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Faster union find #415

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Faster union find #415

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1c4ad95
Use faster, direct array access in UnionFind.fast_find()
markopy Feb 8, 2020
24ee0c3
Fix heap corruption in union find
markopy Feb 10, 2020
682ad87
Fix issue #321
markopy Oct 3, 2020
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17 changes: 9 additions & 8 deletions hdbscan/_hdbscan_linkage.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -178,19 +178,20 @@ cdef class UnionFind (object):
self.size[self.next_label] = self.size[m] + self.size[n]
self.parent[m] = self.next_label
self.parent[n] = self.next_label
self.size[self.next_label] = self.size[m] + self.size[n]
self.next_label += 1

return

cdef np.intp_t fast_find(self, np.intp_t n):
cdef np.intp_t p
cdef np.intp_t p, tmp
p = n
while self.parent_arr[n] != -1:
n = self.parent_arr[n]
# label up to the root
while self.parent_arr[p] != n:
p, self.parent_arr[p] = self.parent_arr[p], n
while self.parent[n] != -1:
n = self.parent[n]
# label up to the root if this is not the root already
if p != n:
while self.parent[p] != n:
tmp = self.parent[p]
self.parent[p] = n
p = tmp
return n


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