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BUG: nan segfault in KDTree, reject non-finite input #18230

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May 21, 2023
Merged

BUG: nan segfault in KDTree, reject non-finite input #18230

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76c6933
BUG: nan segfault in KDTree
tylerjereddy Apr 1, 2023
746d76b
MAINT: PR 18230 revisions
tylerjereddy Apr 4, 2023
a897f5c
MAINT: PR 18230 revisions
tylerjereddy Apr 30, 2023
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3 changes: 3 additions & 0 deletions scipy/spatial/_ckdtree.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -557,6 +557,9 @@ cdef class cKDTree:
if data.ndim != 2:
raise ValueError("data must be 2 dimensions")

if not np.isfinite(data).all():
raise ValueError("data must be finite, check for nan or inf values")

self.data = data
cself.n = data.shape[0]
cself.m = data.shape[1]
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21 changes: 17 additions & 4 deletions scipy/spatial/tests/test_kdtree.py
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Expand Up @@ -1464,7 +1464,20 @@ def test_kdtree_nan():
vals = [1, 5, -10, 7, -4, -16, -6, 6, 3, -11]
n = len(vals)
data = np.concatenate([vals, np.full(n, np.nan)])[:, None]

query_with_nans = KDTree(data).query_pairs(2)
query_without_nans = KDTree(data[:n]).query_pairs(2)
assert query_with_nans == query_without_nans
with pytest.raises(ValueError, match="must be finite"):
KDTree(data)


def test_gh_18223():
rng = np.random.default_rng(12345)
coords = rng.uniform(size=(100, 3), low=0.0, high=0.1)
KDTree(coords, balanced_tree=False, compact_nodes=False)
coords[0, :] = np.nan
with pytest.raises(ValueError, match="must be finite"):
KDTree(coords, balanced_tree=True, compact_nodes=False)
with pytest.raises(ValueError, match="must be finite"):
KDTree(coords, balanced_tree=False, compact_nodes=True)
with pytest.raises(ValueError, match="must be finite"):
KDTree(coords, balanced_tree=True, compact_nodes=True)
with pytest.raises(ValueError, match="must be finite"):
KDTree(coords, balanced_tree=False, compact_nodes=False)