nltk 3.2__zip → 3.3__zip

{nltk-3.2 → nltk-3.3}/nltk/cluster/gaac.py

@@ -1,168 +1,168 @@
-# Natural Language Toolkit: Group Average Agglomerative Clusterer
-#
-# Copyright (C) 2001-2015 NLTK Project
-# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
-# URL: <http://nltk.org/>
-# For license information, see LICENSE.TXT
-from __future__ import print_function, unicode_literals
-
-try:
-    import numpy
-except ImportError:
-    pass
-
-from nltk.cluster.util import VectorSpaceClusterer, Dendrogram, cosine_distance
-from nltk.compat import python_2_unicode_compatible
-
-@python_2_unicode_compatible
-class GAAClusterer(VectorSpaceClusterer):
-    """
-    The Group Average Agglomerative starts with each of the N vectors as singleton
-    clusters. It then iteratively merges pairs of clusters which have the
-    closest centroids.  This continues until there is only one cluster. The
-    order of merges gives rise to a dendrogram: a tree with the earlier merges
-    lower than later merges. The membership of a given number of clusters c, 1
-    <= c <= N, can be found by cutting the dendrogram at depth c.
-
-    This clusterer uses the cosine similarity metric only, which allows for
-    efficient speed-up in the clustering process.
-    """
-
-    def __init__(self, num_clusters=1, normalise=True, svd_dimensions=None):
-        VectorSpaceClusterer.__init__(self, normalise, svd_dimensions)
-        self._num_clusters = num_clusters
-        self._dendrogram = None
-        self._groups_values = None
-
-    def cluster(self, vectors, assign_clusters=False, trace=False):
-        # stores the merge order
-        self._dendrogram = Dendrogram(
-            [numpy.array(vector, numpy.float64) for vector in vectors])
-        return VectorSpaceClusterer.cluster(self, vectors, assign_clusters, trace)
-
-    def cluster_vectorspace(self, vectors, trace=False):
-        # variables describing the initial situation
-        N = len(vectors)
-        cluster_len = [1]*N
-        cluster_count = N
-        index_map = numpy.arange(N)
-
-        # construct the similarity matrix
-        dims = (N, N)
-        dist = numpy.ones(dims, dtype=numpy.float)*numpy.inf
-        for i in range(N):
-            for j in range(i+1, N):
-                dist[i, j] = cosine_distance(vectors[i], vectors[j])
-
-        while cluster_count > max(self._num_clusters, 1):
-            i, j = numpy.unravel_index(dist.argmin(), dims)
-            if trace:
-                print("merging %d and %d" % (i, j))
-
-            # update similarities for merging i and j
-            self._merge_similarities(dist, cluster_len, i, j)
-
-            # remove j
-            dist[:, j] = numpy.inf
-            dist[j, :] = numpy.inf
-
-            # merge the clusters
-            cluster_len[i] = cluster_len[i]+cluster_len[j]
-            self._dendrogram.merge(index_map[i], index_map[j])
-            cluster_count -= 1
-
-            # update the index map to reflect the indexes if we
-            # had removed j
-            index_map[j+1:] -= 1
-            index_map[j] = N
-
-        self.update_clusters(self._num_clusters)
-
-    def _merge_similarities(self, dist, cluster_len, i, j):
-        # the new cluster i merged from i and j adopts the average of
-        # i and j's similarity to each other cluster, weighted by the
-        # number of points in the clusters i and j
-        i_weight = cluster_len[i]
-        j_weight = cluster_len[j]
-        weight_sum = i_weight+j_weight
-
-        # update for x<i
-        dist[:i, i] = dist[:i, i]*i_weight + dist[:i, j]*j_weight
-        dist[:i, i] /= weight_sum
-        # update for i<x<j
-        dist[i, i+1:j] = dist[i, i+1:j]*i_weight + dist[i+1:j, j]*j_weight
-        # update for i<j<x
-        dist[i, j+1:] = dist[i, j+1:]*i_weight + dist[j, j+1:]*j_weight
-        dist[i, i+1:] /= weight_sum
-
-    def update_clusters(self, num_clusters):
-        clusters = self._dendrogram.groups(num_clusters)
-        self._centroids = []
-        for cluster in clusters:
-            assert len(cluster) > 0
-            if self._should_normalise:
-                centroid = self._normalise(cluster[0])
-            else:
-                centroid = numpy.array(cluster[0])
-            for vector in cluster[1:]:
-                if self._should_normalise:
-                    centroid += self._normalise(vector)
-                else:
-                    centroid += vector
-            centroid /= float(len(cluster))
-            self._centroids.append(centroid)
-        self._num_clusters = len(self._centroids)
-
-    def classify_vectorspace(self, vector):
-        best = None
-        for i in range(self._num_clusters):
-            centroid = self._centroids[i]
-            dist = cosine_distance(vector, centroid)
-            if not best or dist < best[0]:
-                best = (dist, i)
-        return best[1]
-
-    def dendrogram(self):
-        """
-        :return: The dendrogram representing the current clustering
-        :rtype:  Dendrogram
-        """
-        return self._dendrogram
-
-    def num_clusters(self):
-        return self._num_clusters
-
-    def __repr__(self):
-        return '<GroupAverageAgglomerative Clusterer n=%d>' % self._num_clusters
-
-def demo():
-    """
-    Non-interactive demonstration of the clusterers with simple 2-D data.
-    """
-
-    from nltk.cluster import GAAClusterer
-
-    # use a set of tokens with 2D indices
-    vectors = [numpy.array(f) for f in [[3, 3], [1, 2], [4, 2], [4, 0], [2, 3], [3, 1]]]
-
-    # test the GAAC clusterer with 4 clusters
-    clusterer = GAAClusterer(4)
-    clusters = clusterer.cluster(vectors, True)
-
-    print('Clusterer:', clusterer)
-    print('Clustered:', vectors)
-    print('As:', clusters)
-    print()
-
-    # show the dendrogram
-    clusterer.dendrogram().show()
-
-    # classify a new vector
-    vector = numpy.array([3, 3])
-    print('classify(%s):' % vector, end=' ')
-    print(clusterer.classify(vector))
-    print()
-
-
-if __name__ == '__main__':
-    demo()
+# Natural Language Toolkit: Group Average Agglomerative Clusterer
+#
+# Copyright (C) 2001-2018 NLTK Project
+# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
+# URL: <http://nltk.org/>
+# For license information, see LICENSE.TXT
+from __future__ import print_function, unicode_literals, division
+
+try:
+    import numpy
+except ImportError:
+    pass
+
+from nltk.cluster.util import VectorSpaceClusterer, Dendrogram, cosine_distance
+from nltk.compat import python_2_unicode_compatible
+
+@python_2_unicode_compatible
+class GAAClusterer(VectorSpaceClusterer):
+    """
+    The Group Average Agglomerative starts with each of the N vectors as singleton
+    clusters. It then iteratively merges pairs of clusters which have the
+    closest centroids.  This continues until there is only one cluster. The
+    order of merges gives rise to a dendrogram: a tree with the earlier merges
+    lower than later merges. The membership of a given number of clusters c, 1
+    <= c <= N, can be found by cutting the dendrogram at depth c.
+
+    This clusterer uses the cosine similarity metric only, which allows for
+    efficient speed-up in the clustering process.
+    """
+
+    def __init__(self, num_clusters=1, normalise=True, svd_dimensions=None):
+        VectorSpaceClusterer.__init__(self, normalise, svd_dimensions)
+        self._num_clusters = num_clusters
+        self._dendrogram = None
+        self._groups_values = None
+
+    def cluster(self, vectors, assign_clusters=False, trace=False):
+        # stores the merge order
+        self._dendrogram = Dendrogram(
+            [numpy.array(vector, numpy.float64) for vector in vectors])
+        return VectorSpaceClusterer.cluster(self, vectors, assign_clusters, trace)
+
+    def cluster_vectorspace(self, vectors, trace=False):
+        # variables describing the initial situation
+        N = len(vectors)
+        cluster_len = [1]*N
+        cluster_count = N
+        index_map = numpy.arange(N)
+
+        # construct the similarity matrix
+        dims = (N, N)
+        dist = numpy.ones(dims, dtype=numpy.float)*numpy.inf
+        for i in range(N):
+            for j in range(i+1, N):
+                dist[i, j] = cosine_distance(vectors[i], vectors[j])
+
+        while cluster_count > max(self._num_clusters, 1):
+            i, j = numpy.unravel_index(dist.argmin(), dims)
+            if trace:
+                print("merging %d and %d" % (i, j))
+
+            # update similarities for merging i and j
+            self._merge_similarities(dist, cluster_len, i, j)
+
+            # remove j
+            dist[:, j] = numpy.inf
+            dist[j, :] = numpy.inf
+
+            # merge the clusters
+            cluster_len[i] = cluster_len[i]+cluster_len[j]
+            self._dendrogram.merge(index_map[i], index_map[j])
+            cluster_count -= 1
+
+            # update the index map to reflect the indexes if we
+            # had removed j
+            index_map[j+1:] -= 1
+            index_map[j] = N
+
+        self.update_clusters(self._num_clusters)
+
+    def _merge_similarities(self, dist, cluster_len, i, j):
+        # the new cluster i merged from i and j adopts the average of
+        # i and j's similarity to each other cluster, weighted by the
+        # number of points in the clusters i and j
+        i_weight = cluster_len[i]
+        j_weight = cluster_len[j]
+        weight_sum = i_weight+j_weight
+
+        # update for x<i
+        dist[:i, i] = dist[:i, i]*i_weight + dist[:i, j]*j_weight
+        dist[:i, i] /= weight_sum
+        # update for i<x<j
+        dist[i, i+1:j] = dist[i, i+1:j]*i_weight + dist[i+1:j, j]*j_weight
+        # update for i<j<x
+        dist[i, j+1:] = dist[i, j+1:]*i_weight + dist[j, j+1:]*j_weight
+        dist[i, i+1:] /= weight_sum
+
+    def update_clusters(self, num_clusters):
+        clusters = self._dendrogram.groups(num_clusters)
+        self._centroids = []
+        for cluster in clusters:
+            assert len(cluster) > 0
+            if self._should_normalise:
+                centroid = self._normalise(cluster[0])
+            else:
+                centroid = numpy.array(cluster[0])
+            for vector in cluster[1:]:
+                if self._should_normalise:
+                    centroid += self._normalise(vector)
+                else:
+                    centroid += vector
+            centroid /= len(cluster)
+            self._centroids.append(centroid)
+        self._num_clusters = len(self._centroids)
+
+    def classify_vectorspace(self, vector):
+        best = None
+        for i in range(self._num_clusters):
+            centroid = self._centroids[i]
+            dist = cosine_distance(vector, centroid)
+            if not best or dist < best[0]:
+                best = (dist, i)
+        return best[1]
+
+    def dendrogram(self):
+        """
+        :return: The dendrogram representing the current clustering
+        :rtype:  Dendrogram
+        """
+        return self._dendrogram
+
+    def num_clusters(self):
+        return self._num_clusters
+
+    def __repr__(self):
+        return '<GroupAverageAgglomerative Clusterer n=%d>' % self._num_clusters
+
+def demo():
+    """
+    Non-interactive demonstration of the clusterers with simple 2-D data.
+    """
+
+    from nltk.cluster import GAAClusterer
+
+    # use a set of tokens with 2D indices
+    vectors = [numpy.array(f) for f in [[3, 3], [1, 2], [4, 2], [4, 0], [2, 3], [3, 1]]]
+
+    # test the GAAC clusterer with 4 clusters
+    clusterer = GAAClusterer(4)
+    clusters = clusterer.cluster(vectors, True)
+
+    print('Clusterer:', clusterer)
+    print('Clustered:', vectors)
+    print('As:', clusters)
+    print()
+
+    # show the dendrogram
+    clusterer.dendrogram().show()
+
+    # classify a new vector
+    vector = numpy.array([3, 3])
+    print('classify(%s):' % vector, end=' ')
+    print(clusterer.classify(vector))
+    print()
+
+
+if __name__ == '__main__':
+    demo()