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avoid use of deprecated numpy.bool alias #1485

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Jul 1, 2023
Merged

avoid use of deprecated numpy.bool alias #1485

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1 change: 1 addition & 0 deletions CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ Next Version
* remove unusable C-linkage with std::vector (#1468)
* fixed compatibility issue with Python 3.10 in endf.py (#1472)
* avoid use of deprecated numpy.int alias (#1479)
* avoid use of deprecated numpy.bool alias (#1485)

v0.7.7
======
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23 changes: 12 additions & 11 deletions pyne/mesh.py
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Expand Up @@ -67,7 +67,8 @@
),
}

_INTEGRAL_TYPES = (int, np.integer, np.bool_)
_INTEGRAL_TYPES = (int, np.integer, bool, np.bool_)
_BOOLEAN_TYPES = (bool, np.bool_)
_SEQUENCE_TYPES = (Sequence, np.ndarray)


Expand Down Expand Up @@ -155,7 +156,7 @@ def __getitem__(self, key):
return getattr(mats[int(key)], name)
elif isinstance(key, slice):
return np.array([getattr(mats[i], name) for i in range(*key.indices(size))])
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
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I believe that setting key.dtype == bool may be more efficient in this case. This comparison checks if the data type (dtype) of key is exactly bool. On the other hand, using key.dtype in (bool, np.bool_) checks if the dtype is either bool or np.bool_. This approach involves iterating over the elements of the tuple to find a match, which could potentially be slower.

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You are right that my proposed change would be technically slower, involving 2 equality checks instead of one, but note that

  • we're talking 10s of nano-seconds here (hopefully this doesn't matter)
  • because bool is the first element in _BOOLEAN_TYPES, the second check is only performed in case key.dtype != bool
  • if performance was important here (again, I'm hoping it's not), key.dtype is bool would be the way to go (identity check is always cheaper than equality check, although here it's 20ns VS 24ns on my machine)

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Considering the potential impact on simulation time when the code is called multiple times (considering large data), it becomes more important to optimize the comparison. In that case, using key.dtype == bool would be more efficient compared to key.dtype in (bool, np.bool_) due to the reduced number of operations involved. However, it's still advisable to measure the actual performance gain before making a decision, as the difference might still be minimal.

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Does the proposed approach ensure some kind of backward compatibility? Are there configurations that may use one vs the other? Or is bool always available so that any invocation will always work if we restrict to bool? Put another way, what's the benefit to this proposed approach?

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My approach is supposed to be 100% backward compatible. Additionally, it survives np.bool_ (current implementation doesn't)

if len(key) != size:
raise KeyError("boolean mask must match the length of the mesh.")
return np.array([getattr(mats[i], name) for i, b in enumerate(key) if b])
Expand All @@ -182,7 +183,7 @@ def __setitem__(self, key, value):
else:
for i in idx:
setattr(mats[i], name, value)
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != size:
raise KeyError("boolean mask must match " "the length of the mesh.")
idx = np.where(key)[0]
Expand Down Expand Up @@ -234,7 +235,7 @@ def __getitem__(self, key):
return np.array(
[getattr(mats[i], name)() for i in range(*key.indices(size))]
)
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != size:
raise KeyError("boolean mask must match the " "length of the mesh.")
return np.array([getattr(mats[i], name)() for i, b in enumerate(key) if b])
Expand Down Expand Up @@ -278,7 +279,7 @@ def __getitem__(self, key):
return mats[key].metadata[name]
elif isinstance(key, slice):
return [mats[i].metadata[name] for i in range(*key.indices(size))]
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != size:
raise KeyError("boolean mask must match the length " "of the mesh.")
return [mats[i].metadata[name] for i, b in enumerate(key) if b]
Expand All @@ -305,7 +306,7 @@ def __setitem__(self, key, value):
else:
for i in idx:
mats[i].metadata[name] = value
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != size:
raise KeyError("boolean mask must match the length " "of the mesh.")
idx = np.where(key)[0]
Expand Down Expand Up @@ -338,7 +339,7 @@ def __delitem__(self, key):
elif isinstance(key, slice):
for i in range(*key.indices(size)):
del mats[i].metadata[name]
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != size:
raise KeyError("boolean mask must match the length " "of the mesh.")
for i, b in enumerate(key):
Expand Down Expand Up @@ -495,7 +496,7 @@ def __getitem__(self, key):
ents = list(miter)[key]
data = self.mesh.mesh.tag_get_data(self.tag, ents, flat=flat)
return data
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != size:
raise KeyError("boolean mask must match the length " "of the mesh.")
return self.mesh.mesh.tag_get_data(
Expand Down Expand Up @@ -542,7 +543,7 @@ def __setitem__(self, key, value):
v.shape = (len(key),)
v[...] = value
self.mesh.mesh.tag_set_data(mtag, key, v)
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != msize:
raise KeyError("boolean mask must match the length " "of the mesh.")
key = [ve for b, ve in zip(key, miter) if b]
Expand Down Expand Up @@ -584,7 +585,7 @@ def __delitem__(self, key):
self.mesh.mesh.tag_delete_data(mtag, i_ve[1])
elif isinstance(key, slice):
self.mesh.mesh.tag_delete_data(mtag, list(miter)[key])
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != size:
raise KeyError("boolean mask must match the " "length of the mesh.")
self.mesh.mesh.tag_delete_data(mtag, [ve for b, ve in zip(key, miter) if b])
Expand Down Expand Up @@ -754,7 +755,7 @@ def __getitem__(self, key):
return f(m, key)
elif isinstance(key, slice):
return [f(m, i) for i in range(*key.indices(size))]
elif isinstance(key, np.ndarray) and key.dtype == np.bool:
elif isinstance(key, np.ndarray) and key.dtype in _BOOLEAN_TYPES:
if len(key) != size:
raise KeyError("boolean mask must match the length " "of the mesh.")
return [f(m, i) for i, b in enumerate(key) if b]
Expand Down