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DOC Update _hdbscan/_linkage.pyx with new inline comments #25656

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DOC Update _hdbscan/_linkage.pyx with new inline comments #25656

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15 changes: 13 additions & 2 deletions sklearn/cluster/_hdbscan/_linkage.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ cpdef cnp.ndarray[MST_edge_t, ndim=1, mode='c'] mst_from_mutual_reachability(
-------
mst : ndarray of shape (n_samples - 1,), dtype=MST_edge_dtype
The MST representation of the mutual-reahability graph. The MST is
represented as a collecteion of edges.
represented as a collection of edges.
"""
cdef:
# Note: we utilize ndarray's over memory-views to make use of numpy
Expand All @@ -59,16 +59,28 @@ cpdef cnp.ndarray[MST_edge_t, ndim=1, mode='c'] mst_from_mutual_reachability(
mst = np.empty(n_samples - 1, dtype=MST_edge_dtype)
current_labels = np.arange(n_samples, dtype=np.int64)
current_node = 0
# Contains the minimum reachability of points to the built tree. This is
# iteratively updated with each node we add.
min_reachability = np.full(n_samples, fill_value=np.infty, dtype=np.float64)
for i in range(0, n_samples - 1):
# Sub-select nodes not-yet in the tree
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Can this be communicate with a better variable name for label_filter?

label_filter = current_labels != current_node
current_labels = current_labels[label_filter]

# Compute the nodes' current min-reachability scores
left = min_reachability[label_filter]
# Compute the nodes' mutual-reachability to current node
right = mutual_reachability[current_node][current_labels]
Comment on lines +70 to 73
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left and right are not computing anything. Is there a better name for left and right such that the comment is not required?

# Update min-reachability, given the new mutual-reachability of all
# nodes from the current node.
Comment on lines +74 to +75
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Also would a better name for left and right remove the need for this comment?

min_reachability = np.minimum(left, right)

# Find node with minimum-reachabiltiy
# Note we perform index-remapping via `current_labels` since it is a
# sub-selection and hence not 1-1
new_node_index = np.argmin(min_reachability)
new_node = current_labels[new_node_index]

mst[i].current_node = current_node
mst[i].next_node = new_node
mst[i].distance = min_reachability[new_node_index]
Expand Down Expand Up @@ -228,7 +240,6 @@ cpdef cnp.ndarray[cnp.float64_t, ndim=2, mode='c'] make_single_linkage(const MST

current_node_cluster = U.fast_find(current_node)
next_node_cluster = U.fast_find(next_node)

# TODO: Update this to an array of structs (AoS).
# Should be done simultaneously in _tree.pyx to ensure compatability.
single_linkage[i][0] = <cnp.float64_t> current_node_cluster
Expand Down