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__init__.py
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__init__.py
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import numpy as np
from sklearn.base import BaseEstimator, ClusterMixin, TransformerMixin
class ConstrainedKMeans(BaseEstimator, ClusterMixin, TransformerMixin):
def __init__(self, n_clusters=8, n_iter=300):
self.n_clusters = n_clusters
self.n_iter = n_iter
def fit(self, X, y=None, must_link=[], cannot_link=[]):
assert type(X).__name__ == 'ndarray', "X must be a ndarray"
assert X.shape[0] >= self.n_clusters, "X can't have less objects than n_clusters"
# Initialize cluster centers
n_samples = X.shape[0]
samples_idx = np.random.choice(range(n_samples), self.n_clusters, replace=False)
centroids = np.array(map(lambda i: X[i], samples_idx))
clusters = [[] for _ in range(self.n_clusters)]
labels = [0 for _ in X]
inertia = 0
for _ in range(self.n_iter):
for i in range(self.n_clusters):
clusters[i] = []
inertia = 0
for i, d in enumerate(X):
rank = _rank_centroids(d, centroids)
violate_constraint = True
for idx in rank:
other_clusters = [clusters[j] for j in range(self.n_clusters) if j != idx]
cluster = clusters[idx]
violate_constraint = _violate_constraints(d, cluster, other_clusters, must_link, cannot_link)
if not violate_constraint:
clusters[idx].append(d)
labels[i] = idx
inertia += _dist(centroids[idx], d)
break
if violate_constraint:
# raise IOError("Unable to cluster")
pass
for idx in range(self.n_clusters):
centroids[idx] = np.array(clusters[idx]).mean(axis=0)
self.cluster_centers_ = centroids
self.labels_ = labels
self.inertia_ = inertia
return self
def predict(self, X):
def predict_single(d):
return _rank_centroids(d, self.cluster_centers_)[0]
return map(predict_single, X)
def transform(self, X):
def transform_single(d):
return np.array([_dist(d, c) for c in self.cluster_centers_])
return map(transform_single, X)
def _dist(a, b=0):
d = a - b
return np.sqrt(d.dot(d))
def _rank_centroids(instance, centroids):
"""
Return a ascendant list of nearest clusters of certain instance
:param instance: Instance to compare
:param centroids: Centroids
:return: the clusters array sorted by distance of instance
"""
deltas = centroids - instance
rank = np.asarray([_dist(d) for d in deltas]).argsort()
return rank
def _violate_constraints(instance, cluster, other_clusters, must_link, cannot_link):
def get_other_instance(instance, link):
if (link[0] == instance).all():
return link[1]
elif (link[1] == instance).all():
return link[0]
for link in must_link:
other_instance = get_other_instance(instance, link)
if other_instance is not None:
for c in other_clusters:
if _contains(other_instance, c):
return True
for link in cannot_link:
other_instance = get_other_instance(instance, link)
if other_instance is not None and _contains(other_instance, cluster):
return True
return False
def _contains(instance, _list):
"""Returns True if the ndarray list contains the specified instance"""
if not _list:
return False
return bool([y for y in (instance == _list) if y.all()])