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Harmonize FillValue and missing_value during encoding and decoding steps #3502

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merged 7 commits into from
Nov 14, 2019
Merged

Harmonize FillValue and missing_value during encoding and decoding steps #3502

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b61deeb
Replace `equivalent()` with `allclose_or_equiv()`
andersy005 Nov 9, 2019
0740853
Ensure _FillValue & missing_value are cast to same dtype as data's
andersy005 Nov 9, 2019
9b5108d
Merge branch 'master' of github.com:pydata/xarray into fix-fill-missi…
andersy005 Nov 12, 2019
404bd75
Use Numpy scalar during type casting
andersy005 Nov 12, 2019
d3e9562
Update ValueError message
andersy005 Nov 12, 2019
3aa18f0
Formatting only
andersy005 Nov 12, 2019
43b84d4
Update whats-new.rst
andersy005 Nov 12, 2019
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13 changes: 11 additions & 2 deletions xarray/coding/variables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@

from ..core import dtypes, duck_array_ops, indexing
from ..core.pycompat import dask_array_type
from ..core.utils import equivalent
from ..core.variable import Variable


Expand Down Expand Up @@ -152,18 +151,28 @@ def encode(self, variable, name=None):
fv = encoding.get("_FillValue")
mv = encoding.get("missing_value")

if fv is not None and mv is not None and not equivalent(fv, mv):
if (
fv is not None
and mv is not None
and not duck_array_ops.allclose_or_equiv(fv, mv)
):
raise ValueError(
"Variable {!r} has multiple fill values {}. "
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"Cannot encode data. ".format(name, [fv, mv])
)

if fv is not None:
encoding["_FillValue"] = np.asarray(encoding["_FillValue"]).astype(
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data.dtype
)
fill_value = pop_to(encoding, attrs, "_FillValue", name=name)
if not pd.isnull(fill_value):
data = duck_array_ops.fillna(data, fill_value)

if mv is not None:
encoding["missing_value"] = np.asarray(encoding["missing_value"]).astype(
data.dtype
)
fill_value = pop_to(encoding, attrs, "missing_value", name=name)
if not pd.isnull(fill_value) and fv is None:
data = duck_array_ops.fillna(data, fill_value)
Expand Down
13 changes: 13 additions & 0 deletions xarray/tests/test_coding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,19 @@ def test_CFMaskCoder_decode():
assert_identical(expected, encoded)


def test_CFMaskCoder_encode_missing_fill_values_conflict():
original = xr.Variable(
("x",),
[0.0, -1.0, 1.0],
encoding={"_FillValue": np.float32(1e20), "missing_value": np.float64(1e20)},
)
coder = variables.CFMaskCoder()
encoded = coder.encode(original)

assert encoded.dtype == encoded.attrs["missing_value"].dtype
assert encoded.dtype == encoded.attrs["_FillValue"].dtype


def test_CFMaskCoder_missing_value():
expected = xr.DataArray(
np.array([[26915, 27755, -9999, 27705], [25595, -9999, 28315, -9999]]),
Expand Down