def climatology_3d():
def jan_offset(day, year):
dt = (datetime(year, 1, day) - datetime(1970, 1, 1))
return dt.total_seconds() / (24. * 3600)
days = range(10, 15)
years = [[year, year + 10] for year in [2001] * 4]
days_since = [[jan_offset(day, yr1),
jan_offset(day, yr2)]
for (day, [yr1, yr2]) in zip(days, years)]
time_bounds = np.array(days_since)
time_points = time_bounds[..., 0]
lon = np.linspace(-25, 25, 5)
lat = np.linspace(0, 60, 3)
time_dim = DimCoord(time_points,
standard_name='time',
bounds=time_bounds,
units='days since 1970-01-01 00:00:00-00',
climatological=True)
lon_dim = DimCoord(lon, standard_name='longitude')
lat_dim = DimCoord(lat, standard_name='latitude')
data_shape = (len(time_points), len(lat), len(lon))
values = np.zeros(shape=data_shape, dtype=np.int8)
cube = Cube(values)
cube.add_dim_coord(time_dim, 0)
cube.add_dim_coord(lat_dim, 1)
cube.add_dim_coord(lon_dim, 2)
cube.rename('climatology test')
cube.units = 'Kelvin'
cube.add_cell_method(CellMethod('mean over years', coords='time'))
return cube
def test_unknown_method(self):
cube = Cube([1, 2], long_name="odd_phenomenon")
cube.add_cell_method(CellMethod(method="oddity", coords=("x",)))
temp_dirpath = tempfile.mkdtemp()
try:
temp_filepath = os.path.join(temp_dirpath, "tmp.nc")
iris.save(cube, temp_filepath)
with warnings.catch_warnings(record=True) as warning_records:
iris.load(temp_filepath)
# Filter to get the warning we are interested in.
warning_messages = [record.message for record in warning_records]
warning_messages = [
warn
for warn in warning_messages
if isinstance(warn, UnknownCellMethodWarning)
]
self.assertEqual(len(warning_messages), 1)
message = warning_messages[0].args[0]
msg = (
"NetCDF variable 'odd_phenomenon' contains unknown cell "
"method 'oddity'"
)
self.assertIn(msg, message)
finally:
shutil.rmtree(temp_dirpath)
def test_climatological_mean_single_year(self):
cube = Cube(np.zeros((3, 4)))
cube.add_aux_coord(AuxCoord(standard_name="forecast_period", units="hours", points=36, bounds=[24, 4 * 24]))
cube.add_aux_coord(
AuxCoord(standard_name="time", units="hours since epoch", points=240 + 36, bounds=[240 + 24, 240 + 4 * 24])
)
cube.add_aux_coord(AuxCoord(long_name="clim_season", points="DUMMY"))
cube.add_cell_method(CellMethod("DUMMY", "clim_season"))
field = self.convert_cube_to_field(cube)
self.assertEqual(field.lbft, 4 * 24)
def create_difference_cube(cube, coord_name, diff_along_axis):
"""
Put the difference array into a cube with the appropriate
metadata.
Parameters
----------
cube : Iris.cube.Cube
Cube from which the differences have been calculated.
coord_name : String
The name of the coordinate over which the difference
have been calculated.
diff_along_axis : numpy array
Array containing the differences.
Returns
-------
diff_cube : Iris.cube.Cube
Cube containing the differences calculated along the
specified axis.
"""
points = cube.coord(coord_name).points
mean_points = (points[1:] + points[:-1]) / 2
# Copy cube metadata and coordinates into a new cube.
# Create a new coordinate for the coordinate along which the
# difference has been calculated.
metadata_dict = copy.deepcopy(cube.metadata._asdict())
diff_cube = Cube(diff_along_axis, **metadata_dict)
for coord in cube.dim_coords:
dims = cube.coord_dims(coord)
if coord.name() in [coord_name]:
coord = coord.copy(points=mean_points)
diff_cube.add_dim_coord(coord.copy(), dims)
for coord in cube.aux_coords:
dims = cube.coord_dims(coord)
diff_cube.add_aux_coord(coord.copy(), dims)
for coord in cube.derived_coords:
dims = cube.coord_dims(coord)
diff_cube.add_aux_coord(coord.copy(), dims)
# Add metadata to indicate that a difference has been calculated.
# TODO: update this metadata when proper conventions have been
# agreed upon.
cell_method = CellMethod("difference",
coords=[coord_name],
intervals='1 grid length')
diff_cube.add_cell_method(cell_method)
diff_cube.attributes["form_of_difference"] = ("forward_difference")
diff_cube.rename('difference_of_' + cube.name())
return diff_cube
def test_climatological_mean_single_year(self):
cube = Cube(np.zeros((3, 4)))
cube.add_aux_coord(AuxCoord(standard_name='forecast_period',
units='hours',
points=36, bounds=[24, 4 * 24]))
cube.add_aux_coord(AuxCoord(standard_name='time',
units='hours since epoch',
points=240 + 36, bounds=[240 + 24,
240 + 4 * 24]))
cube.add_aux_coord(AuxCoord(long_name='clim_season', points='DUMMY'))
cube.add_cell_method(CellMethod('DUMMY', 'clim_season'))
field = self.convert_cube_to_field(cube)
self.assertEqual(field.lbft, 4 * 24)
def test_climatological_mean_single_year(self):
cube = Cube(np.zeros((3, 4)))
cube.add_aux_coord(AuxCoord(standard_name='forecast_period',
units='hours',
points=36, bounds=[24, 4 * 24]))
cube.add_aux_coord(AuxCoord(standard_name='time',
units='hours since epoch',
points=240 + 36, bounds=[240 + 24,
240 + 4 * 24]))
cube.add_aux_coord(AuxCoord(long_name='clim_season', points='DUMMY'))
cube.add_cell_method(CellMethod('DUMMY', 'clim_season'))
field = self.convert_cube_to_field(cube)
self.assertEqual(field.lbft, 4 * 24)
def create_difference_cube(self, cube, coord_name, diff_along_axis):
"""
Put the difference array into a cube with the appropriate
metadata.
Args:
cube (iris.cube.Cube):
Cube from which the differences have been calculated.
coord_name (str):
The name of the coordinate over which the difference
have been calculated.
diff_along_axis (numpy.ndarray):
Array containing the differences.
Returns:
iris.cube.Cube:
Cube containing the differences calculated along the
specified axis.
"""
points = cube.coord(coord_name).points
mean_points = (points[1:] + points[:-1]) / 2
# Copy cube metadata and coordinates into a new cube.
# Create a new coordinate for the coordinate along which the
# difference has been calculated.
metadata_dict = copy.deepcopy(cube.metadata._asdict())
diff_cube = Cube(diff_along_axis, **metadata_dict)
for coord in cube.dim_coords:
dims = cube.coord_dims(coord)
if coord.name() in [coord_name]:
coord = coord.copy(points=mean_points)
diff_cube.add_dim_coord(coord.copy(), dims)
for coord in cube.aux_coords:
dims = cube.coord_dims(coord)
diff_cube.add_aux_coord(coord.copy(), dims)
for coord in cube.derived_coords:
dims = cube.coord_dims(coord)
diff_cube.add_aux_coord(coord.copy(), dims)
# Add metadata to indicate that a difference has been calculated.
# TODO: update metadata for difference and add metadata for gradient
# when proper conventions have been agreed upon.
if not self.is_gradient:
cell_method = CellMethod("difference",
coords=[coord_name],
intervals="1 grid length")
diff_cube.add_cell_method(cell_method)
diff_cube.attributes["form_of_difference"] = "forward_difference"
diff_cube.rename("difference_of_" + cube.name())
return diff_cube
def create_cube(self, fp_min, fp_mid, fp_max, ref_offset, season=None):
cube = Cube(np.zeros((3, 4)))
cube.add_aux_coord(AuxCoord(standard_name='forecast_period',
units='hours',
points=fp_mid, bounds=[fp_min, fp_max]))
cube.add_aux_coord(AuxCoord(standard_name='time',
units='hours since epoch',
points=ref_offset + fp_mid,
bounds=[ref_offset + fp_min,
ref_offset + fp_max]))
if season:
cube.add_aux_coord(AuxCoord(long_name='clim_season',
points=season))
cube.add_cell_method(CellMethod('DUMMY', 'clim_season'))
return cube
def create_cube(self, fp_min, fp_mid, fp_max, ref_offset, season=None):
cube = Cube(np.zeros((3, 4)))
cube.add_aux_coord(AuxCoord(standard_name='forecast_period',
units='hours',
points=fp_mid, bounds=[fp_min, fp_max]))
cube.add_aux_coord(AuxCoord(standard_name='time',
units='hours since epoch',
points=ref_offset + fp_mid,
bounds=[ref_offset + fp_min,
ref_offset + fp_max]))
if season:
cube.add_aux_coord(AuxCoord(long_name='clim_season',
points=season))
cube.add_cell_method(CellMethod('DUMMY', 'clim_season'))
return cube
def create_cube(self, fp_min, fp_mid, fp_max, ref_offset, season=None):
cube = Cube(np.zeros((3, 4)))
cube.add_aux_coord(
AuxCoord(standard_name="forecast_period", units="hours", points=fp_mid, bounds=[fp_min, fp_max])
)
cube.add_aux_coord(
AuxCoord(
standard_name="time",
units="hours since epoch",
points=ref_offset + fp_mid,
bounds=[ref_offset + fp_min, ref_offset + fp_max],
)
)
if season:
cube.add_aux_coord(AuxCoord(long_name="clim_season", points=season))
cube.add_cell_method(CellMethod("DUMMY", "clim_season"))
return cube
def _update_metadata(diff_cube: Cube, coord_name: str, cube_name: str) -> None:
"""Rename cube, add attribute and cell method to describe difference.
Args:
diff_cube
coord_name
cube_name
"""
# Add metadata to indicate that a difference has been calculated.
# TODO: update metadata for difference when
# proper conventions have been agreed upon.
cell_method = CellMethod(
"difference", coords=[coord_name], intervals="1 grid length"
)
diff_cube.add_cell_method(cell_method)
diff_cube.attributes["form_of_difference"] = "forward_difference"
diff_cube.rename("difference_of_" + cube_name)
def test_section_cell_methods(self):
cube = Cube([0], long_name="name", units=1)
cube.add_cell_method(CellMethod("stdev", "area"))
cube.add_cell_method(
CellMethod(
method="mean",
coords=["y", "time"],
intervals=["10m", "3min"],
comments=["vertical", "=duration"],
))
rep = cube_replines(cube)
# Note: not alphabetical -- provided order is significant
expected = [
"name / (1) (-- : 1)",
" Cell methods:",
" stdev area",
" mean y (10m, vertical), time (3min, =duration)",
]
self.assertEqual(rep, expected)
def test_unknown_method(self):
cube = Cube([1, 2], long_name='odd_phenomenon')
cube.add_cell_method(CellMethod(method='oddity', coords=('x',)))
temp_dirpath = tempfile.mkdtemp()
try:
temp_filepath = os.path.join(temp_dirpath, 'tmp.nc')
iris.save(cube, temp_filepath)
with warnings.catch_warnings(record=True) as warning_records:
iris.load(temp_filepath)
# Filter to get the warning we are interested in.
warning_messages = [record.message for record in warning_records]
warning_messages = [warn for warn in warning_messages
if isinstance(warn, UnknownCellMethodWarning)]
self.assertEqual(len(warning_messages), 1)
message = warning_messages[0].args[0]
msg = ("NetCDF variable 'odd_phenomenon' contains unknown cell "
"method 'oddity'")
self.assertIn(msg, message)
finally:
shutil.rmtree(temp_dirpath)
def test_climatological_mean_single_year(self):
cube = Cube(np.zeros((3, 4)))
cube.add_aux_coord(
AuxCoord(
standard_name="forecast_period",
units="hours",
points=36,
bounds=[24, 4 * 24],
))
cube.add_aux_coord(
AuxCoord(
standard_name="time",
units="hours since epoch",
points=240 + 36,
bounds=[240 + 24, 240 + 4 * 24],
))
cube.add_aux_coord(AuxCoord(long_name="clim_season", points="DUMMY"))
cube.add_cell_method(CellMethod("DUMMY", "clim_season"))
field = self.convert_cube_to_field(cube)
self.assertEqual(field.lbft, 4 * 24)
def create_cube(self, fp_min, fp_mid, fp_max, ref_offset, season=None):
cube = Cube(np.zeros((3, 4)))
cube.add_aux_coord(
AuxCoord(
standard_name="forecast_period",
units="hours",
points=fp_mid,
bounds=[fp_min, fp_max],
))
cube.add_aux_coord(
AuxCoord(
standard_name="time",
units="hours since epoch",
points=ref_offset + fp_mid,
bounds=[ref_offset + fp_min, ref_offset + fp_max],
))
if season:
cube.add_aux_coord(AuxCoord(long_name="clim_season",
points=season))
cube.add_cell_method(CellMethod("DUMMY", "clim_season"))
return cube