def test_set_height_levels_single_value():
""" Tests cube generated with single height level is demoted from dimension to
scalar coordinate """
height_levels = [1.5]
cube = generate_metadata(MANDATORY_ATTRIBUTE_DEFAULTS,
height_levels=height_levels)
assert cube.ndim == 3
assert cube.shape == (
ENSEMBLE_MEMBERS_DEFAULT,
NPOINTS_DEFAULT,
NPOINTS_DEFAULT,
)
expected_spatial_grid_attributes = SPATIAL_GRID_ATTRIBUTE_DEFAULTS[
SPATIAL_GRID_DEFAULT]
assert cube.coords()[0].name() == "realization"
assert cube.coords()[1].name() == expected_spatial_grid_attributes["y"]
assert cube.coords()[2].name() == expected_spatial_grid_attributes["x"]
np.testing.assert_array_equal(cube.coord("height").points, height_levels)
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata(MANDATORY_ATTRIBUTE_DEFAULTS)
cube.remove_coord("height")
assert cube == default_cube
def test_name_unknown_no_units():
""" Tests error raised if output variable name not in iris.std_names.STD_NAMES and
no unit provided """
name = "temperature"
with pytest.raises(ValueError, match=name):
generate_metadata(name)
def test_spatial_grid_not_supported():
""" Tests error raised if spatial grid not supported """
spatial_grid = "other"
with pytest.raises(ValueError, match=spatial_grid):
generate_metadata(MANDATORY_ATTRIBUTE_DEFAULTS,
spatial_grid=spatial_grid)
def test_missing_mandatory_attributes(use_attributes):
"""Tests that unspecified mandatory attributes raise an error"""
attributes = {}
for key in use_attributes:
attributes[key] = MANDATORY_ATTRIBUTE_DEFAULTS[key]
msg = "No values for these mandatory attributes: "
with pytest.raises(KeyError, match=msg):
generate_metadata(attributes)
def test_set_attributes():
""" Tests cube generated with specified attributes and the rest of the values set
as default values """
attributes = {"source": "IMPROVER"}
cube = generate_metadata(attributes=attributes)
assert cube.attributes == attributes
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata()
cube.attributes = default_cube.attributes
assert cube == default_cube
def test_set_time():
""" Tests cube generated with specified time and the rest of the values set as
default values """
time = datetime(2020, 1, 1, 0, 0)
cube = generate_metadata(time=time)
assert iris_time_to_datetime(cube.coord("time"))[0] == time
assert cube.coord("forecast_period").points > FORECAST_PERIOD_DEFAULT
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata()
cube.coord("time").points = default_cube.coord("time").points
cube.coord("forecast_period").points = default_cube.coord("forecast_period").points
assert cube == default_cube
def test_default():
""" Tests default metadata cube generated """
cube = generate_metadata()
assert cube.name() == NAME_DEFAULT
assert cube.standard_name == NAME_DEFAULT
assert cube.units == UNITS_DEFAULT
assert cube.ndim == NDIMS_DEFAULT
assert cube.shape == (ENSEMBLE_MEMBERS_DEFAULT, NPOINTS_DEFAULT, NPOINTS_DEFAULT)
spatial_grid_values = SPATIAL_GRID_ATTRIBUTE_DEFAULTS[SPATIAL_GRID_DEFAULT]
assert cube.coords()[0].name() == "realization"
assert cube.coords()[1].name() == spatial_grid_values["y"]
assert cube.coords()[2].name() == spatial_grid_values["x"]
for axis in ("y", "x"):
assert cube.coord(axis=axis).units == spatial_grid_values["units"]
assert cube.coord(axis=axis).coord_system == spatial_grid_values["coord_system"]
assert np.diff(cube.coord(axis=axis).points)[0] == pytest.approx(
spatial_grid_values["grid_spacing"]
)
assert np.count_nonzero(cube.data) == 0
assert iris_time_to_datetime(cube.coord("time"))[0] == TIME_DEFAULT
assert cube.coord("time").bounds is None
assert (
iris_time_to_datetime(cube.coord("forecast_reference_time"))[0] == FRT_DEFAULT
)
assert cube.coord("forecast_period").points == FORECAST_PERIOD_DEFAULT
assert cube.attributes == ATTRIBUTES_DEFAULT
def test_disable_ensemble_set_height_levels():
""" Tests cube generated without realizations dimension but with height dimension """
ensemble_members = 1
height_levels = [1.5, 3.0, 4.5]
cube = generate_metadata(
MANDATORY_ATTRIBUTE_DEFAULTS,
ensemble_members=ensemble_members,
height_levels=height_levels,
)
assert cube.ndim == 3
assert cube.shape == (
len(height_levels),
NPOINTS_DEFAULT,
NPOINTS_DEFAULT,
)
expected_spatial_grid_attributes = SPATIAL_GRID_ATTRIBUTE_DEFAULTS[
SPATIAL_GRID_DEFAULT]
assert cube.coords()[0].name() == "height"
assert cube.coords()[1].name() == expected_spatial_grid_attributes["y"]
assert cube.coords()[2].name() == expected_spatial_grid_attributes["x"]
np.testing.assert_array_equal(cube.coord("height").points, height_levels)
# Assert that cube shape is different from default cube shape but metadata unchanged
_check_cube_shape_different(cube)
def test_set_attributes():
""" Tests cube generated with specified attributes and the rest of the values set
as default values """
attributes = {"test_attribute": "kittens"}
cube = generate_metadata(MANDATORY_ATTRIBUTE_DEFAULTS,
attributes=attributes)
expected_attributes = MANDATORY_ATTRIBUTE_DEFAULTS.copy()
expected_attributes["test_attribute"] = "kittens"
assert cube.attributes == expected_attributes
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata(MANDATORY_ATTRIBUTE_DEFAULTS)
cube.attributes = default_cube.attributes
assert cube == default_cube
def test_set_height_levels():
""" Tests cube generated with specified height levels as an additional dimension """
height_levels = [1.5, 3.0, 4.5]
cube = generate_metadata(height_levels=height_levels)
assert cube.ndim == 4
assert cube.shape == (
ENSEMBLE_MEMBERS_DEFAULT,
len(height_levels),
NPOINTS_DEFAULT,
NPOINTS_DEFAULT,
)
expected_spatial_grid_attributes = SPATIAL_GRID_ATTRIBUTE_DEFAULTS[
SPATIAL_GRID_DEFAULT
]
assert cube.coords()[0].name() == "realization"
assert cube.coords()[1].name() == "height"
assert cube.coords()[2].name() == expected_spatial_grid_attributes["y"]
assert cube.coords()[3].name() == expected_spatial_grid_attributes["x"]
np.testing.assert_array_equal(cube.coord("height").points, height_levels)
# Assert that cube shape is different from default cube shape but metadata unchanged
_check_cube_shape_different(cube)
def test_set_domain_corner():
""" Tests cube generated with specified domain corner and the rest of the values
set as default values """
domain_corner = (0, 0)
cube = generate_metadata(domain_corner=domain_corner)
assert cube.coord(axis="y").points[0] == domain_corner[0]
assert cube.coord(axis="x").points[0] == domain_corner[1]
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata()
cube.coord(axis="y").points = default_cube.coord(axis="y").points
cube.coord(axis="x").points = default_cube.coord(axis="x").points
cube.coord(axis="y").bounds = default_cube.coord(axis="y").bounds
cube.coord(axis="x").bounds = default_cube.coord(axis="x").bounds
assert cube == default_cube
def test_set_name_no_units():
""" Tests cube generated with specified name, automatically setting units, and the
rest of the values set as default values """
name = "air_pressure"
cube = generate_metadata(name=name)
assert cube.name() == name
assert cube.standard_name == name
assert cube.units == "Pa"
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata()
cube.standard_name = default_cube.standard_name
cube.units = default_cube.units
assert cube == default_cube
def test_set_grid_spacing():
""" Tests cube generated with specified grid_spacing and the rest of the values set
as default values """
grid_spacing = 5
cube = generate_metadata(grid_spacing=grid_spacing)
assert np.diff(cube.coord(axis="y").points)[0] == grid_spacing
assert np.diff(cube.coord(axis="x").points)[0] == grid_spacing
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata()
for axis in ("y", "x"):
cube.coord(axis=axis).points = default_cube.coord(axis=axis).points
cube.coord(axis=axis).bounds = default_cube.coord(axis=axis).bounds
assert cube == default_cube
def test_set_npoints():
""" Tests cube generated with specified npoints """
npoints = 500
cube = generate_metadata(npoints=npoints)
assert cube.shape == (ENSEMBLE_MEMBERS_DEFAULT, npoints, npoints)
# Assert that cube shape is different from default cube shape but metadata unchanged
_check_cube_shape_different(cube)
def test_set_spatial_grid(spatial_grid):
""" Tests different spatial grids generates cubes with default values for that
spatial grid """
cube = generate_metadata(
MANDATORY_ATTRIBUTE_DEFAULTS,
spatial_grid=spatial_grid,
)
expected_spatial_grid_attributes = SPATIAL_GRID_ATTRIBUTE_DEFAULTS[
spatial_grid]
assert cube.coords()[0].name() == "realization"
assert cube.coords()[1].name() == expected_spatial_grid_attributes["y"]
assert cube.coords()[2].name() == expected_spatial_grid_attributes["x"]
for axis in ("y", "x"):
assert cube.coord(
axis=axis).units == expected_spatial_grid_attributes["units"]
assert (cube.coord(axis=axis).coord_system ==
expected_spatial_grid_attributes["coord_system"])
assert np.diff(cube.coord(axis=axis).points)[0] == pytest.approx(
expected_spatial_grid_attributes["grid_spacing"])
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata(MANDATORY_ATTRIBUTE_DEFAULTS)
if spatial_grid != SPATIAL_GRID_DEFAULT:
default_spatial_grid_values = SPATIAL_GRID_ATTRIBUTE_DEFAULTS[
SPATIAL_GRID_DEFAULT]
cube.coords()[1].rename(default_spatial_grid_values["y"])
cube.coords()[2].rename(default_spatial_grid_values["x"])
for axis in ("y", "x"):
cube.coord(axis=axis).points = default_cube.coord(axis=axis).points
cube.coord(axis=axis).bounds = default_cube.coord(axis=axis).bounds
cube.coord(axis=axis).units = default_spatial_grid_values["units"]
cube.coord(
axis=axis
).coord_system = default_spatial_grid_values["coord_system"]
assert cube == default_cube
else:
assert cube == default_cube
def test_set_frt():
""" Tests cube generated with specified forecast reference time and the rest of the
values set as default values """
frt = datetime(2017, 1, 1, 0, 0)
cube = generate_metadata(frt=frt)
assert iris_time_to_datetime(cube.coord("forecast_reference_time"))[0] == frt
assert cube.coord("forecast_period").points > 0
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata()
cube.coord("forecast_reference_time").points = default_cube.coord(
"forecast_reference_time"
).points
cube.coord("forecast_period").points = default_cube.coord("forecast_period").points
assert cube == default_cube
def test_set_time_period():
""" Tests cube generated with time bounds calculated using specified time_period
and the rest of the values set as default values """
time_period = 150
cube = generate_metadata(time_period=time_period)
assert iris_time_to_datetime(cube.coord("time"))[0] == TIME_DEFAULT
assert cube.coord("forecast_period").points == FORECAST_PERIOD_DEFAULT
assert cube.coord("time").bounds[0][0] == datetime_to_iris_time(
datetime(2017, 11, 10, 1, 30)
)
assert cube.coord("time").bounds[0][1] == datetime_to_iris_time(TIME_DEFAULT)
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata()
cube.coord("time").bounds = None
cube.coord("forecast_period").bounds = None
assert cube == default_cube
def test_name_unknown_with_units():
""" Tests cube generated with specified name which isn't a CF standard name,
specified units, and the rest of the values set as default values"""
name = "lapse_rate"
units = "K m-1"
cube = generate_metadata(name=name, units=units)
# "lapse_rate" not CF standard so standard_name expected None
assert cube.name() == name
assert cube.standard_name is None
assert cube.units == units
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata()
# Iris.cube.Cube.rename() assigns standard_name if valid
cube.rename(default_cube.standard_name)
cube.units = default_cube.units
assert cube == default_cube
def test_set_ensemble_members():
""" Tests cube generated with specified number of ensemble members """
ensemble_members = 4
cube = generate_metadata(ensemble_members=ensemble_members)
assert cube.ndim == 3
assert cube.shape == (ensemble_members, NPOINTS_DEFAULT, NPOINTS_DEFAULT)
assert cube.coords()[0].name() == "realization"
# Assert that cube shape is different from default cube shape but metadata unchanged
_check_cube_shape_different(cube)
def test_set_name_units():
""" Tests cube generated with specified name and units, and the rest of the values
set as default values"""
name = "air_pressure"
units = "pascal"
cube = generate_metadata(MANDATORY_ATTRIBUTE_DEFAULTS,
name=name,
units=units)
assert cube.name() == name
assert cube.standard_name == name
assert cube.units == units
# Assert that no other values have unexpectedly changed by returning changed values
# to defaults and comparing against default cube
default_cube = generate_metadata(MANDATORY_ATTRIBUTE_DEFAULTS)
cube.standard_name = default_cube.standard_name
cube.units = default_cube.units
assert cube == default_cube
def test_disable_ensemble(ensemble_members):
""" Tests cube generated without realizations dimension """
cube = generate_metadata(ensemble_members=ensemble_members)
assert cube.ndim == 2
assert cube.shape == (NPOINTS_DEFAULT, NPOINTS_DEFAULT)
spatial_grid_values = SPATIAL_GRID_ATTRIBUTE_DEFAULTS[SPATIAL_GRID_DEFAULT]
assert cube.coords()[0].name() == spatial_grid_values["y"]
assert cube.coords()[1].name() == spatial_grid_values["x"]
# Assert that cube shape is different from default cube shape but metadata unchanged
_check_cube_shape_different(cube)
def process(
mandatory_attributes_json: cli.inputjson,
*,
name="air_pressure_at_sea_level",
units=None,
spatial_grid="latlon",
time_period: int = None,
json_input: cli.inputjson = None,
ensemble_members: int = 8,
grid_spacing: float = None,
domain_corner: cli.comma_separated_list_of_float = None,
npoints: int = 71,
):
""" Generate a cube with metadata only.
Args:
mandatory_attributes_json (Dict):
Specifies the values of the mandatory attributes, title, institution and
source.
name (Optional[str]):
Output variable name, or if creating a probability cube the name of the
underlying variable to which the probability field applies.
units (Optional[str]):
Output variable units, or if creating a probability cube the units of the
underlying variable / threshold.
spatial_grid (Optional[str]):
What type of x/y coordinate values to use. Permitted values are
"latlon" or "equalarea".
time_period (Optional[int]):
The period in minutes between the time bounds. This is used to calculate
the lower time bound. If unset the diagnostic will be instantaneous, i.e.
without time bounds.
json_input (Optional[Dict]):
Dictionary containing values for one or more of: "name", "units", "time",
"time_bounds", "frt", "spp__relative_to_threshold", "attributes"
(dictionary of additional metadata attributes) and "coords" (dictionary).
"coords" can contain "height_levels" (list of height/pressure level values),
and one of "realizations", "percentiles" or "thresholds" (list of dimension
values).
ensemble_members (Optional[int]):
Number of ensemble members. Default 8. Will not be used if "realizations",
"percentiles" or "thresholds" provided in json_input.
grid_spacing (Optional[float]):
Resolution of grid (metres or degrees).
domain_corner (Optional[Tuple[float, float]]):
Bottom left corner of grid domain (y,x) (degrees for latlon or metres for
equalarea).
npoints (Optional[int]):
Number of points along each of the y and x spatial axes.
Returns:
iris.cube.Cube:
Output of generate_metadata()
"""
# Set arguments to pass to generate_metadata function and remove json_input for
# processing contents before adding
generate_metadata_args = locals()
for key in ["mandatory_attributes_json", "json_input"]:
generate_metadata_args.pop(key, None)
from improver.synthetic_data.generate_metadata import generate_metadata
from improver.synthetic_data.utilities import (
get_height_levels,
get_leading_dimension,
)
from improver.utilities.temporal import cycletime_to_datetime
if json_input is not None:
# Get leading dimension and height/pressure data from json_input
if "coords" in json_input:
coord_data = json_input["coords"]
(
json_input["leading_dimension"],
json_input["cube_type"],
) = get_leading_dimension(coord_data)
json_input["height_levels"], json_input["pressure"] = get_height_levels(
coord_data
)
json_input.pop("coords", None)
# Convert str time, frt and time_bounds to datetime
if "time" in json_input:
json_input["time"] = cycletime_to_datetime(json_input["time"])
if "frt" in json_input:
json_input["frt"] = cycletime_to_datetime(json_input["frt"])
if "time_bounds" in json_input:
time_bounds = []
for tb in json_input["time_bounds"]:
time_bounds.append(cycletime_to_datetime(tb))
json_input["time_bounds"] = time_bounds
# Update generate_metadata_args with the json_input data
generate_metadata_args.update(json_input)
return generate_metadata(mandatory_attributes_json, **generate_metadata_args)
def test_spatial_grid_not_supported():
""" Tests error raised if spatial grid not supported """
spatial_grid = "other"
with pytest.raises(ValueError, match=spatial_grid):
generate_metadata(spatial_grid=spatial_grid)
def _check_cube_shape_different(cube):
""" Asserts that cube shape has been changed from default but name, units and
attributes are unchanged """
default_cube = generate_metadata()
assert cube.shape != default_cube.shape
assert iris.util.describe_diff(cube, default_cube) is None
def test_leading_dimension(cube_type, spp__relative_to_threshold):
""" Tests cube generated with leading dimension specified using percentile and
probability flags, and different values for spp__relative_to_threshold """
if cube_type == "other":
# Tests that error is raised when cube type isn't supported
msg = 'Cube type {} not supported. Specify one of "variable", "percentile" or "probability".'.format(
cube_type
)
with pytest.raises(ValueError, match=msg):
generate_metadata(
cube_type=cube_type,
spp__relative_to_threshold=spp__relative_to_threshold,
)
else:
leading_dimension = [10, 20, 30, 40, 50, 60, 70, 80]
if spp__relative_to_threshold is not None:
cube = generate_metadata(
leading_dimension=leading_dimension,
cube_type=cube_type,
spp__relative_to_threshold=spp__relative_to_threshold,
)
else:
cube = generate_metadata(
leading_dimension=leading_dimension, cube_type=cube_type,
)
spp__relative_to_threshold = RELATIVE_TO_THRESHOLD_DEFAULT
if cube_type == "percentile":
cube_name = NAME_DEFAULT
coord_name = "percentile"
elif cube_type == "probability":
cube_name = "probability_of_{}_{}_threshold".format(
NAME_DEFAULT, spp__relative_to_threshold
)
coord_name = NAME_DEFAULT
assert cube.coord(coord_name).attributes == {
"spp__relative_to_threshold": spp__relative_to_threshold
}
cube.coord(coord_name).attributes = {}
else:
cube_name = NAME_DEFAULT
coord_name = "realization"
assert cube.name() == cube_name
assert cube.ndim == 3
assert cube.shape == (len(leading_dimension), NPOINTS_DEFAULT, NPOINTS_DEFAULT)
assert cube.coords()[0].name() == coord_name
np.testing.assert_array_equal(cube.coord(coord_name).points, leading_dimension)
# Assert that no other values have unexpectedly changed by returning changed
# values to defaults and comparing against default cube
default_cube = generate_metadata()
cube.coord(coord_name).points = default_cube.coord("realization").points
cube.coord(coord_name).rename("realization")
cube.coord("realization").units = "1"
cube.rename(default_cube.standard_name)
cube.units = default_cube.units
assert cube == default_cube
def test_domain_corner_incorrect_length(domain_corner):
"""Tests error raised if domain corner not length 2"""
msg = "Domain corner"
with pytest.raises(ValueError, match=msg):
generate_metadata(domain_corner=domain_corner)