Fix JSON encoding of complex fill values (zarr-developers#2432)

* Fix JSON encoding of complex fill values

We were not replacing NaNs and Infs with the string versions.

* Fix decoding of complex fill values

* try excluding `math.inf`

* Check complex numbers explicitly

* Update src/zarr/core/metadata/v3.py

Author: dcherian

src/zarr/core/metadata/v3.py

@@ -43,6 +43,13 @@
 
 DEFAULT_DTYPE = "float64"
 
+# Keep in sync with _replace_special_floats
+SPECIAL_FLOATS_ENCODED = {
+    "Infinity": np.inf,
+    "-Infinity": -np.inf,
+    "NaN": np.nan,
+}
+
 
 def parse_zarr_format(data: object) -> Literal[3]:
     if data == 3:
@@ -149,7 +156,7 @@ def default(self, o: object) -> Any:
                 if isinstance(out, complex):
                     # python complex types are not JSON serializable, so we use the
                     # serialization defined in the zarr v3 spec
-                    return [out.real, out.imag]
+                    return _replace_special_floats([out.real, out.imag])
                 elif np.isnan(out):
                     return "NaN"
                 elif np.isinf(out):
@@ -447,8 +454,11 @@ def parse_fill_value(
     if isinstance(fill_value, Sequence) and not isinstance(fill_value, str):
         if data_type in (DataType.complex64, DataType.complex128):
             if len(fill_value) == 2:
+                decoded_fill_value = tuple(
+                    SPECIAL_FLOATS_ENCODED.get(value, value) for value in fill_value
+                )
                 # complex datatypes serialize to JSON arrays with two elements
-                return np_dtype.type(complex(*fill_value))
+                return np_dtype.type(complex(*decoded_fill_value))
             else:
                 msg = (
                     f"Got an invalid fill value for complex data type {data_type.value}."
@@ -475,12 +485,20 @@ def parse_fill_value(
         pass
     elif fill_value in ["Infinity", "-Infinity"] and not np.isfinite(casted_value):
         pass
-    elif np_dtype.kind in "cf":
+    elif np_dtype.kind == "f":
         # float comparison is not exact, especially when dtype <float64
-        # so we us np.isclose for this comparison.
+        # so we use np.isclose for this comparison.
         # this also allows us to compare nan fill_values
         if not np.isclose(fill_value, casted_value, equal_nan=True):
             raise ValueError(f"fill value {fill_value!r} is not valid for dtype {data_type}")
+    elif np_dtype.kind == "c":
+        # confusingly np.isclose(np.inf, np.inf + 0j) is False on numpy<2, so compare real and imag parts
+        # explicitly.
+        if not (
+            np.isclose(np.real(fill_value), np.real(casted_value), equal_nan=True)
+            and np.isclose(np.imag(fill_value), np.imag(casted_value), equal_nan=True)
+        ):
+            raise ValueError(f"fill value {fill_value!r} is not valid for dtype {data_type}")
     else:
         if fill_value != casted_value:
             raise ValueError(f"fill value {fill_value!r} is not valid for dtype {data_type}")

tests/test_array.py

@@ -1,3 +1,5 @@
+import json
+import math
 import pickle
 from itertools import accumulate
 from typing import Any, Literal
@@ -9,6 +11,7 @@
 from zarr import Array, AsyncArray, Group
 from zarr.codecs import BytesCodec, VLenBytesCodec
 from zarr.core.array import chunks_initialized
+from zarr.core.buffer import default_buffer_prototype
 from zarr.core.buffer.cpu import NDBuffer
 from zarr.core.common import JSON, MemoryOrder, ZarrFormat
 from zarr.core.group import AsyncGroup
@@ -624,3 +627,23 @@ def test_array_create_order(
         assert vals.flags.f_contiguous
     else:
         raise AssertionError
+
+
+@pytest.mark.parametrize(
+    ("fill_value", "expected"),
+    [
+        (np.nan * 1j, ["NaN", "NaN"]),
+        (np.nan, ["NaN", 0.0]),
+        (np.inf, ["Infinity", 0.0]),
+        (np.inf * 1j, ["NaN", "Infinity"]),
+        (-np.inf, ["-Infinity", 0.0]),
+        (math.inf, ["Infinity", 0.0]),
+    ],
+)
+async def test_special_complex_fill_values_roundtrip(fill_value: Any, expected: list[Any]) -> None:
+    store = MemoryStore({}, mode="w")
+    Array.create(store=store, shape=(1,), dtype=np.complex64, fill_value=fill_value)
+    content = await store.get("zarr.json", prototype=default_buffer_prototype())
+    assert content is not None
+    actual = json.loads(content.to_bytes())
+    assert actual["fill_value"] == expected