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ENH: Add default fill values for decode_cf #5680

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ENH: Add default fill values for decode_cf #5680

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4ebfb4d
Add f8 default fill value and test for it.
gcaria Aug 6, 2021
26f1b32
Add built-in dictionary for dtype to default fill value
gcaria Aug 8, 2021
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23 changes: 22 additions & 1 deletion xarray/coding/variables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,20 @@
from ..core.pycompat import is_duck_dask_array
from ..core.variable import Variable

NP_TO_NC_TYPE = {
"S1": "\x00",
"i1": -127,
"u1": 255,
"i2": -32767,
"u2": 65535,
"i4": -2147483647,
"u4": 4294967295,
"i8": -9223372036854775806,
"u8": 18446744073709551614,
"f4": 9.969209968386869e36,
"f8": 9.969209968386869e36,
}


class SerializationWarning(RuntimeWarning):
"""Warnings about encoding/decoding issues in serialization."""
Expand Down Expand Up @@ -183,6 +197,14 @@ def decode(self, variable, name=None):
pop_to(attrs, encoding, attr, name=name)
for attr in ("missing_value", "_FillValue")
]
try:
default_fillvalue = NP_TO_NC_TYPE[np.dtype(variable.dtype).str[1:]]
raw_fill_values.append(default_fillvalue)
except KeyError:
warnings.warn(
f"A default fill value for dtype {variable.dtype} could not be found"
)

if raw_fill_values:
encoded_fill_values = {
fv
Expand All @@ -209,7 +231,6 @@ def decode(self, variable, name=None):
dtype=dtype,
)
data = lazy_elemwise_func(data, transform, dtype)

return Variable(dims, data, attrs, encoding)


Expand Down
7 changes: 7 additions & 0 deletions xarray/tests/test_conventions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -232,6 +232,13 @@ def test_decode_cf_with_multiple_missing_values(self):
assert_identical(expected, actual)
assert "has multiple fill" in str(w[0].message)

def test_decode_standard_missing_value(self):

original = Variable(["t"], [coding.variables.NP_TO_NC_TYPE["f8"], 1, 2], {})
expected = Variable(["t"], [np.nan, 1, 2], {})
actual = conventions.decode_cf_variable("t", original)
assert_identical(expected, actual)

def test_decode_cf_with_drop_variables(self):
original = Dataset(
{
Expand Down