handle NaN, Infinity, -Infinity

lindi/LindiH5ZarrStore/_h5_attr_to_zarr_attr.py

@@ -14,6 +14,14 @@ def _h5_attr_to_zarr_attr(attr: Any, *, label: str = '', h5f: h5py.File):
 
     Otherwise, raise NotImplementedError
     """
+
+    # first disallow special strings
+    special_strings = ['NaN', 'Infinity', '-Infinity']
+    if isinstance(attr, str) and attr in special_strings:
+        raise ValueError(f"Special string {attr} not allowed in attribute value at {label}")
+    if isinstance(attr, bytes) and attr in [x.encode('utf-8') for x in special_strings]:
+        raise ValueError(f"Special string {attr} not allowed in attribute value at {label}")
+
     if attr is None:
         return None
     elif isinstance(attr, bytes):
@@ -26,8 +34,8 @@ def _h5_attr_to_zarr_attr(attr: Any, *, label: str = '', h5f: h5py.File):
         return float(attr)
     elif np.issubdtype(type(attr), np.bool_):
         return bool(attr)
-    elif np.issubdtype(type(attr), np.bytes_):
-        return attr.decode('utf-8')
+    elif type(attr) is np.bytes_:
+        return attr.tobytes().decode('utf-8')
     elif isinstance(attr, h5py.Reference):
         return _h5_ref_to_zarr_attr(attr, label=label + '._REFERENCE', h5f=h5f)
     elif isinstance(attr, list):

lindi/LindiH5pyFile/LindiH5pyAttributes.py

@@ -44,18 +44,11 @@ def __getitem__(self, key):
             if isinstance(val, dict) and "_REFERENCE" in val:
                 return LindiH5pyReference(val["_REFERENCE"])
 
-            # Convert special values
-            # @rly: doing this saves a lot of headache when loading the nwb file
-            # but then how can we represent strings that should not be converted?
-            elif val == 'NaN':
-                return float('nan')
-            elif val == 'Infinity':
-                return float('inf')
-            elif val == '-Infinity':
-                return float('-inf')
-
-            else:
-                return val
+            # Convert special float values to actual floats (NaN, Inf, -Inf)
+            # Note that string versions of these values are not supported
+            val = _decode_nan_inf_ninf_in_attr_val(val)
+
+            return val
         else:
             raise ValueError(f"Unknown attrs_type: {self._attrs_type}")
 
@@ -90,3 +83,18 @@ def __repr__(self):
 
     def __str__(self):
         return str(self._attrs)
+
+
+def _decode_nan_inf_ninf_in_attr_val(val):
+    if isinstance(val, list):
+        return [_decode_nan_inf_ninf_in_attr_val(v) for v in val]
+    elif isinstance(val, dict):
+        return {k: _decode_nan_inf_ninf_in_attr_val(v) for k, v in val.items()}
+    elif val == 'NaN':
+        return float('nan')
+    elif val == 'Infinity':
+        return float('inf')
+    elif val == '-Infinity':
+        return float('-inf')
+    else:
+        return val