def setUp(self):
"""Create a class-object containing the necessary cubes.
All cubes are on the target grid. Here this is defined as a 5x5 grid.
The cubes have values of one everywhere except:
input_land: zeroes (sea points) at [0, 1], [4, 4]
output_land: zeroes (sea points) at [0, 0], [1, 1]
input_cube: 0. at [1, 1]; 0.5 at [0, 1]; 0.1 at [4, 4]
These should trigger all the behavior we expect.
"""
self.plugin = AdjustLandSeaPoints(vicinity_radius=2200.0)
self.output_land = squeeze(
set_up_cube(
num_grid_points=5, zero_point_indices=((0, 0, 1, 1), (0, 0, 0, 0))
)
)
self.cube = squeeze(
set_up_cube(num_grid_points=5, zero_point_indices=((0, 0, 1, 1),))
)
self.cube.data[0, 1] = 0.5
self.cube.data[4, 4] = 0.1
self.input_land = squeeze(
set_up_cube(
num_grid_points=5, zero_point_indices=((0, 0, 0, 1), (0, 0, 4, 4))
)
)
# Lat-lon coords for reprojection
# These coords result in a 1:1 regridding with the above cubes.
x_coord = DimCoord(
np.linspace(-3.281, -3.153, 5),
standard_name="longitude",
units="degrees",
coord_system=ELLIPSOID,
)
y_coord = DimCoord(
np.linspace(54.896, 54.971, 5),
standard_name="latitude",
units="degrees",
coord_system=ELLIPSOID,
)
self.input_land_ll = Cube(
self.input_land.data,
long_name="land_sea_mask",
units="1",
dim_coords_and_dims=[(y_coord, 0), (x_coord, 1)],
)
def setUp(self):
"""
Set up a basic cube and linear weights cube for the process
method. Input cube has 2 thresholds and 3 forecast_reference_times
"""
thresholds = [10, 20]
data = np.ones((2, 2, 3), dtype=np.float32)
cycle1 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 0, 0),
)
cycle2 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 1, 0),
)
cycle3 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 2, 0),
)
self.cube_to_collapse = CubeList([cycle1, cycle2, cycle3]).merge_cube()
self.cube_to_collapse = squeeze(self.cube_to_collapse)
self.cube_to_collapse.rename("weights")
# This input array has 3 forecast reference times and 2 thresholds.
# The two thresholds have the same weights.
self.cube_to_collapse.data = np.array(
[
[[[1, 0, 1], [1, 1, 1]], [[1, 0, 1], [1, 1, 1]]],
[[[0, 0, 1], [0, 1, 1]], [[0, 0, 1], [0, 1, 1]]],
[[[1, 1, 1], [1, 1, 1]], [[1, 1, 1], [1, 1, 1]]],
],
dtype=np.float32,
)
self.cube_to_collapse.data = np.ma.masked_equal(self.cube_to_collapse.data, 0)
# Create a one_dimensional weights cube by slicing the larger
# weights cube.
# The resulting cube only has a forecast_reference_time coordinate.
self.one_dimensional_weights_cube = self.cube_to_collapse[:, 0, 0, 0]
self.one_dimensional_weights_cube.remove_coord("projection_x_coordinate")
self.one_dimensional_weights_cube.remove_coord("projection_y_coordinate")
self.one_dimensional_weights_cube.remove_coord(
find_threshold_coordinate(self.one_dimensional_weights_cube)
)
self.one_dimensional_weights_cube.data = np.array(
[0.2, 0.5, 0.3], dtype=np.float32
)
self.plugin = SpatiallyVaryingWeightsFromMask(
"forecast_reference_time", fuzzy_length=2
)
self.plugin_no_fuzzy = SpatiallyVaryingWeightsFromMask(
"forecast_reference_time", fuzzy_length=1
)
def load_multiple_files_callback(cube, field, filename):
from iris.util import squeeze
# We need to remove these global attributes when reading multiple files so that the cubes can be properly merged
cube.attributes.pop('host_name', None)
cube.attributes.pop('date_time', None)
cube.attributes.pop('history', None)
return squeeze(cube)
def setUp(self):
"""Set up an example cube to test with"""
thresholds = [10]
data = np.ones((1, 2, 3), dtype=np.float32)
cycle1 = set_up_probability_cube(
data,
thresholds,
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 0, 0),
)
cycle2 = set_up_probability_cube(
data,
thresholds,
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 1, 0),
)
cycle3 = set_up_probability_cube(
data,
thresholds,
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 2, 0),
)
self.cube = CubeList([cycle1, cycle2, cycle3]).merge_cube()
self.cube = squeeze(self.cube)
self.plugin = SpatiallyVaryingWeightsFromMask()
def squeeze(data):
from iris.cube import Cube
from iris.util import squeeze
from cis.data_io.gridded_data import make_from_cube
if isinstance(data, Cube):
return make_from_cube(squeeze(data))
else:
return data
def load_multiple_files_callback(cube, field, filename):
from iris.util import squeeze
# We need to remove the history field when reading multiple files so that the cubes can be properly merged
cube.attributes.pop('history')
# cube.coord(name_or_coord='Hybrid height').attributes['formula_terms'] = 'a: lev b: b orog: orog'
# We also need to remove the length one time dimension so that the cube can be merged correctly (iris preserves
# the value as a scalar which then gets converted back into a full coordinate again on merge).
return squeeze(cube)
def squeeze(data):
from iris.cube import Cube
from iris.util import squeeze
from cis.data_io.gridded_data import make_from_cube
if isinstance(data, Cube):
return make_from_cube(squeeze(data))
else:
return data
def load_multiple_files_callback(cube, field, filename):
from iris.util import squeeze
# We need to remove the history field when reading multiple files so that the cubes can be properly merged
cube.attributes.pop('history')
# cube.coord(name_or_coord='Hybrid height').attributes['formula_terms'] = 'a: lev b: b orog: orog'
# We also need to remove the length one time dimension so that the cube can be merged correctly (iris preserves
# the value as a scalar which then gets converted back into a full coordinate again on merge).
return squeeze(cube)
def test_ice_large_with_fc(self):
"""Test that large VII probs do increase zero lightning risk when
forecast lead time is non-zero (two forecast_period points)"""
self.ice_cube.data[:, 1, 1] = 1.
self.fg_cube.data[0, 1, 1] = 0.
self.fg_cube.coord('forecast_period').points = [1.] # hours
fg_cube_next = self.fg_cube.copy()
time_pt, = self.fg_cube.coord('time').points
fg_cube_next.coord('time').points = [time_pt + 2.] # hours
fg_cube_next.coord('forecast_period').points = [3.] # hours
self.fg_cube = CubeList([squeeze(self.fg_cube),
squeeze(fg_cube_next)]).merge_cube()
expected = self.fg_cube.copy()
# expected.data contains all ones except:
expected.data[0, 1, 1] = 0.54
expected.data[1, 1, 1] = 0.0
result = self.plugin.apply_ice(self.fg_cube, self.ice_cube)
self.assertArrayAlmostEqual(result.data, expected.data)
def setUp(self):
"""
Set up a basic weights cube with 2 thresholds to multiple with
a cube with one_dimensional weights.
"""
thresholds = [10, 20]
data = np.ones((2, 2, 3), dtype=np.float32)
cycle1 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 0, 0),
)
cycle2 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 1, 0),
)
cycle3 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 2, 0),
)
self.spatial_weights_cube = CubeList([cycle1, cycle2,
cycle3]).merge_cube()
self.spatial_weights_cube = squeeze(self.spatial_weights_cube)
self.spatial_weights_cube.rename("weights")
# This input array has 3 forecast reference times and 2 thresholds.
# The two thresholds have the same weights.
self.spatial_weights_cube.data = np.array(
[
[[[1, 0, 1], [1, 0, 1]], [[1, 0, 1], [1, 0, 1]]],
[[[0, 0, 1], [0, 0, 1]], [[0, 0, 1], [0, 0, 1]]],
[[[1, 1, 1], [1, 1, 1]], [[1, 1, 1], [1, 1, 1]]],
],
dtype=np.float32,
)
# Create a one_dimensional weights cube by slicing the
# larger weights cube.
# The resulting cube only has a forecast_reference_time coordinate.
self.one_dimensional_weights_cube = self.spatial_weights_cube[:, 0, 0,
0]
self.one_dimensional_weights_cube.remove_coord(
"projection_x_coordinate")
self.one_dimensional_weights_cube.remove_coord(
"projection_y_coordinate")
self.one_dimensional_weights_cube.remove_coord(
find_threshold_coordinate(self.one_dimensional_weights_cube))
self.one_dimensional_weights_cube.data = np.array([0.2, 0.5, 0.3],
dtype=np.float32)
self.plugin = SpatiallyVaryingWeightsFromMask()
def _remove_length_one_dimensions(self, packed_data):
from iris.util import squeeze
from cis.data_io.gridded_data import GriddedData
listify(packed_data)
new_data_list = []
for data in packed_data:
if data.is_gridded:
new_data_list.append(GriddedData.make_from_cube(squeeze(data)))
else:
new_data_list.append(data)
return new_data_list
def main():
arguments = docopt.docopt(__doc__)
print(arguments)
cubes = iris.cube.CubeList(
[squeeze(cube) for cube in irise.load(arguments["<model_data>"])])
with open(arguments["<yaml_file>"]) as f:
info = yaml.safe_load(f)
generate_overview(cubes, info, path=arguments["--output_path"])
def test_not_in_vicinity(self):
"""Test for no change if the matching point is too far away."""
# We need larger arrays for this.
# Define 5 x 5 arrays with output sea point at [1, 1] and input sea
# point at [4, 4]. The alternative value of 0.5 at [4, 4] should not
# be selected with a small vicinity_radius.
self.plugin = AdjustLandSeaPoints(vicinity_radius=2200.0)
cube = squeeze(
set_up_cube(num_grid_points=5,
zero_point_indices=((0, 0, 1, 1), )))
self.plugin.output_land = cube.copy()
self.plugin.nearest_cube = cube.copy()
self.plugin.nearest_cube.data[4, 4] = 0.5
self.plugin.output_cube = self.plugin.nearest_cube.copy()
self.plugin.input_land = squeeze(
set_up_cube(num_grid_points=5,
zero_point_indices=((0, 0, 4, 4), )))
output_cube = self.plugin.output_cube.copy()
self.plugin.correct_where_input_true(0)
self.assertArrayEqual(output_cube.data, self.plugin.output_cube.data)
def setUp(self):
"""Create a class-object containing the necessary cubes.
All cubes are on the target grid. Here this is defined as a 3x3 grid.
The grid contains ones everywhere except the centre point (a zero).
The output_cube has a value of 0.5 at [0, 1].
The move_sea_point cube has the zero value at [0, 1] instead of [1, 1],
this allows it to be used in place of input_land to trigger the
expected behaviour in the function.
"""
self.plugin = AdjustLandSeaPoints(vicinity_radius=2200.0)
cube = squeeze(
set_up_cube(num_grid_points=3,
zero_point_indices=((0, 0, 1, 1), )))
self.plugin.input_land = cube.copy()
self.plugin.output_land = cube.copy()
self.plugin.nearest_cube = cube.copy()
self.plugin.nearest_cube.data[0, 1] = 0.5
self.plugin.output_cube = self.plugin.nearest_cube.copy()
self.move_sea_point = squeeze(
set_up_cube(num_grid_points=3,
zero_point_indices=((0, 0, 0, 1), )))
def load_single_file_callback(cube, field, filename):
from iris.util import squeeze
from datetime import datetime
from iris.coords import AuxCoord
datetime = datetime(cube.attributes['HDFEOS_ADDITIONAL_FILE_ATTRIBUTES.GranuleYear'],
cube.attributes['HDFEOS_ADDITIONAL_FILE_ATTRIBUTES.GranuleMonth'],
cube.attributes['HDFEOS_ADDITIONAL_FILE_ATTRIBUTES.GranuleDay'],
12, 0, 0)
cube.add_aux_coord(AuxCoord([datetime], standard_name='time'))
cube.units = 'dobson'
cube.convert_units()
# Sometimes it's useful to remove length one dimensions from cubes, squeeze does this for us...
return squeeze(cube)
def load_single_file_callback(cube, field, filename):
from iris.util import squeeze
from datetime import datetime
from iris.coords import AuxCoord
datetime = datetime(
cube.attributes['HDFEOS_ADDITIONAL_FILE_ATTRIBUTES.GranuleYear'],
cube.attributes['HDFEOS_ADDITIONAL_FILE_ATTRIBUTES.GranuleMonth'],
cube.attributes['HDFEOS_ADDITIONAL_FILE_ATTRIBUTES.GranuleDay'],
12, 0, 0)
cube.add_aux_coord(AuxCoord([datetime], standard_name='time'))
cube.units = 'dobson'
cube.convert_units()
# Sometimes it's useful to remove length one dimensions from cubes, squeeze does this for us...
return squeeze(cube)
def setUp(self):
"""
Set up a basic 2D cube with a large enough grid to see the
effect of the fuzzy weights.
"""
thresholds = [10]
data = np.ones((1, 7, 7), dtype=np.float32)
self.cube = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 0, 0),
)
self.cube = squeeze(self.cube)
def setUp(self):
"""Set up a cube with 2 thresholds to test normalisation. We are
testing normalising along the leading dimension in this cube."""
thresholds = [10, 20]
data = np.ones((2, 2, 3), dtype=np.float32)
cycle1 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 0, 0),
)
cycle2 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 1, 0),
)
cycle3 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 2, 0),
)
self.spatial_weights_cube = CubeList([cycle1, cycle2,
cycle3]).merge_cube()
self.spatial_weights_cube = squeeze(self.spatial_weights_cube)
self.spatial_weights_cube.rename("weights")
# This input array has 3 forecast reference times and 2 thresholds.
# The two thresholds have the same weights.
self.spatial_weights_cube.data = np.array(
[
[[[0.2, 0, 0.2], [0.2, 0, 0.2]], [[0.2, 0, 0.2], [0.2, 0, 0.2]]
],
[[[0, 0, 0.5], [0, 0, 0.5]], [[0, 0, 0.5], [0, 0, 0.5]]],
[
[[0.3, 0.3, 0.3], [0.3, 0.3, 0.3]],
[[0.3, 0.3, 0.3], [0.3, 0.3, 0.3]],
],
],
dtype=np.float32,
)
self.plugin = SpatiallyVaryingWeightsFromMask()
def setUp(self):
"""
Set up a basic input cube. Input cube has 2 thresholds on and 3
forecast_reference_times
"""
thresholds = [10, 20]
data = np.ones((2, 2, 3), dtype=np.float32)
cycle1 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 0, 0),
)
cycle2 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 1, 0),
)
cycle3 = set_up_probability_cube(
data,
thresholds,
spatial_grid="equalarea",
time=datetime(2017, 11, 10, 4, 0),
frt=datetime(2017, 11, 10, 2, 0),
)
self.cube_to_collapse = CubeList([cycle1, cycle2, cycle3]).merge_cube()
self.cube_to_collapse = squeeze(self.cube_to_collapse)
self.cube_to_collapse.rename("weights")
# This input array has 3 forecast reference times and 2 thresholds.
# The two thresholds have the same weights.
self.cube_to_collapse.data = np.array(
[
[[[1, 0, 1], [1, 1, 1]], [[1, 0, 1], [1, 1, 1]]],
[[[0, 0, 1], [0, 1, 1]], [[0, 0, 1], [0, 1, 1]]],
[[[1, 1, 1], [1, 1, 1]], [[1, 1, 1], [1, 1, 1]]],
],
dtype=np.float32,
)
self.cube_to_collapse.data = np.ma.masked_equal(
self.cube_to_collapse.data, 0)
self.plugin = SpatiallyVaryingWeightsFromMask(
"forecast_reference_time")
def test_ice_large_with_fc(self):
"""Test that large VII probs do increase zero lightning risk when
forecast lead time is non-zero (three forecast_period points)"""
self.ice_cube.data[:, 1, 1] = 1.0
self.fg_cube.data[1, 1] = 0.0
frt_point = self.fg_cube.coord("forecast_reference_time").points[0]
fg_cube_input = CubeList([])
for fc_time in np.array([1, 2.5, 3]) * 3600: # seconds
fg_cube_next = self.fg_cube.copy()
fg_cube_next.coord("time").points = [frt_point + fc_time]
fg_cube_next.coord("forecast_period").points = [fc_time]
fg_cube_input.append(squeeze(fg_cube_next))
fg_cube_input = fg_cube_input.merge_cube()
expected = fg_cube_input.copy()
# expected.data contains all ones except:
expected.data[0, 1, 1] = 0.54
expected.data[1, 1, 1] = 0.0
expected.data[2, 1, 1] = 0.0
result = self.plugin.apply_ice(fg_cube_input, self.ice_cube)
self.assertArrayAlmostEqual(result.data, expected.data)
def setUp(self):
"""Create cubes with a single zero prob(precip) point.
The cubes look like this:
precipitation_amount / (kg m^-2)
Dimension coordinates:
time: 1;
projection_y_coordinate: 3;
projection_x_coordinate: 3;
Auxiliary coordinates:
forecast_period (on time coord): 0.0 hours (simulates nowcast data)
Scalar coordinates:
forecast_reference_time: 2015-11-23 03:00:00
Data:
self.fg_cube:
All points contain float(1.)
Cube name is "probability_of_lightning".
self.ice_cube:
With extra coordinate of length(3) "threshold" containing
points [0.5, 1., 2.] kg m^-2.
Time and forecast_period dimensions "sqeezed" to be Scalar coords.
All points contain float(0.)
Cube name is "probability_of_vertical_integral_of_ice".
"""
self.fg_cube = add_forecast_reference_time_and_forecast_period(
set_up_cube_with_no_realizations(zero_point_indices=[],
num_grid_points=3),
fp_point=0.0)
self.fg_cube.rename("probability_of_lightning")
self.ice_cube = squeeze(
add_forecast_reference_time_and_forecast_period(set_up_cube(
num_realization_points=3,
zero_point_indices=[],
num_grid_points=3),
fp_point=0.0))
threshold_coord = self.ice_cube.coord('realization')
threshold_coord.points = [0.5, 1.0, 2.0]
threshold_coord.rename('threshold')
threshold_coord.units = cf_units.Unit('kg m^-2')
self.ice_cube.data = np.zeros_like(self.ice_cube.data)
self.ice_cube.rename("probability_of_vertical_integral_of_ice")
self.plugin = Plugin()
def load_single_file_callback(cube, field, filename):
from iris.util import squeeze
# We need to remove the history field when reading multiple files so that the cubes can be properly merged
cube.attributes.pop('history')
# Fix the altitude coordinate
alt_coord = cube.coords(name_or_coord='hybrid_ht_1')
if alt_coord:
alt_coord[0].rename('altitude')
alt_coord[0].attributes = {}
alt_coord[0].units = Unit('m')
# Remove the scalar time coord
if len(cube.coord('t').points) == 1:
cube.remove_coord(cube.coord(name_or_coord='t'))
else:
cube.coord(name_or_coord='t').rename('time')
# We also need to remove the length one time dimension so that the cube can be merged correctly (iris preserves
# the value as a scalar which then gets converted back into a full coordinate again on merge).
return squeeze(cube)
def correct_analyses(cubes):
newcubes = CubeList()
for cube in cubes:
# Squeeze cubes dimensions
newcube = squeeze(cube)
# Give time coordinate proper name
newcube.coord('t').rename('time')
# Correct dimensional coordinates
z, y, x, t = newcube.coords()
z.rename('level_height')
z.units = 'm'
z.attributes = {'positive': 'up'}
y.rename('latitude')
y.coord_system = lat.coord_system
y.units = lat.units
x.rename('longitude')
x.coord_system = lon.coord_system
x.units = lon.units
newcubes.append(newcube)
# Correct cube names
for before, after in name_pairs:
newcubes.extract(before)[0].rename(after)
# Correct units
for name, unit in units:
newcubes.extract(name)[0].units = unit
return newcubes
def test_missing_dim(self):
"""Check that an error is raised if missing dimensional coordinate"""
single_percentile = squeeze(self.percentiles_land[0])
message = "Input cubes do not have the same dimension coordinates"
with self.assertRaisesRegex(ValueError, message):
merge_land_and_sea(single_percentile, self.percentiles_sea)
def setUp(self):
"""Create cubes with a single zero prob(precip) point.
The cubes look like this:
precipitation_amount / (kg m^-2)
Dimension coordinates:
time: 1;
projection_y_coordinate: 3;
projection_x_coordinate: 3;
Auxiliary coordinates:
forecast_period (on time coord): 4.0 hours (simulates UM data)
Scalar coordinates:
forecast_reference_time: 2015-11-23 03:00:00
Data:
self.cube:
Describes the nowcast fields to be calculated.
forecast_period (on time coord): 0.0 hours (simulates nowcast data)
All points contain float(1.) except the
zero point [0, 1, 1] which is float(0.)
self.fg_cube:
All points contain float(1.)
self.ltng_cube:
forecast_period (on time coord): 0.0 hours (simulates nowcast data)
All points contain float(1.)
self.precip_cube:
With extra coordinate of length(3) "threshold" containing
points [0.5, 7., 35.] mm hr-1.
All points contain float(1.) except the
zero point [0, 0, 1, 1] which is float(0.)
and [1:, 0, ...] which are float(0.)
self.vii_cube:
With extra coordinate of length(3) "threshold" containing
points [0.5, 1., 2.] kg m^-2.
forecast_period (on time coord): 0.0 hours (simulates nowcast data)
Time and forecast_period dimensions "sqeezed" to be Scalar coords.
All points contain float(0.)
"""
self.cube = add_forecast_reference_time_and_forecast_period(
set_up_cube_with_no_realizations(zero_point_indices=((0, 1, 1), ),
num_grid_points=3),
fp_point=0.0)
self.fg_cube = add_forecast_reference_time_and_forecast_period(
set_up_cube_with_no_realizations(zero_point_indices=[],
num_grid_points=3))
self.ltng_cube = add_forecast_reference_time_and_forecast_period(
set_up_cube_with_no_realizations(zero_point_indices=[],
num_grid_points=3),
fp_point=0.0)
self.precip_cube = (add_forecast_reference_time_and_forecast_period(
set_up_cube(num_realization_points=3,
zero_point_indices=((0, 1, 1), ),
num_grid_points=3),
fp_point=0.0))
threshold_coord = self.precip_cube.coord('realization')
threshold_coord.points = [0.5, 7.0, 35.0]
threshold_coord.rename('threshold')
threshold_coord.units = cf_units.Unit('mm hr-1')
self.precip_cube.data[1:, 0, ...] = 0.
# iris.util.queeze is applied here to demote the singular coord "time"
# to a scalar coord.
self.vii_cube = squeeze(
add_forecast_reference_time_and_forecast_period(set_up_cube(
num_realization_points=3,
zero_point_indices=[],
num_grid_points=3),
fp_point=0.0))
threshold_coord = self.vii_cube.coord('realization')
threshold_coord.points = [0.5, 1.0, 2.0]
threshold_coord.rename('threshold')
threshold_coord.units = cf_units.Unit('kg m^-2')
self.vii_cube.data = np.zeros_like(self.vii_cube.data)
self.plugin = Plugin()
def set_up_lightning_test_cubes(validity_time=dt(2015, 11, 23, 7),
fg_frt=dt(2015, 11, 23, 3),
grid_points=3):
"""Set up five cubes for testing nowcast lightning.
The cube coordinates look like this:
Dimension coordinates:
projection_y_coordinate: grid_points;
projection_x_coordinate: grid_points;
Scalar coordinates:
time: 2015-11-23 07:00:00
forecast_reference_time: 2015-11-23 07:00:00
forecast_period: 0 seconds
Args:
grid_points (int):
Number of points along each spatial axis (square grid)
validity_time (datetime.datetime):
Time to use for test cubes
fg_frt (datetime.datetime):
Forecast reference time for first_guess_cube, which needs
to have different forecast periods for different tests
Returns:
template_cube (iris.cube.Cube)
first_guess_cube (iris.cube.Cube)
lightning_rate_cube (iris.cube.Cube)
prob_precip_cube (iris.cube.Cube):
Has extra coordinate of length(3) "threshold" containing
points [0.5, 7., 35.] mm h-1
prob_vii_cube (iris.cube.Cube):
Has extra coordinate of length(3) "threshold" containing
points [0.5, 1., 2.] kg m-2
"""
# template cube with metadata matching desired output
data = np.ones((grid_points, grid_points), dtype=np.float32)
template_cube = set_up_variable_cube(
data.copy(),
name="metadata_template",
units=None,
time=validity_time,
frt=validity_time,
spatial_grid="equalarea",
)
# first guess lightning rate probability cube with flexible forecast
# period (required for level 2 lighting risk index)
prob_fg = np.array([data.copy()], dtype=np.float32)
first_guess_cube = set_up_probability_cube(
prob_fg,
np.array([0], dtype=np.float32),
threshold_units="s-1",
variable_name="rate_of_lightning",
time=validity_time,
frt=fg_frt,
spatial_grid="equalarea",
)
first_guess_cube = squeeze(first_guess_cube)
# lightning rate cube full of ones
lightning_rate_cube = set_up_variable_cube(
data.copy(),
name="rate_of_lightning",
units="min-1",
time=validity_time,
frt=validity_time,
spatial_grid="equalarea",
)
# probability of precip rate exceedance cube with higher rate probabilities
# set to zero, and central point of low rate probabilities set to zero
precip_data = np.ones((3, grid_points, grid_points), dtype=np.float32)
precip_thresholds = np.array([0.5, 7.0, 35.0], dtype=np.float32)
prob_precip_cube = set_up_probability_cube(
precip_data,
precip_thresholds,
variable_name="lwe_precipitation_rate",
threshold_units="mm h-1",
time=validity_time,
frt=validity_time,
spatial_grid="equalarea",
)
prob_precip_cube.data[0, 1, 1] = 0.0
prob_precip_cube.data[1:, ...] = 0.0
# probability of VII exceedance cube full of zeros
vii_data = np.zeros((3, grid_points, grid_points), dtype=np.float32)
vii_thresholds = np.array([0.5, 1.0, 2.0], dtype=np.float32)
prob_vii_cube = set_up_probability_cube(
vii_data,
vii_thresholds,
variable_name="vertical_integral_of_ice",
threshold_units="kg m-2",
time=validity_time,
frt=validity_time,
spatial_grid="equalarea",
)
return (
template_cube,
first_guess_cube,
lightning_rate_cube,
prob_precip_cube,
prob_vii_cube,
)
def generate_metadata(
name="air_pressure_at_sea_level",
units=None,
time_period=None,
ensemble_members=8,
leading_dimension=None,
cube_type="variable",
spp__relative_to_threshold="greater_than",
npoints=71,
**kwargs,
):
""" Generate a cube with metadata only.
Args:
name (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.
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.
ensemble_members (Optional[int]):
Number of ensemble members. Default 8, unless percentile or probability set
to True.
leading_dimension (Optional[List[float]]):
List of realizations, percentiles or thresholds.
cube_type (Optional[str]):
The type of cube to be generated. Permitted values are "variable",
"percentile" or "probability".
spp__relative_to_threshold (Optional[str]):
Value of the attribute "spp__relative_to_threshold" which is required for
IMPROVER probability cubes.
npoints (Optional[int]):
Number of points along each of the y and x spatial axes.
**kwargs:
Additional keyword arguments to pass to the required cube setup function.
Returns:
iris.cube.Cube:
Output of set_up_variable_cube(), set_up_percentile_cube() or
set_up_probability_cube()
"""
if cube_type not in CUBE_TYPES:
raise ValueError(
'Cube type {} not supported. Specify one of "variable", "percentile" or "probability".'
.format(cube_type))
if "spatial_grid" in kwargs and kwargs["spatial_grid"] not in (
"latlon",
"equalarea",
):
raise ValueError(
"Spatial grid {} not supported. Specify either latlon or equalarea."
.format(kwargs["spatial_grid"]))
if ("domain_corner" in kwargs and kwargs["domain_corner"] is not None
and len(kwargs["domain_corner"]) != 2):
raise ValueError("Domain corner must be a list or tuple of length 2.")
if units is None:
units = _get_units(name)
# If time_period specified, create time bounds using time as upper bound
if time_period is not None:
if "time" not in kwargs:
kwargs["time"] = DEFAULT_TIME
time_bounds = _create_time_bounds(kwargs["time"], time_period)
kwargs["time_bounds"] = time_bounds
# If grid_spacing not specified, use default for requested spatial grid
if "grid_spacing" not in kwargs or kwargs["grid_spacing"] is None:
if "spatial_grid" not in kwargs:
kwargs["spatial_grid"] = DEFAULT_SPATIAL_GRID
kwargs["grid_spacing"] = DEFAULT_GRID_SPACING[kwargs["spatial_grid"]]
# Create ndimensional array of zeros
if "height_levels" not in kwargs:
kwargs["height_levels"] = None
data = _create_data_array(ensemble_members, leading_dimension, npoints,
kwargs["height_levels"])
# Set up requested cube
if cube_type == "percentile":
metadata_cube = set_up_percentile_cube(
data,
percentiles=leading_dimension,
name=name,
units=units,
**kwargs,
)
elif cube_type == "probability":
metadata_cube = set_up_probability_cube(
data,
leading_dimension,
variable_name=name,
threshold_units=units,
spp__relative_to_threshold=spp__relative_to_threshold,
**kwargs,
)
else:
metadata_cube = set_up_variable_cube(
data,
name=name,
units=units,
realizations=leading_dimension,
**kwargs,
)
metadata_cube = squeeze(metadata_cube)
return metadata_cube
def setUp(self):
"""Create cubes with a single zero prob(precip) point.
The cubes look like this:
precipitation_amount / (kg m^-2)
Dimension coordinates:
time: 1;
projection_y_coordinate: 16;
projection_x_coordinate: 16;
Auxiliary coordinates:
forecast_period (on time coord): 4.0 hours (simulates UM data)
Scalar coordinates:
forecast_reference_time: 2015-11-23 03:00:00
Data:
self.fg_cube:
All points contain float(1.)
Cube name is "probability_of_lightning".
self.ltng_cube:
forecast_period (on time coord): 0.0 hours (simulates nowcast data)
All points contain float(1.)
Cube name is "rate_of_lightning".
Cube units are "min^-1".
self.precip_cube:
With extra coordinate of length(3) "threshold" containing
points [0.5, 7., 35.] mm hr-1.
All points contain float(1.) except the
zero point [0, 0, 7, 7] which is float(0.)
and [1:, 0, ...] which are float(0.)
Cube name is "probability_of_precipitation".
Cube has added attribute {'relative_to_threshold': 'above'}
self.vii_cube:
forecast_period (on time coord): 0.0 hours (simulates nowcast data)
With extra coordinate of length(3) "threshold" containing
points [0.5, 1., 2.] kg m^-2.
forecast_period (on time coord): 0.0 hours (simulates nowcast data)
Time and forecast_period dimensions "sqeezed" to be Scalar coords.
All points contain float(0.)
Cube name is "probability_of_vertical_integral_of_ice".
"""
self.fg_cube = add_forecast_reference_time_and_forecast_period(
set_up_cube_with_no_realizations(zero_point_indices=[]))
self.fg_cube.rename("probability_of_lightning")
self.ltng_cube = add_forecast_reference_time_and_forecast_period(
set_up_cube_with_no_realizations(zero_point_indices=[]),
fp_point=0.0)
self.ltng_cube.rename("rate_of_lightning")
self.ltng_cube.units = cf_units.Unit("min^-1")
self.precip_cube = (add_forecast_reference_time_and_forecast_period(
set_up_cube(num_realization_points=3)))
threshold_coord = self.precip_cube.coord('realization')
threshold_coord.points = [0.5, 7.0, 35.0]
threshold_coord.rename('threshold')
threshold_coord.units = cf_units.Unit('mm hr-1')
self.precip_cube.rename("probability_of_precipitation")
self.precip_cube.attributes.update({'relative_to_threshold': 'above'})
self.precip_cube.data[1:, 0, ...] = 0.
self.vii_cube = squeeze(
add_forecast_reference_time_and_forecast_period(set_up_cube(
num_realization_points=3, zero_point_indices=[]),
fp_point=0.0))
threshold_coord = self.vii_cube.coord('realization')
threshold_coord.points = [0.5, 1.0, 2.0]
threshold_coord.rename('threshold')
threshold_coord.units = cf_units.Unit('kg m^-2')
self.vii_cube.data = np.zeros_like(self.vii_cube.data)
self.vii_cube.rename("probability_of_vertical_integral_of_ice")
self.plugin = Plugin()
def load(uris, constraints=None, callback=None):
cubes = iris.load(uris, constraints=constraints, callback=callback)
fix_by_stash(cubes)
cubes.sort(key=get_stash)
return iris.cube.CubeList([squeeze(cube) for cube in cubes])
def load_single_file_callback(cube, field, filename):
from iris.util import squeeze
# Sometimes it's useful to remove length one dimensions from cubes, squeeze does this for us...
return squeeze(cube)
def load_single_file_callback(cube, field, filename):
from iris.util import squeeze
# Sometimes it's useful to remove length one dimensions from cubes, squeeze does this for us...
return squeeze(cube)