def test_is_vertical_coordinate(self):
'''
Section 4.3 Qualifiers for Vertical Coordinate
NOTE: The standard doesn't explicitly say that vertical coordinates must be a
coordinate type.
'''
# Make something that I can attach attrs to
mock_variable = MockVariable
# Proper name/standard_name
known_name = mock_variable()
known_name.standard_name = 'depth'
self.assertTrue(is_vertical_coordinate('not_known', known_name))
# Proper Axis
axis_set = mock_variable()
axis_set.axis = 'Z'
self.assertTrue(is_vertical_coordinate('not_known', axis_set))
# Proper units
units_set = mock_variable()
units_set.units = 'dbar'
self.assertTrue(is_vertical_coordinate('not_known', units_set))
# Proper units/positive
positive = mock_variable()
positive.units = 'm'
positive.positive = 'up'
self.assertTrue(is_vertical_coordinate('not_known', positive))
def test_is_vertical_coordinate(self):
'''
Section 4.3 Qualifiers for Vertical Coordinate
NOTE: The standard doesn't explicitly say that vertical coordinates must be a
coordinate type.
'''
# Make something that I can attach attrs to
mock_variable = MockVariable
# Proper name/standard_name
known_name = mock_variable()
known_name.standard_name = 'depth'
self.assertTrue(is_vertical_coordinate('not_known', known_name))
# Proper Axis
axis_set = mock_variable()
axis_set.axis = 'Z'
self.assertTrue(is_vertical_coordinate('not_known', axis_set))
# Proper units
units_set = mock_variable()
units_set.units = 'dbar'
self.assertTrue(is_vertical_coordinate('not_known', units_set))
# Proper units/positive
positive = mock_variable()
positive.units = 'm'
positive.positive = 'up'
self.assertTrue(is_vertical_coordinate('not_known', positive))
def test_is_vertical_coordinate(self):
"""
Section 4.3 Qualifiers for Vertical Coordinate
NOTE: The standard doesn't explicitly say that vertical coordinates must be a
coordinate type.
"""
# Make something that I can attach attrs to
mock_variable = MockVariable
# Proper name/standard_name
known_name = mock_variable()
known_name.standard_name = "depth"
self.assertTrue(is_vertical_coordinate("not_known", known_name))
# Proper Axis
axis_set = mock_variable()
axis_set.axis = "Z"
self.assertTrue(is_vertical_coordinate("not_known", axis_set))
# Proper units
units_set = mock_variable()
units_set.units = "dbar"
self.assertTrue(is_vertical_coordinate("not_known", units_set))
# Proper units/positive
positive = mock_variable()
positive.units = "m"
positive.positive = "up"
self.assertTrue(is_vertical_coordinate("not_known", positive))
def check_vertical_extents(self, ds):
"""
Check that the values of geospatial_vertical_min/geospatial_vertical_max approximately match the data.
"""
if not (hasattr(ds, 'geospatial_vertical_min')
and hasattr(ds, 'geospatial_vertical_max')):
return
vert_min = ds.geospatial_vertical_min
vert_max = ds.geospatial_vertical_max
# identify vertical vars as per CF 4.3
v_vars = [
var for name, var in ds.variables.items()
if is_vertical_coordinate(name, var)
]
if len(v_vars) == 0:
return Result(
BaseCheck.MEDIUM, False, 'geospatial_vertical_extents_match', [
'Could not find vertical variable to test extent of geospatial_vertical_min/geospatial_vertical_max, see CF-1.6 spec chapter 4.3'
])
obs_mins = {
var._name: np.nanmin(var)
for var in v_vars if not np.isnan(var).all()
}
obs_maxs = {
var._name: np.nanmax(var)
for var in v_vars if not np.isnan(var).all()
}
min_pass = any(
(np.isclose(vert_min, min_val) for min_val in obs_mins.values()))
max_pass = any(
(np.isclose(vert_max, max_val) for max_val in obs_maxs.values()))
allpass = sum((min_pass, max_pass))
msgs = []
if not min_pass:
msgs.append(
"Data for possible vertical variables (%s) did not match geospatial_vertical_min value (%s)"
% (obs_mins, vert_min))
if not max_pass:
msgs.append(
"Data for possible vertical variables (%s) did not match geospatial_vertical_max value (%s)"
% (obs_maxs, vert_max))
return Result(BaseCheck.MEDIUM, (allpass, 2),
'geospatial_vertical_extents_match', msgs)
def check_vertical_extents(self, ds):
"""
Check that the values of geospatial_vertical_min/geospatial_vertical_max approximately match the data.
"""
if not (hasattr(ds, "geospatial_vertical_min") and hasattr(ds, "geospatial_vertical_max")):
return
vert_min = ds.geospatial_vertical_min
vert_max = ds.geospatial_vertical_max
# identify vertical vars as per CF 4.3
v_vars = [var for name, var in ds.variables.items() if is_vertical_coordinate(name, var)]
if len(v_vars) == 0:
return Result(
BaseCheck.MEDIUM,
False,
"geospatial_vertical_extents_match",
[
"Could not find vertical variable to test extent of geospatial_vertical_min/geospatial_vertical_max, see CF-1.6 spec chapter 4.3"
],
)
obs_mins = {var._name: np.nanmin(var) for var in v_vars if not np.isnan(var).all()}
obs_maxs = {var._name: np.nanmax(var) for var in v_vars if not np.isnan(var).all()}
min_pass = any((np.isclose(vert_min, min_val) for min_val in obs_mins.values()))
max_pass = any((np.isclose(vert_max, max_val) for max_val in obs_maxs.values()))
allpass = sum((min_pass, max_pass))
msgs = []
if not min_pass:
msgs.append(
"Data for possible vertical variables (%s) did not match geospatial_vertical_min value (%s)"
% (obs_mins, vert_min)
)
if not max_pass:
msgs.append(
"Data for possible vertical variables (%s) did not match geospatial_vertical_max value (%s)"
% (obs_maxs, vert_max)
)
return Result(BaseCheck.MEDIUM, (allpass, 2), "geospatial_vertical_extents_match", msgs)