def test_cf_set_cf_specs():
cf.reset_cache(disk=False)
cfspecs = cf.get_cf_specs()
cf.set_cf_specs(cfspecs)
cf_cache = cf._get_cache_()
assert cf_cache["current"] is cfspecs
assert cf.get_cf_specs() is cfspecs
def test_cf_set_cf_specs():
cf._CACHE.clear()
cfspecs = cf.get_cf_specs()
cf.set_cf_specs(cfspecs)
assert "specs" in cf._CACHE
assert cf._CACHE["specs"] is cfspecs
assert cf.get_cf_specs() is cfspecs
def test_cf_get_cfg_specs_var():
specs = cf.get_cf_specs("temp", "data_vars")
assert specs["name"][0] == "temp"
assert specs["standard_name"][0] == "sea_water_temperature"
assert specs["cmap"] == "cmo.thermal"
new_specs = cf.get_cf_specs("temp")
assert new_specs is specs
def test_cf_get_cfg_specs_var():
specs = cf.get_cf_specs().data_vars["temp"]
assert specs["alt_names"][0] == "temperature"
assert specs["attrs"]["standard_name"][0] == "sea_water_temperature"
assert specs["cmap"] == "cmo.thermal"
new_specs = cf.get_cf_specs()["temp"]
assert new_specs is specs
def test_cf_set_cf_specs_context():
cfspecs0 = cf.get_cf_specs()
cfspecs1 = cf.CFSpecs({"data_vars": {"temp": {"name": "tempouille"}}})
assert cf.get_cf_specs() is cfspecs0
with cf.set_cf_specs(cfspecs1) as cfspecs:
assert cfspecs is cfspecs1
assert cf.get_cf_specs() is cfspecs1
assert cf.get_cf_specs() is cfspecs0
def test_cf_cfspecs_format_data_var_loc():
temp = xr.DataArray(0,
name='xtemp',
attrs={'standard_name': 'banana_at_x_location'})
cfspecs = cf.get_cf_specs()
temp_fmt = cfspecs.format_data_var(temp,
"temp",
format_coords=False,
replace_attrs=True)
assert temp_fmt.name == "temp"
assert temp_fmt.standard_name == "sea_water_temperature_at_x_location"
temp_fmt = cfspecs.format_data_var(temp,
"temp",
format_coords=False,
replace_attrs=True,
add_loc_to_name=True)
assert temp_fmt.name == "temp_x"
cfspecs = cf.CFSpecs({"data_vars": {"temp": {"add_loc": True}}})
temp_fmt = cfspecs.format_data_var(temp,
"temp",
format_coords=False,
replace_attrs=True)
assert temp_fmt.name == "temp_x"
def test_cf_cfspecs_coords_search_dim():
cfspecs = cf.get_cf_specs().coords
# from name
temp = xr.DataArray(np.arange(2 * 3).reshape(1, 2, 3),
dims=('aa', 'ny', 'x'))
assert cfspecs.search_dim(temp, 'y') == 'ny'
assert cfspecs.search_dim(temp) is None
# from explicit axis attribute
depth = xr.DataArray([1], dims='aa', attrs={'axis': 'z'})
temp.coords['aa'] = depth
assert cfspecs.search_dim(temp, 'z') == 'aa'
assert cfspecs.search_dim(temp) is None
# from known coordinate
del temp.coords['aa'].attrs['axis']
temp.coords['aa'].attrs['standard_name'] = 'ocean_layer_depth'
assert cfspecs.search_dim(temp, 'z') == 'aa'
assert cfspecs.search_dim(temp) is None
# subcoords
level = xr.DataArray(np.arange(2), dims='level')
depth = xr.DataArray(np.arange(2 * 3).reshape(2, 3),
dims=('level', 'x'),
name='depth',
coords={'level': level})
assert cfspecs.search_dim(depth) == ('level', 'z')
assert cfspecs.search_dim(depth.level) == ('level', 'z')
depth = depth.rename(level='aa')
depth.aa.attrs['axis'] = 'Z'
assert cfspecs.search_dim(depth) == ('aa', 'z')
assert cfspecs.search_dim(xr.DataArray([5], dims='bb')) == ('bb', None)
def test_cf_cfspecs_match_coord(cf_name, in_name, in_attrs):
lon = xr.DataArray(range(5), dims=in_name, name=in_name, attrs=in_attrs)
res = cf.get_cf_specs().match_coord(lon, cf_name)
if cf_name is None:
assert res == 'lon'
else:
assert res is True
def test_cf_cfspecs_format_coord(cf_name, in_name, in_attrs):
lon = xr.DataArray(range(5), dims=in_name, name=in_name, attrs=in_attrs)
lon = cf.get_cf_specs().format_coord(lon, cf_name)
assert lon.name == "lon"
assert lon.standard_name == "longitude"
assert lon.long_name == "Longitude"
assert lon.units == "degrees_east"
def test_cf_cfspecs_search_coord(cf_name, in_name, in_attrs):
lon = xr.DataArray(range(5), dims=in_name, name=in_name, attrs=in_attrs)
temp = xr.DataArray(range(20, 25),
dims=in_name,
coords={in_name: lon},
name='temp')
res = cf.get_cf_specs().search_coord(temp, cf_name, get="name")
assert res == 'lon'
def test_cf_cfspecs_format_coord_unknown():
coord = xr.DataArray(range(5), name='foo')
cfspecs = cf.get_cf_specs()
coord_fmt = cfspecs.format_coord(coord, rename=False)
assert coord_fmt is None
coord_fmt = cfspecs.format_coord(coord, rename=True)
assert coord_fmt.name == "foo"
def test_cf_cfspecs_format_data_var_loc():
temp = xr.DataArray(0,
name='xtemp_t',
attrs={'standard_name': 'banana_at_x_location'})
cfspecs = cf.get_cf_specs()
temp_fmt = cfspecs.format_data_var(temp, "temp", format_coords=False)
assert temp_fmt.name == "temp_t"
assert temp_fmt.standard_name == "sea_water_temperature_at_x_location"
def test_cf_cfspecs_format_data_var_unkown():
da = xr.DataArray(range(5), name='foo')
cfspecs = cf.get_cf_specs()
da_fmt = cfspecs.format_data_var(da, rename=False)
assert da_fmt is None
da_fmt = cfspecs.format_data_var(da, rename=True)
assert da_fmt.name == "foo"
def test_cf_cfspecs_search_data_var(cf_name, in_name, in_attrs):
lon = xr.DataArray(range(5), dims='lon', name='lon')
temp = xr.DataArray(range(20, 25),
dims='lon',
coords={'lon': lon},
name=in_name,
attrs=in_attrs)
ds = temp.to_dataset()
assert cf.get_cf_specs().search_data_var(ds, cf_name, get="name") == 'temp'
def test_cf_cfspecs_coords_get_dim_type():
cfspecs = cf.get_cf_specs().coords
# from name
assert cfspecs.get_dim_type('aa') is None
assert cfspecs.get_dim_type('xi') == "x"
# from a known coordinate
coord = xr.DataArray([1], dims='aa', attrs={'standard_name': 'longitude'})
da = xr.DataArray([1], dims='aa', coords={'aa': coord})
assert cfspecs.get_dim_type('aa', da=da) == "x"
def test_cf_cfspecs_copy():
cfspecs0 = cf.get_cf_specs()
cfspecs1 = cfspecs0.copy()
assert id(cfspecs0._dict) != id(cfspecs1._dict)
assert sorted(list(cfspecs0._dict["data_vars"])) == sorted(
list(cfspecs1._dict["data_vars"]))
assert cfspecs0._dict["coords"] == cfspecs1._dict["coords"]
assert (cfspecs0._dict["data_vars"]["temp"] == cfspecs1._dict["data_vars"]
["temp"])
assert "temp" in cfspecs1["data_vars"]
assert "temperature" in cfspecs1["data_vars"]["temp"]["name"]
def test_cf_cfspecs_coords_get_dim_type():
cfspecs = cf.get_cf_specs().coords
# from attrs
depth = xr.DataArray([1], dims='aa', attrs={'axis': 'z'})
assert cfspecs.get_dim_type(depth) == 'z'
# from CF specs
depth = xr.DataArray([1],
dims='aa',
attrs={'standard_name': 'ocean_layer_depth'})
assert cfspecs.get_dim_type(depth) == 'z'
def test_cf_cfspecs_match_data_var(cf_name, in_name, in_attrs):
lon = xr.DataArray(range(5), dims='lon', name='lon')
temp = xr.DataArray(range(20, 25),
dims='lon',
coords={'lon': lon},
name=in_name,
attrs=in_attrs)
res = cf.get_cf_specs().match_data_var(temp, cf_name)
if cf_name is None:
assert res == 'temp'
else:
assert res is True
def test_cf_cfspecs_coords_get_dim_types():
cfspecs = cf.get_cf_specs().coords
aa = xr.DataArray([0, 1], dims="aa", attrs={"standard_name": "latitude"})
da = xr.DataArray(np.ones((2, 2, 2)),
dims=('foo', 'aa', 'xi'),
coords={'aa': aa})
assert cfspecs.get_dim_types(da) == (None, 'y', 'x')
assert cfspecs.get_dim_types(da, unknown='-') == ("-", 'y', 'x')
assert cfspecs.get_dim_types(da, asdict=True) == {
"foo": None,
"aa": "y",
"xi": "x"
}
def test_cf_cfspecs_coords_get_dims():
lat = xr.DataArray([4, 5], dims='yy', attrs={'units': 'degrees_north'})
depth = xr.DataArray([4, 5], dims='level', attrs={'axis': 'Z'})
da = xr.DataArray(np.ones((2, 2, 2, 2)),
dims=('r', 'level', 'yy', 'xi'),
coords={
'level': depth,
'yy': lat
})
cfspecs = cf.get_cf_specs().coords
dims = cfspecs.get_dims(da, 'xyzt', allow_positional=True)
assert dims == ('xi', 'yy', 'level', 'r')
dims = cfspecs.get_dims(da, 'f', errors="ignore")
assert dims == (None, )
def test_cf_get_cf_specs_registered():
cf_cache = cf._get_cache_()
cf_cache["registered"].clear()
content = """
[register]
name=myname
[data_vars]
[[temp]]
name=mytemp
"""
cf_specs_in = cf.CFSpecs(content)
cf.register_cf_specs(cf_specs_in)
cf_specs_out = cf.get_cf_specs(name='myname')
assert cf_specs_out is cf_specs_in
def test_cf_cfspecs_format_data_var(cf_name, in_name, in_attrs):
lon = xr.DataArray(range(5),
dims='xxx',
name='xxx',
attrs={'standard_name': 'longitude'})
temp = xr.DataArray(range(20, 25),
dims='xxx',
coords={'xxx': lon},
name=in_name,
attrs=in_attrs)
temp = cf.get_cf_specs().format_data_var(temp, cf_name)
assert temp.name == "temp"
assert temp.standard_name == "sea_water_temperature"
assert temp.long_name == "Temperature"
assert temp.units == "degrees_celsius"
assert temp.lon.standard_name == "longitude"
def test_cf_cfspecs_coords_search_from_dim():
lon = xr.DataArray([1, 2], dims='lon')
level = xr.DataArray([1, 2, 3],
dims='aa',
attrs={'standard_name': 'ocean_sigma_coordinate'})
mem = xr.DataArray(range(3), dims='mem')
temp = xr.DataArray(np.zeros((mem.size, level.size, lon.size)),
dims=('mem', 'aa', 'lon'),
coords={
'mem': mem,
'aa': level,
'lon': lon
})
cfspecs = cf.get_cf_specs().coords
# Direct coordinate
assert cfspecs.search_from_dim(temp, 'aa').name == 'aa'
# Depth coordinate because the only one with this dim
depth = xr.DataArray(np.ones((level.size, lon.size)),
dims=('aa', 'lon'),
coords={
'aa': level,
'lon': lon
})
temp.coords['depth'] = depth
assert cfspecs.search_from_dim(temp, 'aa').name == 'depth'
# Cannot get dim_type and we have multiple coords with this dim
del temp.coords['aa']
fake = xr.DataArray(np.ones((level.size, lon.size)),
dims=('aa', 'lon'),
coords={'lon': lon})
temp.coords['fake'] = fake
assert cfspecs.search_from_dim(temp, 'aa') is None
# Can get dim_type back from name
temp = temp.rename(aa='level')
assert cfspecs.search_from_dim(temp, 'level').name == 'depth'
# Nothing identifiable
temp = xr.DataArray([3], dims='banana')
assert cfspecs.search_from_dim(temp, "banana") is None
def test_cf_cfspecs_infer_coords():
ds = xr.Dataset({"temp": ("nx", [1, 2]), "lon": ("nx", [4, 5])})
ds = cf.get_cf_specs().infer_coords(ds)
assert "lon" in ds.coords
def test_cf_get_cfg_specs(cache):
assert isinstance(cf.get_cf_specs(cache=cache), cf.CFSpecs)
def test_cf_get_cfg_specs_var_inherit():
specs = cf.get_cf_specs("sst", "data_vars")
assert specs["standard_name"][0] == "sea_surface_temperature"
assert specs["units"][0] == "degrees_celsius"
def test_cf_get_cfg_specs_coord():
specs = cf.get_cf_specs("lon", "coords")
assert specs["name"][0] == "lon"
assert "longitude" in specs["name"]
new_specs = cf.get_cf_specs("lon")
assert new_specs is specs
def test_cf_cfspecs_load_cfg(cfg, key, name):
cfspecs = cf.get_cf_specs()
cfspecs.load_cfg(cfg)
assert name in cfspecs["data_vars"][key]["name"]
def test_cf_get_cfg_specs_coord_inherit():
specs = cf.get_cf_specs("depth", "coords")
assert specs["name"][0] == "depth"
assert specs["long_name"][0] == "Depth"
def test_cf_cfspecs_format_data_var_coord():
da = xr.DataArray(0, attrs={'standard_name': 'longitude_at_u_location'})
da = cf.get_cf_specs().format_data_var(da)
