube)
cubes = filter(None, [i_cube, j_cube, k_cube])
# get the names of all coords binned into useful comparison groups
coord_comparison = iris.analysis.coord_comparison(*cubes)
bad_coords = coord_comparison['ungroupable_and_dimensioned']
if bad_coords:
raise ValueError("Coordinates found in one cube that describe a data dimension which weren't in the other "
"cube (%s), try removing this coordinate." % ', '.join([group.name() for group in bad_coords]))
bad_coords = coord_comparison['resamplable']
if bad_coords:
raise ValueError('Some coordinates are different (%s), consider resampling.' % ', '.join([group.name() for group in bad_coords]))
ignore_string = ''
if coord_comparison['ignorable']:
ignore_string = ' (ignoring %s)' % ', '.join([group.name() for group in bad_coords])
# Get the dim_coord, or None if none exist, for the xyz dimensions
x_coord = i_cube.coord(axis='X')
y_coord = i_cube.coord(axis='Y')
z_coord = i_cube.coord(axis='Z')
y_dim = i_cube.coord_dims(y_coord)[0]
horiz_cs = i_cube.coord_system('HorizontalCS')
if horiz_cs is None:
raise ValueError('Could not get the horizontal CS of the cubes provided.')
if horiz_cs.cs_type == iris.coord_systems.CARTESIAN_CS:
# TODO Implement some mechanism for conforming to a common grid
dj_dx = _curl_differentiate(j_cube, x_coord)
prototype_diff = dj_dx
# i curl component (dk_dy - dj_dz)
dk_dy = _curl_differentiate(k_cube, y_coord)
dk_dy = _curl_regrid(dk_dy, prototype_diff)
dj_dz = _curl_differentiate(j_cube, z_coord)
dj_dz = _curl_regrid(dj_dz, prototype_diff)
# TODO Implement resampling in the vertical (which regridding does not support).
if dj_dz is not None and dj_dz.data.shape != prototype_diff.data.shape:
dj_dz = _curl_change_z(dj_dz, z_coord, prototype_diff)
i_cmpt = _curl_subtract(dk_dy, dj_dz)
dj_dz = dk_dy = None
# j curl component (di_dz - dk_dx)
di_dz = _curl_differentiate(i_cube, z_coord)
di_dz = _curl_regrid(di_dz, prototype_diff)
# TODO Implement resampling in the vertical (which regridding does not support).
if di_dz is not None and di_dz.data.shape != prototype_diff.data.shape:
di_dz = _curl_change_z(di_dz, z_coord, prototype_diff)
dk_dx = _curl_differentiate(k_cube, x_coord)
dk_dx = _curl_regrid(dk_dx, prototype_diff)
j_cmpt = _curl_subtract(di_dz, dk_dx)
di_dz = dk_dx = None
# k curl component ( dj_dx - di_dy)
di_dy = _curl_differentiate(i_cube, y_coord)
di_dy = _curl_regrid(di_dy, prototype_diff)
# Since prototype_diff == dj_dx we don't need to recalculate dj_dx
# dj_dx = _curl_differentiate(j_cube, x_coord)
# dj_dx = _curl_regrid(dj_dx, prototype_diff)
k_cmpt = _curl_subtract(dj_dx, di_dy)
di_dy = dj_dx = None
result = [i_cmpt, j_cmpt, k_cmpt]
elif horiz_cs.cs_type == iris.coord_systems.SPHERICAL_CS:
# A_\phi = i ; A_\theta = j ; A_\r = k
# theta = lat ; phi = long ;
# r_cmpt = 1/ ( r * cos(lat) ) * ( d/dtheta ( i_cube * sin( lat ) ) - d_j_cube_dphi )
# phi_cmpt = 1/r * ( d/dr (r * j_cube) - d_k_cube_dtheta)
# theta_cmpt = 1/r * ( 1/cos(lat) * d_k_cube_dphi - d/dr (r * i_cube)
if not horiz_cs.datum.is_spherical():
raise NotImplementedError('Cannot take the curl over a non-spherical datum.')
if y_coord.name() != 'latitude' or x_coord.name() != 'longitude':
raise ValueError('Expecting latitude as the y coord and longitude as the x coord for spherical curl.')
lon_coord = x_coord.unit_converted('radians')
lat_coord = y_coord.unit_converted('radians')
lat_cos_coord = _coord_cos(lat_coord)
# TODO Implement some mechanism for conforming to a common grid
temp = iris.analysis.maths.multiply(i_cube, lat_cos_coord, y_dim)
dicos_dtheta = _curl_differentiate(temp, lat_coord)
prototype_diff = dicos_dtheta
# r curl component: 1/ ( r * cos(lat) ) * ( dicos_dtheta - d_j_cube_dphi )
# Since prototype_diff == dicos_dtheta we don't need to recalculate dicos_dtheta
d_j_cube_dphi = _curl_differentiate(j_cube, lon_coord)
d_j_cube_dphi = _curl_regrid(d_j_cube_dphi, prototype_diff)
new_lat_coord = d_j_cube_dphi.coord(name='latitude')
new_lat_cos_coord = _coord_cos(new_lat_coord)
lat_dim = d_j_cube_dphi.coord_dims(new_lat_coord)[0]
r_cmpt = iris.analysis.maths.divide(_curl_subtract(dicos_dtheta, d_j_cube_dphi), r * new_lat_cos_coord, dim=lat_dim)
r_cmpt.units = r_cmpt.units / r_unit
d_j_cube_dphi = dicos_dtheta = None
# phi curl component: 1/r * ( drj_dr - d_k_cube_dtheta)
drj_dr = _curl_differentiate(r * j_cube, z_coord)
if drj_dr is not None:
drj_dr.units = drj_dr.units * r_unit
drj_dr = _curl_regrid(drj_dr, prototype_diff)
d_k_cube_dtheta = _curl_differentiate(k_cube, lat_coord)
d_k_cube_dtheta = _curl_regrid(d_k_cube_dtheta, prototype_diff)
if drj_dr is None and d_k_cube_dtheta is None:
phi_cmpt = None
else:
phi_cmpt = 1/r * _curl_subtract(drj_dr, d_k_cube_dtheta)
phi_cmpt.units = phi_cmpt.units / r_unit
drj_dr = d_k_cube_dtheta = None
# theta curl component: 1/r * ( 1/cos(lat) * d_k_cube_dphi - dri_dr )
d_k_cube_dphi = _curl_differentiate(k_cube, lon_coord)
d_k_cube_dphi = _curl_regrid(d_k_cube_dphi, prototype_diff)
if d_k_cube_dphi is not None:
d_k_cube_dphi = iris.analysis.maths.divide(d_k_cube_dphi, lat_cos_coord)
dri_dr = _curl_differentiate(r * i_cube, z_coord)
if dri_dr is not None:
dri_dr.units = dri_dr.units * r_unit
dri_dr = _curl_regrid(dri_dr, prototype_diff)
if d_k_cube_dphi is None and dri_dr is None:
theta_cmpt = None
else:
theta_cmpt = 1/r * _curl_subtract(d_k_cube_dphi, dri_dr)
theta_cmpt.units = theta_cmpt.units / r_unit
d_k_cube_dphi = dri_dr = None
result = [phi_cmpt, theta_cmpt, r_cmpt]
else:
raise ValueError("Horizontal coord system neither cartesian nor spherical spheroid: %s %s (%s)" \
% (type(horiz_cs), horiz_cs.cs_type, horiz_cs.datum))
for direction, cube in zip(vector_quantity_names, result):
if cube is not None:
cube.rename('%s curl of %s' % (direction, phenomenon_name))
if update_history:
# Add history in place
if k_cube is None:
cube.add_history('%s cmpt of the curl of %s and %s%s' % \
(direction, i_cube.name(), j_cube.name(), ignore_string))
else:
cube.add_history('%s cmpt of the curl of %s, %s and %s%s' % \
(direction, i_cube.name(), j_cube.name(), k_cube.name(), ignore_string))
return result
def load_NAMEIII_trajectory(filename):
"""
Load a NAME III trajectory file returning a
generator of :class:`iris.cube.Cube` instances.
Args:
* filename (string):
Name of file to load.
Returns:
A generator :class:`iris.cube.Cube` instances.
"""
time_unit = iris.unit.Unit('hours since epoch',
calendar=iris.unit.CALENDAR_GREGORIAN)
with open(filename, 'r') as infile:
header = read_header(infile)
# read the column headings
for line in infile:
if line.startswith(" "):
break
headings = [heading.strip() for heading in line.split(",")]
# read the columns
columns = [[] for i in range(len(headings))]
for line in infile:
values = [v.strip() for v in line.split(",")]
for c, v in enumerate(values):
if "UTC" in v:
v = v.replace(":00 ", " ") # Strip out milliseconds.
v = datetime.datetime.strptime(v, NAMEIII_DATETIME_FORMAT)
else:
try:
v = float(v)
except ValueError:
pass
columns[c].append(v)
# Where's the Z column?
z_column = None
for i, heading in enumerate(headings):
if heading.startswith("Z "):
z_column = i
break
if z_column is None:
raise iris.exceptions.TranslationError("Expected a Z column")
# Every column up to Z becomes a coordinate.
coords = []
for name, values in izip(headings[:z_column + 1], columns[:z_column + 1]):
values = np.array(values)
if np.all(np.array(values) == values[0]):
values = [values[0]]
standard_name = long_name = units = None
if isinstance(values[0], datetime.datetime):
values = time_unit.date2num(values)
units = time_unit
if name == "Time":
name = "time"
elif " (Lat-Long)" in name:
if name.startswith("X"):
name = "longitude"
elif name.startswith("Y"):
name = "latitude"
units = "degrees"
elif name == "Z (m asl)":
name = "height"
units = "m"
try:
coord = DimCoord(values, units=units)
except ValueError:
coord = AuxCoord(values, units=units)
coord.rename(name)
coords.append(coord)
# Every numerical column after the Z becomes a cube.
for name, values in izip(headings[z_column + 1:], columns[z_column + 1:]):
try:
float(values[0])
except ValueError:
continue
# units embedded in column heading?
name, units = _split_name_and_units(name)
cube = iris.cube.Cube(values, units=units)
cube.rename(name)
for coord in coords:
dim = 0 if len(coord.points) > 1 else None
if isinstance(coord, DimCoord) and coord.name() == "time":
cube.add_dim_coord(coord.copy(), dim)
else:
cube.add_aux_coord(coord.copy(), dim)
yield cube
def test_handmade(self):
# Test xml output of a handmade cube.
data = numpy.array( [ [1, 2, 3, 4, 5],
[2, 3, 4, 5, 6],
[3, 4, 5, 6, 7],
[4, 5, 6, 7, 8],
[5, 6, 7, 8, 9] ], dtype=numpy.int32)
cubes = []
# Different types of test
for ll_dtype in [numpy.float32, numpy.int32]:
for rotated in [False, True]:
for forecast_or_time_mean in ["forecast", "time_mean"]:
for TEST_COMPAT_i in xrange(2): # TODO: remove with TEST_COMPAT purge -
# adds two copies of each cube to cube list
# in line with redundant data first option
cube = iris.cube.Cube(data)
cube.attributes['my_attribute'] = 'foobar'
if rotated == False:
pole_pos = coord_systems.GeoPosition(90, 0)
else:
pole_pos = coord_systems.GeoPosition(30, 150)
lonlat_cs = coord_systems.LatLonCS("datum?", "prime_meridian?", pole_pos, "reference_longitude?")
cube.add_dim_coord(coords.DimCoord(numpy.array([-180, -90, 0, 90, 180], dtype=ll_dtype),
'longitude', units='degrees', coord_system=lonlat_cs), 1)
cube.add_dim_coord(coords.DimCoord(numpy.array([-90, -45, 0, 45, 90], dtype=ll_dtype),
'latitude', units='degrees', coord_system=lonlat_cs), 0)
# height
cube.add_aux_coord(coords.AuxCoord(numpy.array([1000], dtype=numpy.int32),
long_name='pressure', units='Pa'))
# phenom
cube.rename("temperature")
cube.units = "K"
# source
cube.add_aux_coord(coords.AuxCoord(points=["itbb"], long_name='source', units="no_unit"))
# forecast dates
if forecast_or_time_mean == "forecast":
unit = iris.unit.Unit('hours since epoch', calendar=iris.unit.CALENDAR_GREGORIAN)
dt = datetime.datetime(2010, 12, 31, 12, 0)
cube.add_aux_coord(coords.AuxCoord(numpy.array([6], dtype=numpy.int32),
standard_name='forecast_period', units='hours'))
cube.add_aux_coord(coords.AuxCoord(numpy.array([unit.date2num(dt)], dtype=numpy.float64),
standard_name='time', units=unit))
# time mean dates
if forecast_or_time_mean == "time_mean":
unit = iris.unit.Unit('hours since epoch', calendar=iris.unit.CALENDAR_GREGORIAN)
dt1 = datetime.datetime(2010, 12, 31, 6, 0)
dt2 = datetime.datetime(2010, 12, 31, 12, 0)
dt_mid = datetime.datetime(2010, 12, 31, 9, 0)
cube.add_aux_coord(coords.AuxCoord(numpy.array([6], dtype=numpy.int32),
standard_name='forecast_period', units='hours'))
cube.add_aux_coord(coords.AuxCoord(numpy.array(unit.date2num(dt_mid), dtype=numpy.float64),
standard_name='time', units=unit,
bounds=numpy.array([unit.date2num(dt1), unit.date2num(dt2)],
dtype=numpy.float64)))
cube.add_cell_method(coords.CellMethod('mean', cube.coord('forecast_period')))
cubes.append(cube)
# Now we've made all sorts of cube, check the xml...
self.assertCML(cubes, ('xml', 'handmade.cml'))
def _generate_cubes(header,
column_headings,
coords,
data_arrays,
cell_methods=None):
"""
Yield :class:`iris.cube.Cube` instances given
the headers, column headings, coords and data_arrays extracted
from a NAME file.
"""
for i, data_array in enumerate(data_arrays):
# Turn the dictionary of column headings with a list of header
# information for each field into a dictionary of headings for
# just this field.
field_headings = {k: v[i] for k, v in column_headings.iteritems()}
# Make a cube.
cube = iris.cube.Cube(data_array)
# Determine the name and units.
name = '{} {}'.format(field_headings['Species'],
field_headings['Quantity'])
name = name.upper().replace(' ', '_')
cube.rename(name)
# Some units are not in SI units, are missing spaces or typed
# in the wrong case. _parse_units returns units that are
# recognised by Iris.
cube.units = _parse_units(field_headings['Unit'])
# Define and add the singular coordinates of the field (flight
# level, time etc.)
z_coord = _cf_height_from_name(field_headings['Z'])
cube.add_aux_coord(z_coord)
# Define the time unit and use it to serialise the datetime for
# the time coordinate.
time_unit = iris.unit.Unit('hours since epoch',
calendar=iris.unit.CALENDAR_GREGORIAN)
# Build time, latitude and longitude coordinates.
for coord in coords:
pts = coord.values
coord_sys = None
if coord.name == 'latitude' or coord.name == 'longitude':
coord_units = 'degrees'
coord_sys = iris.coord_systems.GeogCS(EARTH_RADIUS)
if coord.name == 'time':
coord_units = time_unit
pts = time_unit.date2num(coord.values)
if coord.dimension is not None:
icoord = DimCoord(points=pts,
standard_name=coord.name,
units=coord_units,
coord_system=coord_sys)
if coord.name == 'time' and 'Av or Int period' in \
field_headings:
dt = coord.values - \
field_headings['Av or Int period']
bnds = time_unit.date2num(np.vstack((dt, coord.values)).T)
icoord.bounds = bnds
else:
icoord.guess_bounds()
cube.add_dim_coord(icoord, coord.dimension)
else:
icoord = AuxCoord(points=pts[i],
standard_name=coord.name,
coord_system=coord_sys,
units=coord_units)
if coord.name == 'time' and 'Av or Int period' in \
field_headings:
dt = coord.values - \
field_headings['Av or Int period']
bnds = time_unit.date2num(np.vstack((dt, coord.values)).T)
icoord.bounds = bnds[i, :]
cube.add_aux_coord(icoord)
# Headings/column headings which are encoded elsewhere.
headings = [
'X',
'Y',
'Z',
'Time',
'Unit',
'Av or Int period',
'X grid origin',
'Y grid origin',
'X grid size',
'Y grid size',
'X grid resolution',
'Y grid resolution',
]
# Add the Main Headings as attributes.
for key, value in header.iteritems():
if value is not None and value != '' and \
key not in headings:
cube.attributes[key] = value
# Add the Column Headings as attributes
for key, value in field_headings.iteritems():
if value is not None and value != '' and \
key not in headings:
cube.attributes[key] = value
if cell_methods is not None:
cube.add_cell_method(cell_methods[i])
yield cube
def curl(i_cube, j_cube, k_cube=None, ignore=None):
r'''
Calculate the 3d curl of the given vector of cubes.
Args:
* i_cube
The i cube of the vector to operate on
* j_cube
The j cube of the vector to operate on
Kwargs:
* k_cube
The k cube of the vector to operate on
Return (i_cmpt_curl_cube, j_cmpt_curl_cube, k_cmpt_curl_cube)
The calculation of curl is dependent on the type of :func:`iris.coord_systems.CoordSystem` in the cube:
Cartesian curl
The Cartesian curl is defined as:
.. math::
\nabla\times \vec u = (\frac{\delta w}{\delta y} - \frac{\delta v}{\delta z}) \vec a_i - (\frac{\delta w}{\delta x} - \frac{\delta u}{\delta z})\vec a_j + (\frac{\delta v}{\delta x} - \frac{\delta u}{\delta y})\vec a_k
Spherical curl
When spherical calculus is used, i_cube is the phi vector component (e.g. eastward), j_cube is the theta component
(e.g. northward) and k_cube is the radial component.
The spherical curl is defined as:
.. math::
\nabla\times \vec A = \frac{1}{r cos \theta}(\frac{\delta}{\delta \theta}(\vec A_\phi cos \theta) - \frac{\delta \vec A_\theta}{\delta \phi}) \vec r + \frac{1}{r}(\frac{1}{cos \theta} \frac{\delta \vec A_r}{\delta \phi} - \frac{\delta}{\delta r} (r \vec A_\phi))\vec \theta + \frac{1}{r}(\frac{\delta}{\delta r}(r \vec A_\theta) - \frac{\delta \vec A_r}{\delta \theta}) \vec \phi
where phi is longitude, theta is latitude.
'''
if ignore is not None:
ignore = None
warnings.warn(
'The ignore keyword to iris.analysis.calculus.curl is deprecated, ignoring is now done automatically.'
)
# Get the vector quantity names (i.e. ['easterly', 'northerly', 'vertical'])
vector_quantity_names, phenomenon_name = spatial_vectors_with_phenom_name(
i_cube, j_cube, k_cube)
cubes = filter(None, [i_cube, j_cube, k_cube])
# get the names of all coords binned into useful comparison groups
coord_comparison = iris.analysis.coord_comparison(*cubes)
bad_coords = coord_comparison['ungroupable_and_dimensioned']
if bad_coords:
raise ValueError(
"Coordinates found in one cube that describe a data dimension which weren't in the other "
"cube (%s), try removing this coordinate." %
', '.join([group.name() for group in bad_coords]))
bad_coords = coord_comparison['resamplable']
if bad_coords:
raise ValueError(
'Some coordinates are different (%s), consider resampling.' %
', '.join([group.name() for group in bad_coords]))
ignore_string = ''
if coord_comparison['ignorable']:
ignore_string = ' (ignoring %s)' % ', '.join(
[group.name() for group in bad_coords])
# Get the dim_coord, or None if none exist, for the xyz dimensions
x_coord = i_cube.coord(axis='X')
y_coord = i_cube.coord(axis='Y')
z_coord = i_cube.coord(axis='Z')
y_dim = i_cube.coord_dims(y_coord)[0]
horiz_cs = i_cube.coord_system('CoordSystem')
# Planar (non spherical) coords?
ellipsoidal = isinstance(
horiz_cs,
(iris.coord_systems.GeogCS, iris.coord_systems.RotatedGeogCS))
if not ellipsoidal:
# TODO Implement some mechanism for conforming to a common grid
dj_dx = _curl_differentiate(j_cube, x_coord)
prototype_diff = dj_dx
# i curl component (dk_dy - dj_dz)
dk_dy = _curl_differentiate(k_cube, y_coord)
dk_dy = _curl_regrid(dk_dy, prototype_diff)
dj_dz = _curl_differentiate(j_cube, z_coord)
dj_dz = _curl_regrid(dj_dz, prototype_diff)
# TODO Implement resampling in the vertical (which regridding does not support).
if dj_dz is not None and dj_dz.data.shape != prototype_diff.data.shape:
dj_dz = _curl_change_z(dj_dz, z_coord, prototype_diff)
i_cmpt = _curl_subtract(dk_dy, dj_dz)
dj_dz = dk_dy = None
# j curl component (di_dz - dk_dx)
di_dz = _curl_differentiate(i_cube, z_coord)
di_dz = _curl_regrid(di_dz, prototype_diff)
# TODO Implement resampling in the vertical (which regridding does not support).
if di_dz is not None and di_dz.data.shape != prototype_diff.data.shape:
di_dz = _curl_change_z(di_dz, z_coord, prototype_diff)
dk_dx = _curl_differentiate(k_cube, x_coord)
dk_dx = _curl_regrid(dk_dx, prototype_diff)
j_cmpt = _curl_subtract(di_dz, dk_dx)
di_dz = dk_dx = None
# k curl component ( dj_dx - di_dy)
di_dy = _curl_differentiate(i_cube, y_coord)
di_dy = _curl_regrid(di_dy, prototype_diff)
# Since prototype_diff == dj_dx we don't need to recalculate dj_dx
# dj_dx = _curl_differentiate(j_cube, x_coord)
# dj_dx = _curl_regrid(dj_dx, prototype_diff)
k_cmpt = _curl_subtract(dj_dx, di_dy)
di_dy = dj_dx = None
result = [i_cmpt, j_cmpt, k_cmpt]
# Spherical coords (GeogCS or RotatedGeogCS).
else:
# A_\phi = i ; A_\theta = j ; A_\r = k
# theta = lat ; phi = long ;
# r_cmpt = 1/ ( r * cos(lat) ) * ( d/dtheta ( i_cube * sin( lat ) ) - d_j_cube_dphi )
# phi_cmpt = 1/r * ( d/dr (r * j_cube) - d_k_cube_dtheta)
# theta_cmpt = 1/r * ( 1/cos(lat) * d_k_cube_dphi - d/dr (r * i_cube)
if y_coord.name() != 'latitude' or x_coord.name() != 'longitude':
raise ValueError(
'Expecting latitude as the y coord and longitude as the x coord for spherical curl.'
)
# Get the radius of the earth - and check for sphericity
ellipsoid = horiz_cs
if isinstance(horiz_cs, iris.coord_systems.RotatedGeogCS):
ellipsoid = horiz_cs.ellipsoid
if ellipsoid:
# TODO: Add a test for this
r = ellipsoid.semi_major_axis
r_unit = iris.unit.Unit("m")
spherical = (ellipsoid.inverse_flattening == 0.0)
else:
r = iris.analysis.cartography.DEFAULT_SPHERICAL_EARTH_RADIUS
r_unit = iris.analysis.cartography.DEFAULT_SPHERICAL_EARTH_RADIUS_UNIT
spherical = True
if not spherical:
raise ValueError(
"Cannot take the curl over a non-spherical ellipsoid.")
lon_coord = x_coord.copy()
lat_coord = y_coord.copy()
lon_coord.convert_units('radians')
lat_coord.convert_units('radians')
lat_cos_coord = _coord_cos(lat_coord)
# TODO Implement some mechanism for conforming to a common grid
temp = iris.analysis.maths.multiply(i_cube, lat_cos_coord, y_dim)
dicos_dtheta = _curl_differentiate(temp, lat_coord)
prototype_diff = dicos_dtheta
# r curl component: 1/ ( r * cos(lat) ) * ( dicos_dtheta - d_j_cube_dphi )
# Since prototype_diff == dicos_dtheta we don't need to recalculate dicos_dtheta
d_j_cube_dphi = _curl_differentiate(j_cube, lon_coord)
d_j_cube_dphi = _curl_regrid(d_j_cube_dphi, prototype_diff)
new_lat_coord = d_j_cube_dphi.coord(name='latitude')
new_lat_cos_coord = _coord_cos(new_lat_coord)
lat_dim = d_j_cube_dphi.coord_dims(new_lat_coord)[0]
r_cmpt = iris.analysis.maths.divide(_curl_subtract(
dicos_dtheta, d_j_cube_dphi),
r * new_lat_cos_coord,
dim=lat_dim)
r_cmpt.units = r_cmpt.units / r_unit
d_j_cube_dphi = dicos_dtheta = None
# phi curl component: 1/r * ( drj_dr - d_k_cube_dtheta)
drj_dr = _curl_differentiate(r * j_cube, z_coord)
if drj_dr is not None:
drj_dr.units = drj_dr.units * r_unit
drj_dr = _curl_regrid(drj_dr, prototype_diff)
d_k_cube_dtheta = _curl_differentiate(k_cube, lat_coord)
d_k_cube_dtheta = _curl_regrid(d_k_cube_dtheta, prototype_diff)
if drj_dr is None and d_k_cube_dtheta is None:
phi_cmpt = None
else:
phi_cmpt = 1 / r * _curl_subtract(drj_dr, d_k_cube_dtheta)
phi_cmpt.units = phi_cmpt.units / r_unit
drj_dr = d_k_cube_dtheta = None
# theta curl component: 1/r * ( 1/cos(lat) * d_k_cube_dphi - dri_dr )
d_k_cube_dphi = _curl_differentiate(k_cube, lon_coord)
d_k_cube_dphi = _curl_regrid(d_k_cube_dphi, prototype_diff)
if d_k_cube_dphi is not None:
d_k_cube_dphi = iris.analysis.maths.divide(d_k_cube_dphi,
lat_cos_coord)
dri_dr = _curl_differentiate(r * i_cube, z_coord)
if dri_dr is not None:
dri_dr.units = dri_dr.units * r_unit
dri_dr = _curl_regrid(dri_dr, prototype_diff)
if d_k_cube_dphi is None and dri_dr is None:
theta_cmpt = None
else:
theta_cmpt = 1 / r * _curl_subtract(d_k_cube_dphi, dri_dr)
theta_cmpt.units = theta_cmpt.units / r_unit
d_k_cube_dphi = dri_dr = None
result = [phi_cmpt, theta_cmpt, r_cmpt]
for direction, cube in zip(vector_quantity_names, result):
if cube is not None:
cube.rename('%s curl of %s' % (direction, phenomenon_name))
return result
def curl(i_cube, j_cube, k_cube=None):
r"""
Calculate the 2-dimensional or 3-dimensional spherical or cartesian
curl of the given vector of cubes.
As well as the standard x and y coordinates, this function requires each
cube to possess a vertical or z-like coordinate (representing some form
of height or pressure). This can be a scalar or dimension coordinate.
Args:
* i_cube
The i cube of the vector to operate on
* j_cube
The j cube of the vector to operate on
Kwargs:
* k_cube
The k cube of the vector to operate on
Return (i_cmpt_curl_cube, j_cmpt_curl_cube, k_cmpt_curl_cube)
If the k-cube is not passed in then the 2-dimensional curl will
be calculated, yielding the result: [None, None, k_cube].
If the k-cube is passed in, the 3-dimensional curl will
be calculated, returning 3 component cubes.
All cubes passed in must have the same data units, and those units
must be spatially-derived (e.g. 'm/s' or 'km/h').
The calculation of curl is dependent on the type of
:func:`~iris.coord_systems.CoordSystem` in the cube.
If the :func:`~iris.coord_systems.CoordSystem` is either
GeogCS or RotatedGeogCS, the spherical curl will be calculated; otherwise
the cartesian curl will be calculated:
Cartesian curl
When cartesian calculus is used, i_cube is the u component,
j_cube is the v component and k_cube is the w component.
The Cartesian curl is defined as:
.. math::
\nabla\times \vec u =
(\frac{\delta w}{\delta y} - \frac{\delta v}{\delta z})\vec a_i
-
(\frac{\delta w}{\delta x} - \frac{\delta u}{\delta z})\vec a_j
+
(\frac{\delta v}{\delta x} - \frac{\delta u}{\delta y})\vec a_k
Spherical curl
When spherical calculus is used, i_cube is the :math:`\phi` vector
component (e.g. eastward), j_cube is the :math:`\theta` component
(e.g. northward) and k_cube is the radial component.
The spherical curl is defined as:
.. math::
\nabla\times \vec A = \frac{1}{r cos \theta}
(\frac{\delta}{\delta \theta}
(\vec A_\phi cos \theta) -
\frac{\delta \vec A_\theta}{\delta \phi}) \vec r +
\frac{1}{r}(\frac{1}{cos \theta}
\frac{\delta \vec A_r}{\delta \phi} -
\frac{\delta}{\delta r} (r \vec A_\phi))\vec \theta +
\frac{1}{r}
(\frac{\delta}{\delta r}(r \vec A_\theta) -
\frac{\delta \vec A_r}{\delta \theta}) \vec \phi
where phi is longitude, theta is latitude.
"""
# Get the vector quantity names.
# (i.e. ['easterly', 'northerly', 'vertical'])
vector_quantity_names, phenomenon_name = \
spatial_vectors_with_phenom_name(i_cube, j_cube, k_cube)
cubes = filter(None, [i_cube, j_cube, k_cube])
# get the names of all coords binned into useful comparison groups
coord_comparison = iris.analysis.coord_comparison(*cubes)
bad_coords = coord_comparison['ungroupable_and_dimensioned']
if bad_coords:
raise ValueError("Coordinates found in one cube that describe "
"a data dimension which weren't in the other "
"cube ({}), try removing this coordinate.".format(
', '.join(group.name() for group in bad_coords)))
bad_coords = coord_comparison['resamplable']
if bad_coords:
raise ValueError('Some coordinates are different ({}), consider '
'resampling.'.format(', '.join(
group.name() for group in bad_coords)))
ignore_string = ''
if coord_comparison['ignorable']:
ignore_string = ' (ignoring {})'.format(', '.join(
group.name() for group in bad_coords))
# Get the dim_coord, or None if none exist, for the xyz dimensions
x_coord = i_cube.coord(axis='X')
y_coord = i_cube.coord(axis='Y')
z_coord = i_cube.coord(axis='Z')
y_dim = i_cube.coord_dims(y_coord)[0]
horiz_cs = i_cube.coord_system('CoordSystem')
# Non-spherical coords?
spherical_coords = isinstance(
horiz_cs,
(iris.coord_systems.GeogCS, iris.coord_systems.RotatedGeogCS))
if not spherical_coords:
# TODO Implement some mechanism for conforming to a common grid
dj_dx = _curl_differentiate(j_cube, x_coord)
prototype_diff = dj_dx
# i curl component (dk_dy - dj_dz)
dk_dy = _curl_differentiate(k_cube, y_coord)
dk_dy = _curl_regrid(dk_dy, prototype_diff)
dj_dz = _curl_differentiate(j_cube, z_coord)
dj_dz = _curl_regrid(dj_dz, prototype_diff)
# TODO Implement resampling in the vertical (which regridding
# does not support).
if dj_dz is not None and dj_dz.data.shape != prototype_diff.data.shape:
dj_dz = _curl_change_z(dj_dz, z_coord, prototype_diff)
i_cmpt = _curl_subtract(dk_dy, dj_dz)
dj_dz = dk_dy = None
# j curl component (di_dz - dk_dx)
di_dz = _curl_differentiate(i_cube, z_coord)
di_dz = _curl_regrid(di_dz, prototype_diff)
# TODO Implement resampling in the vertical (which regridding
# does not support).
if di_dz is not None and di_dz.data.shape != prototype_diff.data.shape:
di_dz = _curl_change_z(di_dz, z_coord, prototype_diff)
dk_dx = _curl_differentiate(k_cube, x_coord)
dk_dx = _curl_regrid(dk_dx, prototype_diff)
j_cmpt = _curl_subtract(di_dz, dk_dx)
di_dz = dk_dx = None
# k curl component ( dj_dx - di_dy)
di_dy = _curl_differentiate(i_cube, y_coord)
di_dy = _curl_regrid(di_dy, prototype_diff)
# Since prototype_diff == dj_dx we don't need to recalculate dj_dx
# dj_dx = _curl_differentiate(j_cube, x_coord)
# dj_dx = _curl_regrid(dj_dx, prototype_diff)
k_cmpt = _curl_subtract(dj_dx, di_dy)
di_dy = dj_dx = None
result = [i_cmpt, j_cmpt, k_cmpt]
# Spherical coords (GeogCS or RotatedGeogCS).
else:
# A_\phi = i ; A_\theta = j ; A_\r = k
# theta = lat ; phi = long ;
# r_cmpt = 1 / (r * cos(lat)) *
# (d/dtheta (i_cube * sin(lat)) - d_j_cube_dphi)
# phi_cmpt = 1/r * ( d/dr (r * j_cube) - d_k_cube_dtheta)
# theta_cmpt = 1/r * ( 1/cos(lat) * d_k_cube_dphi - d/dr (r * i_cube)
if y_coord.name() not in ['latitude', 'grid_latitude'] \
or x_coord.name() not in ['longitude', 'grid_longitude']:
raise ValueError('Expecting latitude as the y coord and '
'longitude as the x coord for spherical curl.')
# Get the radius of the earth - and check for sphericity
ellipsoid = horiz_cs
if isinstance(horiz_cs, iris.coord_systems.RotatedGeogCS):
ellipsoid = horiz_cs.ellipsoid
if ellipsoid:
# TODO: Add a test for this
r = ellipsoid.semi_major_axis
r_unit = cf_units.Unit("m")
spherical = (ellipsoid.inverse_flattening == 0.0)
else:
r = DEFAULT_SPHERICAL_EARTH_RADIUS
r_unit = DEFAULT_SPHERICAL_EARTH_RADIUS_UNIT
spherical = True
if not spherical:
raise ValueError('Cannot take the curl over a non-spherical '
'ellipsoid.')
lon_coord = x_coord.copy()
lat_coord = y_coord.copy()
lon_coord.convert_units('radians')
lat_coord.convert_units('radians')
lat_cos_coord = _coord_cos(lat_coord)
# TODO Implement some mechanism for conforming to a common grid
temp = iris.analysis.maths.multiply(i_cube, lat_cos_coord, y_dim)
dicos_dtheta = _curl_differentiate(temp, lat_coord)
prototype_diff = dicos_dtheta
# r curl component: 1 / (r * cos(lat)) * (d_j_cube_dphi - dicos_dtheta)
# Since prototype_diff == dicos_dtheta we don't need to
# recalculate dicos_dtheta.
d_j_cube_dphi = _curl_differentiate(j_cube, lon_coord)
d_j_cube_dphi = _curl_regrid(d_j_cube_dphi, prototype_diff)
new_lat_coord = d_j_cube_dphi.coord(axis='Y')
new_lat_cos_coord = _coord_cos(new_lat_coord)
lat_dim = d_j_cube_dphi.coord_dims(new_lat_coord)[0]
r_cmpt = iris.analysis.maths.divide(_curl_subtract(
d_j_cube_dphi, dicos_dtheta),
r * new_lat_cos_coord,
dim=lat_dim)
r_cmpt.units = r_cmpt.units / r_unit
d_j_cube_dphi = dicos_dtheta = None
# phi curl component: 1/r * ( drj_dr - d_k_cube_dtheta)
drj_dr = _curl_differentiate(r * j_cube, z_coord)
if drj_dr is not None:
drj_dr.units = drj_dr.units * r_unit
drj_dr = _curl_regrid(drj_dr, prototype_diff)
d_k_cube_dtheta = _curl_differentiate(k_cube, lat_coord)
d_k_cube_dtheta = _curl_regrid(d_k_cube_dtheta, prototype_diff)
if drj_dr is None and d_k_cube_dtheta is None:
phi_cmpt = None
else:
phi_cmpt = 1 / r * _curl_subtract(drj_dr, d_k_cube_dtheta)
phi_cmpt.units = phi_cmpt.units / r_unit
drj_dr = d_k_cube_dtheta = None
# theta curl component: 1/r * ( 1/cos(lat) * d_k_cube_dphi - dri_dr )
d_k_cube_dphi = _curl_differentiate(k_cube, lon_coord)
d_k_cube_dphi = _curl_regrid(d_k_cube_dphi, prototype_diff)
if d_k_cube_dphi is not None:
d_k_cube_dphi = iris.analysis.maths.divide(d_k_cube_dphi,
lat_cos_coord)
dri_dr = _curl_differentiate(r * i_cube, z_coord)
if dri_dr is not None:
dri_dr.units = dri_dr.units * r_unit
dri_dr = _curl_regrid(dri_dr, prototype_diff)
if d_k_cube_dphi is None and dri_dr is None:
theta_cmpt = None
else:
theta_cmpt = 1 / r * _curl_subtract(d_k_cube_dphi, dri_dr)
theta_cmpt.units = theta_cmpt.units / r_unit
d_k_cube_dphi = dri_dr = None
result = [phi_cmpt, theta_cmpt, r_cmpt]
for direction, cube in zip(vector_quantity_names, result):
if cube is not None:
cube.rename('%s curl of %s' % (direction, phenomenon_name))
return result
def _generate_cubes(header, column_headings, coords, data_arrays, cell_methods=None):
"""
Yield :class:`iris.cube.Cube` instances given
the headers, column headings, coords and data_arrays extracted
from a NAME file.
"""
for i, data_array in enumerate(data_arrays):
# Turn the dictionary of column headings with a list of header
# information for each field into a dictionary of headings for
# just this field.
field_headings = {k: v[i] for k, v in six.iteritems(column_headings)}
# Make a cube.
cube = iris.cube.Cube(data_array)
# Determine the name and units.
name = "{} {}".format(field_headings["Species"], field_headings["Quantity"])
name = name.upper().replace(" ", "_")
cube.rename(name)
# Some units are not in SI units, are missing spaces or typed
# in the wrong case. _parse_units returns units that are
# recognised by Iris.
cube.units = _parse_units(field_headings["Units"])
# Define and add the singular coordinates of the field (flight
# level, time etc.)
if "Z" in field_headings:
upper_bound, = [field_headings["... to [Z]"] if "... to [Z]" in field_headings else None]
lower_bound, = [field_headings["... from [Z]"] if "... from [Z]" in field_headings else None]
z_coord = _cf_height_from_name(field_headings["Z"], upper_bound=upper_bound, lower_bound=lower_bound)
cube.add_aux_coord(z_coord)
# Define the time unit and use it to serialise the datetime for
# the time coordinate.
time_unit = cf_units.Unit("hours since epoch", calendar=cf_units.CALENDAR_GREGORIAN)
# Build time, height, latitude and longitude coordinates.
for coord in coords:
pts = coord.values
coord_sys = None
if coord.name == "latitude" or coord.name == "longitude":
coord_units = "degrees"
coord_sys = iris.coord_systems.GeogCS(EARTH_RADIUS)
if coord.name == "projection_x_coordinate" or coord.name == "projection_y_coordinate":
coord_units = "m"
coord_sys = iris.coord_systems.OSGB()
if coord.name == "height":
coord_units = "m"
long_name = "height above ground level"
pts = coord.values
if coord.name == "altitude":
coord_units = "m"
long_name = "altitude above sea level"
pts = coord.values
if coord.name == "air_pressure":
coord_units = "Pa"
pts = coord.values
if coord.name == "flight_level":
pts = coord.values
long_name = "flight_level"
coord_units = _parse_units("FL")
if coord.name == "time":
coord_units = time_unit
pts = time_unit.date2num(coord.values)
if coord.dimension is not None:
if coord.name == "longitude":
circular = iris.util._is_circular(pts, 360.0)
else:
circular = False
if coord.name == "flight_level":
icoord = DimCoord(points=pts, units=coord_units, long_name=long_name)
else:
icoord = DimCoord(
points=pts,
standard_name=coord.name,
units=coord_units,
coord_system=coord_sys,
circular=circular,
)
if coord.name == "height" or coord.name == "altitude":
icoord.long_name = long_name
if coord.name == "time" and "Av or Int period" in field_headings:
dt = coord.values - field_headings["Av or Int period"]
bnds = time_unit.date2num(np.vstack((dt, coord.values)).T)
icoord.bounds = bnds
else:
icoord.guess_bounds()
cube.add_dim_coord(icoord, coord.dimension)
else:
icoord = AuxCoord(points=pts[i], standard_name=coord.name, coord_system=coord_sys, units=coord_units)
if coord.name == "time" and "Av or Int period" in field_headings:
dt = coord.values - field_headings["Av or Int period"]
bnds = time_unit.date2num(np.vstack((dt, coord.values)).T)
icoord.bounds = bnds[i, :]
cube.add_aux_coord(icoord)
# Headings/column headings which are encoded elsewhere.
headings = [
"X",
"Y",
"Z",
"Time",
"T",
"Units",
"Av or Int period",
"... from [Z]",
"... to [Z]",
"X grid origin",
"Y grid origin",
"X grid size",
"Y grid size",
"X grid resolution",
"Y grid resolution",
"Number of field cols",
"Number of preliminary cols",
"Number of fields",
"Number of series",
"Output format",
]
# Add the Main Headings as attributes.
for key, value in six.iteritems(header):
if value is not None and value != "" and key not in headings:
cube.attributes[key] = value
# Add the Column Headings as attributes
for key, value in six.iteritems(field_headings):
if value is not None and value != "" and key not in headings:
cube.attributes[key] = value
if cell_methods is not None:
cube.add_cell_method(cell_methods[i])
yield cube
