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ENH Remember predecessor in OPTICS #12135

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Oct 7, 2018
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ENH Remember predecessor in OPTICS #12135

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16 changes: 14 additions & 2 deletions sklearn/cluster/optics_.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

Authors: Shane Grigsby <[email protected]>
Amy X. Zhang <[email protected]>
Erich Schubert <[email protected]>
License: BSD 3 clause
"""

Expand Down Expand Up @@ -317,6 +318,10 @@ class OPTICS(BaseEstimator, ClusterMixin):
Distance at which each sample becomes a core point.
Points which will never be core have a distance of inf.

predecessor_ : array, shape (n_samples,)
Point that a sample was reached from.
Seed points have a predecessor of -1.

See also
--------

Expand All @@ -329,6 +334,10 @@ class OPTICS(BaseEstimator, ClusterMixin):
Ankerst, Mihael, Markus M. Breunig, Hans-Peter Kriegel, and Jörg Sander.
"OPTICS: ordering points to identify the clustering structure." ACM SIGMOD
Record 28, no. 2 (1999): 49-60.

Schubert, Erich, Michael Gertz.
"Improving the Cluster Structure Extracted from OPTICS Plots." Proc. of
the Conference "Lernen, Wissen, Daten, Analysen" (LWDA) (2018): 318-329.
"""

def __init__(self, min_samples=5, max_eps=np.inf, metric='euclidean',
Expand Down Expand Up @@ -396,6 +405,8 @@ def fit(self, X, y=None):
# Start all points as 'unprocessed' ##
self.reachability_ = np.empty(n_samples)
self.reachability_.fill(np.inf)
self.predecessor_ = np.empty(n_samples, dtype=int)
self.predecessor_.fill(-1)
# Start all points as noise ##
self.labels_ = np.full(n_samples, -1, dtype=int)

Expand Down Expand Up @@ -499,8 +510,9 @@ def _set_reach_dist(self, point_index, processed, X, nbrs):
self.metric, n_jobs=None).ravel()

rdists = np.maximum(dists, self.core_distances_[point_index])
new_reach = np.minimum(np.take(self.reachability_, unproc), rdists)
self.reachability_[unproc] = new_reach
improved = np.where(rdists < np.take(self.reachability_, unproc))
self.reachability_[unproc[improved]] = rdists[improved]
self.predecessor_[unproc[improved]] = point_index

# Define return order based on reachability distance
return (unproc[quick_scan(np.take(self.reachability_, unproc),
Expand Down