disallow inf and nan values

map them to None in data.range

Author: FynnBe

bioimageio/spec/_internal/node.py

@@ -27,15 +27,16 @@ def _node_title_generator(node: Type[Node]) -> str:
 
 class Node(
     pydantic.BaseModel,
+    allow_inf_nan=False,
     extra="forbid",
     frozen=False,
+    model_title_generator=_node_title_generator,
     populate_by_name=True,
     revalidate_instances="never",
+    use_attribute_docstrings=True,
     validate_assignment=True,
     validate_default=False,
     validate_return=True,  # TODO: check if False here would bring a speedup and can still be safe
-    use_attribute_docstrings=True,
-    model_title_generator=_node_title_generator,
 ):
     """"""  # empty docstring to remove all pydantic docstrings from the pdoc spec docs
 

bioimageio/spec/model/v0_5.py

@@ -76,6 +76,7 @@
 )
 from .._internal.io_utils import load_array
 from .._internal.node_converter import Converter
+from .._internal.type_guards import is_dict, is_sequence
 from .._internal.types import (
     AbsoluteTolerance,
     LowerCaseIdentifier,
@@ -878,6 +879,27 @@ class IntervalOrRatioDataDescr(Node):
     offset: Optional[float] = None
     """Offset for data on a ratio scale."""
 
+    @model_validator(mode="before")
+    def _replace_inf(cls, data: Any):
+        if is_dict(data):
+            if "range" in data and is_sequence(data["range"]):
+                forbidden = (
+                    "inf",
+                    "-inf",
+                    ".inf",
+                    "-.inf",
+                    float("inf"),
+                    float("-inf"),
+                )
+                if any(v in forbidden for v in data["range"]):
+                    issue_warning("replaced 'inf' value", value=data["range"])
+
+                data["range"] = tuple(
+                    (None if v in forbidden else v) for v in data["range"]
+                )
+
+        return data
+
 
 TensorDataDescr = Union[NominalOrOrdinalDataDescr, IntervalOrRatioDataDescr]
 

tests/test_model/test_v0_5.py

@@ -129,7 +129,7 @@ def test_tensor_base_invalid(kwargs: Dict[str, Any]):
         {
             "id": "input_1",
             "description": "Input 1",
-            "data": {"type": "float32"},
+            "data": {"type": "float32", "range": ["-inf", float("inf")]},
             "axes": [
                 dict(type="space", id="x", size=10),
                 dict(type="space", id="y", size=11),
@@ -146,7 +146,7 @@ def test_tensor_base_invalid(kwargs: Dict[str, Any]):
                 }
             ],
             "test_tensor": {"source": UNET2D_ROOT / "test_input.npy"},
-        },
+        }
     ],
 )
 def test_input_tensor(kwargs: Dict[str, Any]):