class TestAll(unittest.TestCase):
"""Test fixes for allvars."""
def setUp(self):
"""Prepare tests."""
self.cube = Cube([[1.0, 2.0], [3.0, 4.0]], var_name='co2', units='J')
self.cube.add_dim_coord(
DimCoord([0, 1],
standard_name='time',
units=Unit('days since 0000-01-01 00:00:00',
calendar='gregorian')), 0)
self.cube.add_dim_coord(DimCoord([0, 1], long_name='AR5PL35'), 1)
self.fix = AllVars()
def test_get(self):
"""Test fix get"""
self.assertListEqual(Fix.get_fixes('CMIP5', 'MIROC-ESM', 'tos'),
[AllVars()])
def test_fix_metadata_plev(self):
"""Test plev fix."""
time = self.cube.coord('time')
time.units = Unit("days since 1-1-1", time.units.calendar)
cube = self.fix.fix_metadata([self.cube])[0]
cube.coord('air_pressure')
def test_fix_metadata_no_plev(self):
"""Test plev fix wotk with no plev."""
self.cube.remove_coord('AR5PL35')
cube = self.fix.fix_metadata([self.cube])[0]
with self.assertRaises(CoordinateNotFoundError):
cube.coord('air_pressure')
def _remove_scalar_coords(cube: Cube, coords_to_remove: List[str]) -> None:
"""Removes named coordinates from the input cube."""
for coord in coords_to_remove:
try:
cube.remove_coord(coord)
except CoordinateNotFoundError:
continue
def _create_template_cube(self, cube: Cube) -> Cube:
"""
Create a template cube to store the timezone masks. This cube has only
one scalar coordinate which is time, denoting when it is valid; this is
only relevant if using daylight savings. The attribute
includes_daylight_savings is set to indicate this.
Args:
cube:
A cube with the desired grid from which coordinates are taken
for inclusion in the template.
Returns:
A template cube in which each timezone mask can be stored.
"""
time_point = np.array(self.time.timestamp(), dtype=np.int64)
time_coord = iris.coords.DimCoord(
time_point,
"time",
units=Unit("seconds since 1970-01-01 00:00:00", calendar="gregorian"),
)
for crd in cube.coords(dim_coords=False):
cube.remove_coord(crd)
cube.add_aux_coord(time_coord)
attributes = generate_mandatory_attributes([cube])
attributes["includes_daylight_savings"] = str(self.include_dst)
return create_new_diagnostic_cube(
"timezone_mask", 1, cube, attributes, dtype=np.int8
)
def _set_blended_time_coords(blended_cube: Cube,
cycletime: Optional[str]) -> None:
"""
For cycle and model blending:
- Add a "blend_time" coordinate equal to the current cycletime
- Update the forecast reference time and forecast period coordinate points
to reflect the current cycle time (behaviour is DEPRECATED)
- Remove any bounds from the forecast reference time (behaviour is DEPRECATED)
- Mark the forecast reference time and forecast period as DEPRECATED
Modifies cube in place.
Args:
blended_cube
cycletime:
Current cycletime in YYYYMMDDTHHmmZ format
"""
try:
cycletime_point = _get_cycletime_point(blended_cube, cycletime)
except TypeError:
raise ValueError(
"Current cycle time is required for cycle and model blending")
add_blend_time(blended_cube, cycletime)
blended_cube.coord("forecast_reference_time").points = [cycletime_point]
blended_cube.coord("forecast_reference_time").bounds = None
if blended_cube.coords("forecast_period"):
blended_cube.remove_coord("forecast_period")
new_forecast_period = forecast_period_coord(blended_cube)
time_dim = blended_cube.coord_dims("time")
blended_cube.add_aux_coord(new_forecast_period, data_dims=time_dim)
for coord in ["forecast_period", "forecast_reference_time"]:
msg = f"{coord} will be removed in future and should not be used"
blended_cube.coord(coord).attributes.update(
{"deprecation_message": msg})
class TestAll(unittest.TestCase):
"""Test fixes for all vars."""
def setUp(self):
"""Prepare tests."""
self.cube = Cube([1.0, 2.0], var_name='co2', units='J')
self.cube.add_dim_coord(
DimCoord([0.0, 1.0],
standard_name='time',
units=Unit('days since 0001-01', calendar='gregorian')),
0)
self.fix = AllVars()
def test_get(self):
"""Test fix get"""
self.assertListEqual(Fix.get_fixes('CMIP5', 'FGOALS-G2', 'tas'),
[AllVars()])
def test_fix_metadata(self):
"""Test calendar fix."""
cube = self.fix.fix_metadata([self.cube])[0]
time = cube.coord('time')
self.assertEqual(time.units.origin,
'day since 1-01-01 00:00:00.000000')
self.assertEqual(time.units.calendar, 'gregorian')
def test_fix_metadata_dont_gail_if_not_time(self):
"""Test calendar fix."""
self.cube.remove_coord('time')
self.fix.fix_metadata([self.cube])
class TestAll(unittest.TestCase):
def setUp(self):
self.cube = Cube([[1.0, 2.0], [3.0, 4.0]], var_name='co2', units='J')
self.cube.add_dim_coord(
DimCoord(
[0, 1],
standard_name='time',
units=Unit(
'days since 0000-01-01 00:00:00', calendar='gregorian')),
0)
self.cube.add_dim_coord(DimCoord([0, 1], long_name='AR5PL35'), 1)
self.fix = allvars()
def test_fix_metadata_plev(self):
time = self.cube.coord('time')
time.units = Unit("days since 1-1-1", time.units.calendar)
cube = self.fix.fix_metadata([self.cube])[0]
cube.coord('air_pressure')
def test_fix_metadata_no_plev(self):
self.cube.remove_coord('AR5PL35')
cube = self.fix.fix_metadata([self.cube])[0]
with self.assertRaises(CoordinateNotFoundError):
cube.coord('air_pressure')
class Test_convert_number_of_grid_cells_into_distance(IrisTest):
"""Test the convert_number_of_grid_cells_into_distance method"""
def setUp(self):
"""Set up a cube with x and y coordinates"""
data = np.ones((3, 4))
self.cube = Cube(data, standard_name="air_temperature",)
self.cube.add_dim_coord(
DimCoord(np.linspace(2000.0, 6000.0, 3),
'projection_x_coordinate', units='m'), 0)
self.cube.add_dim_coord(
DimCoord(np.linspace(2000.0, 8000.0, 4),
"projection_y_coordinate", units='m'), 1)
def test_basic(self):
"""Test the function does what it's meant to in a simple case."""
result_radius = convert_number_of_grid_cells_into_distance(
self.cube, 2)
expected_result = 4000.0
self.assertAlmostEqual(result_radius, expected_result)
self.assertIs(type(expected_result), float)
def test_check_input_in_km(self):
"""
Test that the output is still in metres when the input coordinates
are in a different unit.
"""
result_radius = convert_number_of_grid_cells_into_distance(
self.cube, 2)
for coord in self.cube.coords():
coord.convert_units("km")
expected_result = 4000.0
self.assertAlmostEqual(result_radius, expected_result)
self.assertIs(type(expected_result), float)
def test_not_equal_areas(self):
"""
Check it raises an error when the input is not an equal areas grid.
"""
self.cube.remove_coord("projection_x_coordinate")
self.cube.add_dim_coord(
DimCoord(np.linspace(200.0, 600.0, 3),
'projection_x_coordinate', units='m'), 0)
with self.assertRaisesRegex(
ValueError,
"The size of the intervals along the x and y axis"
" should be equal."):
convert_number_of_grid_cells_into_distance(self.cube, 2)
def test_check_different_input_radius(self):
"""Check it works for different input values."""
result_radius = convert_number_of_grid_cells_into_distance(
self.cube, 5)
expected_result = 10000.0
self.assertAlmostEqual(result_radius, expected_result)
self.assertIs(type(expected_result), float)
def update_blended_metadata(
cube: Cube,
blend_coord: str,
coords_to_remove: Optional[List[str]] = None,
cycletime: Optional[str] = None,
attributes_dict: Optional[Dict[str, str]] = None,
model_id_attr: Optional[str] = None,
) -> None:
"""
Update metadata as required after blending
- For cycle and model blending, set a single forecast reference time
and period using current cycletime
- For model blending, add attribute detailing the contributing models
- Remove scalar coordinates that were previously associated with the
blend dimension
- Update attributes as specified via process arguments
- Set any missing mandatory arguments to their default values
Modifies cube in place.
Args:
cube:
Blended cube
blend_coord:
Name of coordinate over which blending has been performed
coords_to_remove:
Name of scalar coordinates to be removed from the blended cube
cycletime:
Current cycletime in YYYYMMDDTHHmmZ format
model_id_attr:
Name of attribute for use in model blending, to record the names of
contributing models on the blended output
attributes_dict:
Optional user-defined attributes to add to the cube
"""
if blend_coord in ["forecast_reference_time", MODEL_BLEND_COORD]:
_set_blended_time_coords(cube, cycletime)
if blend_coord == MODEL_BLEND_COORD:
(contributing_models,) = cube.coord(MODEL_NAME_COORD).points
# iris concatenates string coordinates as a "|"-separated string
cube.attributes[model_id_attr] = " ".join(
sorted(contributing_models.split("|"))
)
if coords_to_remove is not None:
for coord in coords_to_remove:
cube.remove_coord(coord)
if attributes_dict is not None:
amend_attributes(cube, attributes_dict)
for attr in MANDATORY_ATTRIBUTES:
if attr not in cube.attributes:
cube.attributes[attr] = MANDATORY_ATTRIBUTE_DEFAULTS[attr]
def _add_forecast_period(advected_cube: Cube, timestep: timedelta) -> None:
"""Add or replace a forecast period on the advected cube"""
try:
advected_cube.remove_coord("forecast_period")
except CoordinateNotFoundError:
pass
forecast_period_seconds = np.int32(timestep.total_seconds())
forecast_period_coord = AuxCoord(forecast_period_seconds,
standard_name="forecast_period",
units="seconds")
advected_cube.add_aux_coord(forecast_period_coord)
def _add_forecast_reference_time(input_time: Coord, advected_cube: Cube) -> None:
"""Add or replace a forecast reference time on the advected cube"""
try:
advected_cube.remove_coord("forecast_reference_time")
except CoordinateNotFoundError:
pass
frt_coord_name = "forecast_reference_time"
frt_coord_spec = TIME_COORDS[frt_coord_name]
frt_coord = input_time.copy()
frt_coord.rename(frt_coord_name)
frt_coord.convert_units(frt_coord_spec.units)
frt_coord.points = round_close(frt_coord.points, dtype=frt_coord_spec.dtype)
advected_cube.add_aux_coord(frt_coord)
class TestAllVars(unittest.TestCase):
"""Tests for fixes of all variables."""
def setUp(self):
"""Set up tests."""
vardef = get_var_info('CMIP6', 'Omon', 'tos')
self.fix = AllVars(vardef)
self.cube = Cube(np.random.rand(2, 2, 2), var_name='tos')
self.cube.add_aux_coord(
AuxCoord(np.random.rand(2, 2),
var_name='nav_lat',
standard_name='latitude'), (1, 2))
self.cube.add_aux_coord(
AuxCoord(np.random.rand(2, 2),
var_name='nav_lon',
standard_name='longitude'), (1, 2))
def test_fix_metadata_ocean_var(self):
"""Test ``fix_metadata`` for ocean variables."""
cell_area = Cube(np.random.rand(2, 2), standard_name='cell_area')
cubes = self.fix.fix_metadata(CubeList([self.cube, cell_area]))
self.assertEqual(len(cubes), 1)
cube = cubes[0]
self.assertEqual(cube.var_name, 'tos')
self.assertEqual(cube.coord('latitude').var_name, 'lat')
self.assertEqual(cube.coord('longitude').var_name, 'lon')
def test_fix_data_no_lat(self):
"""Test ``fix_metadata`` when no latitude is present."""
self.cube.remove_coord('latitude')
cubes = self.fix.fix_metadata(CubeList([self.cube]))
self.assertEqual(len(cubes), 1)
cube = cubes[0]
self.assertEqual(cube.coord('longitude').var_name, 'lon')
with self.assertRaises(CoordinateNotFoundError):
self.cube.coord('latitude')
def test_fix_data_no_lon(self):
"""Test ``fix_metadata`` when no longitude is present."""
self.cube.remove_coord('longitude')
cubes = self.fix.fix_metadata(CubeList([self.cube]))
self.assertEqual(len(cubes), 1)
cube = cubes[0]
self.assertEqual(cube.coord('latitude').var_name, 'lat')
with self.assertRaises(CoordinateNotFoundError):
self.cube.coord('longitude')
def test_fix_data_no_lat_lon(self):
"""Test ``fix_metadata`` for cubes with no latitude and longitude."""
self.cube.remove_coord('latitude')
self.cube.remove_coord('longitude')
cubes = self.fix.fix_metadata(CubeList([self.cube]))
self.assertEqual(len(cubes), 1)
with self.assertRaises(CoordinateNotFoundError):
self.cube.coord('latitude')
with self.assertRaises(CoordinateNotFoundError):
self.cube.coord('longitude')
class TestAllVars(unittest.TestCase):
"""Test fixes for all vars."""
def setUp(self):
"""Prepare tests."""
self.cube = Cube([1.0, 2.0], var_name='co2', units='J')
reference_dates = [
datetime(300, 1, 16, 12), # e.g. piControl
datetime(1850, 1, 16, 12) # e.g. historical
]
esgf_time_units = {
'unit': 'days since 0001-01-01',
'calendar': 'proleptic_gregorian'
}
time_points = date2num(reference_dates, **esgf_time_units)
self.cube.add_dim_coord(
DimCoord(time_points, 'time', 'time', 'time',
Unit(**esgf_time_units)), data_dim=0)
self.fix = AllVars(None)
def test_get(self):
"""Test getting of fix."""
self.assertListEqual(
Fix.get_fixes('CMIP5', 'ACCESS1-3', 'Amon', 'tas'),
[AllVars(None)])
def test_fix_metadata(self):
"""Test fix for bad calendar."""
cube = self.fix.fix_metadata([self.cube])[0]
time = cube.coord('time')
dates = num2date(time.points, time.units.name, time.units.calendar)
self.assertEqual(time.units.calendar, 'gregorian')
self.assertEqual(dates[0].strftime('%Y%m%d%H%M'), '30001161200')
self.assertEqual(dates[1].strftime('%Y%m%d%H%M'), '185001161200')
def test_fix_metadata_if_not_time(self):
"""Test calendar fix do not fail if no time coord present."""
self.cube.remove_coord('time')
self.fix.fix_metadata([self.cube])
def create_coefficient_cube(
self, data: ndarray, template: Cube, cube_name: str, attributes: Dict
) -> Cube:
"""
Update metadata in smoothing_coefficients cube. Remove any time
coordinates and rename.
Args:
data:
The smoothing coefficient data to store in the cube.
template:
A gradient cube, the dimensions of which are used as a template
for the coefficient cube.
cube_name:
A name for the resultant cube
attributes:
A dictionary of attributes for the new cube.
Returns:
A new cube of smoothing_coefficients
"""
for coord in template.coords(dim_coords=False):
for coord_name in ["time", "period", "realization"]:
if coord_name in coord.name():
template.remove_coord(coord)
attributes["title"] = "Recursive filter smoothing coefficients"
attributes.pop("history", None)
attributes["power"] = self.power
return create_new_diagnostic_cube(
cube_name,
"1",
template,
MANDATORY_ATTRIBUTE_DEFAULTS.copy(),
optional_attributes=attributes,
data=data,
)
class TestAllVars(unittest.TestCase):
"""Test all vars fixes."""
def setUp(self):
"""Prepare tests."""
self.cube = Cube([1.0], var_name='co2', units='J')
self.cube.add_aux_coord(
AuxCoord(0, 'time', 'time', 'time',
Unit('days since 1850-01-01', 'julian')))
self.fix = AllVars()
def test_get(self):
self.assertListEqual(Fix.get_fixes('CMIP5', 'ACCESS1-0', 'tas'),
[AllVars()])
def test_fix_metadata(self):
"""Test fix for bad calendar."""
cube = self.fix.fix_metadata([self.cube])[0]
self.assertEqual(cube.coord('time').units.calendar, 'gregorian')
def test_fix_metadata_if_not_time(self):
"""Test calendar fix do not fail if no time coord present."""
self.cube.remove_coord('time')
self.fix.fix_metadata([self.cube])
def _remove_blend_time(cube: Cube) -> Cube:
"""If present on input, remove existing blend time coordinate (as this will
be replaced on blending)"""
if "blend_time" in get_coord_names(cube):
cube.remove_coord("blend_time")
return cube