[Boost-commit] svn:boost r45219 - sandbox/boost/algorithm/cluster

From: franklin.jonathan_at_[hidden]
Date: 2008-05-08 13:09:19

Author: jfranklin
Date: 2008-05-08 13:09:19 EDT (Thu, 08 May 2008)
New Revision: 45219
URL: http://svn.boost.org/trac/boost/changeset/45219

Log:
Initial cut at dbscan clustering algorithm.

Added:
   sandbox/boost/algorithm/cluster/dbscan.hpp   (contents, props changed)

Added: sandbox/boost/algorithm/cluster/dbscan.hpp
==============================================================================
--- (empty file)
+++ sandbox/boost/algorithm/cluster/dbscan.hpp	2008-05-08 13:09:19 EDT (Thu, 08 May 2008)
@@ -0,0 +1,190 @@
+#if ! defined BOOST_ALGORITHM_CLUSTER_DBSCAN_HPP
+#define BOOST_ALGORITHM_CLUSTER_DBSCAN_HPP
+
+#include <boost/range/begin.hpp>
+#include <boost/range/end.hpp>
+#include <boost/shared_ptr.hpp>
+#include <vector>
+#include <list>
+
+namespace boost
+{
+namespace algorithm
+{
+namespace cluster
+{
+
+namespace detail
+{
+
+// TODO: Replace this naive query function w/ R*-tree or fractional cascading.
+// It makes the runtime quadratic.
+template<typename NTupleIter, typename DistFun>
+static void query(
+  NTupleIter const & query_pt,
+  NTupleIter const & begin,
+  NTupleIter const & end,
+  float eps,
+  DistFun const & d,
+  std::vector<NTupleIter> & v)
+{
+  for(NTupleIter cur_pt = begin; cur_pt != end; ++cur_pt)
+  {
+    if (query_pt == cur_pt)
+      continue;
+
+    if (d(*query_pt->tuple, *cur_pt->tuple) > eps)
+      continue;
+
+    v.push_back(cur_pt);
+  }
+}
+
+// TODO: Replace this so we don't have to store the cluster info for each tuple.
+template<typename NTupleIter>
+struct node
+{
+  node(NTupleIter const & t) : tuple(t), cluster(UNCLASSIFIED) {}
+
+  NTupleIter tuple;
+  int cluster;
+};
+
+} // End of namespace detail.
+
+// TODO: Document this type.
+template<typename Cluster>
+struct cluster_data
+{
+  typedef Cluster value_type;
+  typedef std::vector<value_type> clusters;
+  cluster_data() : m_pClusters(new clusters) {}
+  ~cluster_data() {}
+
+  cluster_data(cluster_data const & c) : m_pClusters(c.m_pClusters) {}
+  cluster_data const & cluster_data::operator=(cluster_data const & rhs)
+  { m_pClusters = rhs.m_pClusters; }
+
+  typedef typename clusters::iterator iterator;
+  typedef typename clusters::const_iterator const_iterator;
+  typedef typename clusters::reverse_iterator reverse_iterator;
+
+  iterator begin() { return m_pClusters->begin(); }
+  iterator end() { return m_pClusters->end(); }
+
+  const_iterator begin() const { return m_pClusters->begin(); }
+  const_iterator end() const { return m_pClusters->end(); }
+
+  iterator rbegin() { return m_pClusters->rbegin(); }
+  iterator rend() { return m_pClusters->rend(); }
+
+  iterator insert(iterator loc, value_type const & val)
+  { return m_pClusters->insert(loc, val); }
+
+  void push_back(value_type const & v) { m_pClusters->push_back(v); }
+  void pop_back() { m_pClusters->pop_back(); }
+
+  value_type & back() { return m_pClusters->back(); }
+  value_type const & back() const { return m_pClusters->back(); }
+
+private:
+  boost::shared_ptr<clusters> m_pClusters;
+};
+
+/**
+ */
+template<typename Cluster, typename NTupleIter, typename DistFun>
+cluster_data<Cluster>
+dbscan(NTupleIter const & begin,
+       NTupleIter const & end, 
+       typename NTupleIter::difference_type const & eps,
+       size_t min_points,
+       DistFun const & d)
+{
+  // TODO: Rework the algorithm to NOT make this extra collection.
+  typedef detail::node<NTupleIter> node;
+  typedef std::vector<node> ntuple_nodes;
+  ntuple_nodes tuples;
+
+  // Initialize algorithm.
+  //size_t num_elems = 0;
+  for(NTupleIter it = begin; it != end; ++it)
+  {
+    //++num_elems;
+    //it->cluster = UNCLASSIFIED;
+    tuples.push_back(node(it));
+  }
+
+  typedef cluster_data<std::vector<NTupleIter> > cluster_data;
+  cluster_data p;
+
+  // Do it...
+  int cluster_num = 0;
+  for(ntuple_nodes::iterator it = tuples.begin(); it != tuples.end(); ++it)
+  {
+    if (it->cluster != UNCLASSIFIED) // Been classified.
+      continue;
+
+    // Expand cluster.
+
+    std::vector<ntuple_nodes::iterator> seeds;
+    detail::query(it, tuples.begin(), tuples.end(), eps, d, seeds);
+    if (seeds.size() < min_points)
+    {
+      it->cluster = NOISE;
+      continue;
+    }
+
+    // Start the next cluster.
+    ++cluster_num;
+    p.push_back(Cluster());
+    Cluster & cur_cluster = p.back();
+
+    // Mark entire neighborhood as part of current cluster.
+    it->cluster = cluster_num;
+    cur_cluster.push_back(it->tuple);
+    // TODO: Remove it from noise.
+    for (size_t n = 0; n < seeds.size(); ++n)
+    {
+      seeds[n]->cluster = cluster_num;
+      cur_cluster.push_back(seeds[n]->tuple);
+      // TODO: Remove it from noise.
+    }
+
+    while (! seeds.empty())
+    {
+      ntuple_nodes::iterator cur = seeds.back();
+      seeds.pop_back();
+
+      std::vector<ntuple_nodes::iterator> results;
+      detail::query(cur, tuples.begin(), tuples.end(), eps, d, results);
+
+      if (results.size() >= min_points)
+      {
+        for (size_t n = 0; n < results.size(); ++n)
+        {
+          if (results[n]->cluster < 1) // Not assigned to cluster yet.
+          {
+            if (UNCLASSIFIED == results[n]->cluster)
+              seeds.push_back(results[n]);
+            results[n]->cluster = cluster_num;
+            cur_cluster.push_back(results[n]->tuple);
+          }
+        }
+      }
+    }
+
+  } // Outer loop for all tuples.
+
+  return p;
+}
+
+} // End of namespace cluster
+
+using namespace cluster;
+
+} // End of namespace algorithm
+
+} // End of namespace boost
+
+#endif // BOOST_ALGORITHM_CLUSTER_DBSCAN_HPP