EVOLUTION-MANAGER

Edit File: minimum_degree_ordering.hpp

//-*-c++-*-
//=======================================================================
// Copyright 1997-2001 University of Notre Dame.
// Authors: Lie-Quan Lee, Jeremy Siek
//
// Distributed under the Boost Software License, Version 1.0. (See
// accompanying file LICENSE_1_0.txt or copy at
// http://www.boost.org/LICENSE_1_0.txt)
//=======================================================================
//
#ifndef MINIMUM_DEGREE_ORDERING_HPP
#define MINIMUM_DEGREE_ORDERING_HPP

#include <vector>
#include <boost/assert.hpp>
#include <boost/config.hpp>
#include <boost/pending/bucket_sorter.hpp>
#include <boost/detail/numeric_traits.hpp> // for integer_traits
#include <boost/graph/graph_traits.hpp>
#include <boost/property_map/property_map.hpp>

namespace boost {

namespace detail {

// 
    // Given a set of n integers (where the integer values range from
    // zero to n-1), we want to keep track of a collection of stacks
    // of integers. It so happens that an integer will appear in at
    // most one stack at a time, so the stacks form disjoint sets.
    // Because of these restrictions, we can use one big array to
    // store all the stacks, intertwined with one another.
    // No allocation/deallocation happens in the push()/pop() methods
    // so this is faster than using std::stack's.
    //
    template <class SignedInteger>
    class Stacks {
      typedef SignedInteger value_type;
      typedef typename std::vector<value_type>::size_type size_type;
    public:
      Stacks(size_type n) : data(n) {}
      
      //: stack 
      class stack {
        typedef typename std::vector<value_type>::iterator Iterator;
      public:
        stack(Iterator _data, const value_type& head)
          :  data(_data), current(head) {}

// did not use default argument here to avoid internal compiler error
        // in g++.
        stack(Iterator _data)
          : data(_data), current(-(std::numeric_limits<value_type>::max)()) {}
        
        void pop() {
          BOOST_ASSERT(! empty());
          current = data[current];
        }
        void push(value_type v) {
          data[v] = current; 
          current = v;
        }
        bool empty() {
          return current == -(std::numeric_limits<value_type>::max)(); 
        }
        value_type& top() { return current; }
      private:
        Iterator data;
        value_type current;
      };

// To return a stack object 
      stack make_stack()
        { return stack(data.begin()); }
    protected:
      std::vector<value_type> data;
    };

// marker class, a generalization of coloring. 
    //
    // This class is to provide a generalization of coloring which has
    // complexity of amortized constant time to set all vertices' color
    // back to be untagged. It implemented by increasing a tag.
    //
    // The colors are:
    //   not tagged 
    //   tagged
    //   multiple_tagged
    //   done
    //
    template <class SignedInteger, class Vertex, class VertexIndexMap>
    class Marker {
      typedef SignedInteger value_type;
      typedef typename std::vector<value_type>::size_type size_type;
      
      static value_type done() 
      { return (std::numeric_limits<value_type>::max)()/2; }
    public:
      Marker(size_type _num, VertexIndexMap index_map) 
        : tag(1 - (std::numeric_limits<value_type>::max)()),
          data(_num, - (std::numeric_limits<value_type>::max)()),
          id(index_map) {}
      
      void mark_done(Vertex node) { data[get(id, node)] = done(); }
      
      bool is_done(Vertex node) { return data[get(id, node)] == done(); }
      
      void mark_tagged(Vertex node) { data[get(id, node)] = tag; }
      
      void mark_multiple_tagged(Vertex node) { data[get(id, node)] = multiple_tag; }
  
      bool is_tagged(Vertex node) const { return data[get(id, node)] >= tag; }

bool is_not_tagged(Vertex node) const { return data[get(id, node)] < tag; }

bool is_multiple_tagged(Vertex node) const 
        { return data[get(id, node)] >= multiple_tag; }

void increment_tag() {
        const size_type num = data.size();
        ++tag;
        if ( tag >= done() ) {
          tag = 1 - (std::numeric_limits<value_type>::max)();
          for (size_type i = 0; i < num; ++i)
            if ( data[i] < done() ) 
              data[i] = - (std::numeric_limits<value_type>::max)();
        }
      }
      
      void set_multiple_tag(value_type mdeg0) 
      { 
        const size_type num = data.size();
        multiple_tag = tag + mdeg0; 
        
        if ( multiple_tag >= done() ) {
          tag = 1-(std::numeric_limits<value_type>::max)();
          
          for (size_type i=0; i<num; i++)
            if ( data[i] < done() ) 
              data[i] = -(std::numeric_limits<value_type>::max)();
          
          multiple_tag = tag + mdeg0; 
        }
      }
      
      void set_tag_as_multiple_tag() { tag = multiple_tag; }
      
    protected:
      value_type tag;
      value_type multiple_tag;
      std::vector<value_type> data;
      VertexIndexMap id;
    };
    
    template< class Iterator, class SignedInteger, 
       class Vertex, class VertexIndexMap, int offset = 1 >
    class Numbering {
      typedef SignedInteger number_type;
      number_type num; //start from 1 instead of zero
      Iterator   data;
      number_type max_num;
      VertexIndexMap id;
    public:
      Numbering(Iterator _data, number_type _max_num, VertexIndexMap id) 
        : num(1), data(_data), max_num(_max_num), id(id) {}
      void operator()(Vertex node) { data[get(id, node)] = -num; }
      bool all_done(number_type i = 0) const { return num + i > max_num; }
      void increment(number_type i = 1) { num += i; }
      bool is_numbered(Vertex node) const {
        return data[get(id, node)] < 0;
      }
      void indistinguishable(Vertex i, Vertex j) {
        data[get(id, i)] = - (get(id, j) + offset);
      }
    };

template <class SignedInteger, class Vertex, class VertexIndexMap>
    class degreelists_marker {
    public:
      typedef SignedInteger value_type;
      typedef typename std::vector<value_type>::size_type size_type;
      degreelists_marker(size_type n, VertexIndexMap id)
        : marks(n, 0), id(id) {}
      void mark_need_update(Vertex i) { marks[get(id, i)] = 1;  }
      bool need_update(Vertex i) { return marks[get(id, i)] == 1; }
      bool outmatched_or_done (Vertex i) { return marks[get(id, i)] == -1; }
      void mark(Vertex i) { marks[get(id, i)] = -1; }
      void unmark(Vertex i) { marks[get(id, i)] = 0; }
    private:
      std::vector<value_type> marks;
      VertexIndexMap id;
    };

// Helper function object for edge removal
    template <class Graph, class MarkerP, class NumberD, class Stack,
      class VertexIndexMap>
    class predicateRemoveEdge1 {
      typedef typename graph_traits<Graph>::vertex_descriptor vertex_t;
      typedef typename graph_traits<Graph>::edge_descriptor edge_t;
    public:
      predicateRemoveEdge1(Graph& _g, MarkerP& _marker, 
                           NumberD _numbering, Stack& n_e, VertexIndexMap id)
        : g(&_g), marker(&_marker), numbering(_numbering),
          neighbor_elements(&n_e), id(id) {}

bool operator()(edge_t e) {
        vertex_t dist = target(e, *g);
        if ( marker->is_tagged(dist) )
          return true;
        marker->mark_tagged(dist);
        if (numbering.is_numbered(dist)) {
          neighbor_elements->push(get(id, dist));
          return true;
        }
        return false;
      }
    private:
      Graph*   g;
      MarkerP* marker;
      NumberD  numbering;
      Stack*   neighbor_elements;
      VertexIndexMap id;
    };

// Helper function object for edge removal
    template <class Graph, class MarkerP>
    class predicate_remove_tagged_edges
    {
      typedef typename graph_traits<Graph>::vertex_descriptor vertex_t;
      typedef typename graph_traits<Graph>::edge_descriptor edge_t;
    public:
      predicate_remove_tagged_edges(Graph& _g, MarkerP& _marker)
        : g(&_g), marker(&_marker) {}

bool operator()(edge_t e) {
        vertex_t dist = target(e, *g);
        if ( marker->is_tagged(dist) )
          return true;
        return false;
      }
    private:
      Graph*   g;
      MarkerP* marker;
    };

template<class Graph, class DegreeMap, 
             class InversePermutationMap, 
             class PermutationMap,
             class SuperNodeMap, 
             class VertexIndexMap>
    class mmd_impl
    {
      // Typedefs
      typedef graph_traits<Graph> Traits;
      typedef typename Traits::vertices_size_type size_type;
      typedef typename detail::integer_traits<size_type>::difference_type 
        diff_t;
      typedef typename Traits::vertex_descriptor vertex_t;
      typedef typename Traits::adjacency_iterator adj_iter;
      typedef iterator_property_map<vertex_t*, 
        identity_property_map, vertex_t, vertex_t&> IndexVertexMap;
      typedef detail::Stacks<diff_t> Workspace;
      typedef bucket_sorter<size_type, vertex_t, DegreeMap, VertexIndexMap> 
        DegreeLists;
      typedef Numbering<InversePermutationMap, diff_t, vertex_t,VertexIndexMap>
        NumberingD;
      typedef degreelists_marker<diff_t, vertex_t, VertexIndexMap> 
        DegreeListsMarker;
      typedef Marker<diff_t, vertex_t, VertexIndexMap> MarkerP;

// Data Members
      bool has_no_edges;

// input parameters
      Graph& G;
      int delta;
      DegreeMap degree;
      InversePermutationMap inverse_perm;
      PermutationMap perm;
      SuperNodeMap supernode_size;
      VertexIndexMap vertex_index_map;

// internal data-structures
      std::vector<vertex_t> index_vertex_vec;
      size_type n;
      IndexVertexMap index_vertex_map;
      DegreeLists degreelists;
      NumberingD numbering;
      DegreeListsMarker degree_lists_marker;
      MarkerP marker;
      Workspace work_space;
    public:
      mmd_impl(Graph& g, size_type n_, int delta, DegreeMap degree, 
               InversePermutationMap inverse_perm, 
               PermutationMap perm,
               SuperNodeMap supernode_size, 
               VertexIndexMap id) 
        : has_no_edges(true), G(g), delta(delta), degree(degree), 
        inverse_perm(inverse_perm), 
        perm(perm), 
        supernode_size(supernode_size), 
        vertex_index_map(id),
        index_vertex_vec(n_), 
        n(n_),
        degreelists(n_ + 1, n_, degree, id),
        numbering(inverse_perm, n_, vertex_index_map),
        degree_lists_marker(n_, vertex_index_map), 
        marker(n_, vertex_index_map),
        work_space(n_)
      {
        typename graph_traits<Graph>::vertex_iterator v, vend;
        size_type vid = 0;
        for (boost::tie(v, vend) = vertices(G); v != vend; ++v, ++vid)
          index_vertex_vec[vid] = *v;
        index_vertex_map = IndexVertexMap(&index_vertex_vec[0]);

// Initialize degreelists.  Degreelists organizes the nodes
        // according to their degree.
        for (boost::tie(v, vend) = vertices(G); v != vend; ++v) {
          typename Traits::degree_size_type d = out_degree(*v, G);
          put(degree, *v, d);
          if (0 < d) has_no_edges = false;
          degreelists.push(*v);
        }
      }

void do_mmd()
      {
        // Eliminate the isolated nodes -- these are simply the nodes
        // with no neighbors, which are accessible as a list (really, a
        // stack) at location 0.  Since these don't affect any other
        // nodes, we can eliminate them without doing degree updates.
        typename DegreeLists::stack list_isolated = degreelists[0];
        while (!list_isolated.empty()) {
          vertex_t node = list_isolated.top();
          marker.mark_done(node);
          numbering(node);
          numbering.increment();
          list_isolated.pop();
        }

if (has_no_edges)
        {
          return;
        }

size_type min_degree = 1;
        typename DegreeLists::stack list_min_degree = degreelists[min_degree];

while (list_min_degree.empty()) {
          ++min_degree;
          list_min_degree = degreelists[min_degree];
        }

// check if the whole eliminating process is done
        while (!numbering.all_done()) {

size_type min_degree_limit = min_degree + delta; // WARNING
          typename Workspace::stack llist = work_space.make_stack();

// multiple elimination
          while (delta >= 0) {

// Find the next non-empty degree
            for (list_min_degree = degreelists[min_degree]; 
                 list_min_degree.empty() && min_degree <= min_degree_limit; 
                 ++min_degree, list_min_degree = degreelists[min_degree])
              ;
            if (min_degree > min_degree_limit)
              break;

const vertex_t node = list_min_degree.top();
            const size_type node_id = get(vertex_index_map, node);
            list_min_degree.pop();
            numbering(node);

// check if node is the last one
            if (numbering.all_done(supernode_size[node])) {
              numbering.increment(supernode_size[node]);
              break;
            }
            marker.increment_tag();
            marker.mark_tagged(node);

this->eliminate(node);

numbering.increment(supernode_size[node]);
            llist.push(node_id);
          } // multiple elimination

if (numbering.all_done()) 
            break;

this->update( llist, min_degree);
        }

} // do_mmd()

void eliminate(vertex_t node)
      {
        typename Workspace::stack element_neighbor = work_space.make_stack();

// Create two function objects for edge removal
        typedef typename Workspace::stack WorkStack;
        predicateRemoveEdge1<Graph, MarkerP, NumberingD, 
                             WorkStack, VertexIndexMap>
          p(G, marker, numbering, element_neighbor, vertex_index_map);

predicate_remove_tagged_edges<Graph, MarkerP> p2(G, marker);

// Reconstruct the adjacent node list, push element neighbor in a List.
        remove_out_edge_if(node, p, G);
        //during removal element neighbors are collected.

while (!element_neighbor.empty()) {
          // element absorb
          size_type e_id = element_neighbor.top();
          vertex_t element = get(index_vertex_map, e_id);
          adj_iter i, i_end;
          for (boost::tie(i, i_end) = adjacent_vertices(element, G); i != i_end; ++i){
            vertex_t i_node = *i;
            if (!marker.is_tagged(i_node) && !numbering.is_numbered(i_node)) {
              marker.mark_tagged(i_node);
              add_edge(node, i_node, G);
            }
          }
          element_neighbor.pop();
        }
        adj_iter v, ve;
        for (boost::tie(v, ve) = adjacent_vertices(node, G); v != ve; ++v) {
          vertex_t v_node = *v;
          if (!degree_lists_marker.need_update(v_node) 
              && !degree_lists_marker.outmatched_or_done(v_node)) {
            degreelists.remove(v_node);
          }
          //update out edges of v_node
          remove_out_edge_if(v_node, p2, G);

if ( out_degree(v_node, G) == 0 ) { // indistinguishable nodes
            supernode_size[node] += supernode_size[v_node];
            supernode_size[v_node] = 0;
            numbering.indistinguishable(v_node, node);
            marker.mark_done(v_node);
            degree_lists_marker.mark(v_node);
          } else {                           // not indistinguishable nodes
            add_edge(v_node, node, G);
            degree_lists_marker.mark_need_update(v_node);
          }
        }
      } // eliminate()

template <class Stack>
      void update(Stack llist, size_type& min_degree)
      {
        size_type min_degree0 = min_degree + delta + 1;

while (! llist.empty()) {
          size_type deg, deg0 = 0;

marker.set_multiple_tag(min_degree0);
          typename Workspace::stack q2list = work_space.make_stack();
          typename Workspace::stack qxlist = work_space.make_stack();

vertex_t current = get(index_vertex_map, llist.top());
          adj_iter i, ie;
          for (boost::tie(i,ie) = adjacent_vertices(current, G); i != ie; ++i) {
            vertex_t i_node = *i;
            const size_type i_id = get(vertex_index_map, i_node);
            if (supernode_size[i_node] != 0) {
              deg0 += supernode_size[i_node];
              marker.mark_multiple_tagged(i_node);
              if (degree_lists_marker.need_update(i_node)) {
                if (out_degree(i_node, G) == 2)
                  q2list.push(i_id);
                else
                  qxlist.push(i_id);
              }
            }
          }

while (!q2list.empty()) {
            const size_type u_id = q2list.top();
            vertex_t u_node = get(index_vertex_map, u_id);
            // if u_id is outmatched by others, no need to update degree
            if (degree_lists_marker.outmatched_or_done(u_node)) {
              q2list.pop();
              continue;
            }
            marker.increment_tag();
            deg = deg0;

adj_iter nu = adjacent_vertices(u_node, G).first;
            vertex_t neighbor = *nu;
            if (neighbor == u_node) {
              ++nu;
              neighbor = *nu;
            }
            if (numbering.is_numbered(neighbor)) {
              adj_iter i, ie;
              for (boost::tie(i,ie) = adjacent_vertices(neighbor, G);
                   i != ie; ++i) {
                const vertex_t i_node = *i;
                if (i_node == u_node || supernode_size[i_node] == 0)
                  continue;
                if (marker.is_tagged(i_node)) {
                  if (degree_lists_marker.need_update(i_node)) {
                    if ( out_degree(i_node, G) == 2 ) { // is indistinguishable
                      supernode_size[u_node] += supernode_size[i_node];
                      supernode_size[i_node] = 0;
                      numbering.indistinguishable(i_node, u_node);
                      marker.mark_done(i_node);
                      degree_lists_marker.mark(i_node);
                    } else                        // is outmatched
                      degree_lists_marker.mark(i_node);
                  }
                } else {
                  marker.mark_tagged(i_node);
                  deg += supernode_size[i_node];
                }
              }
            } else
              deg += supernode_size[neighbor];

deg -= supernode_size[u_node];
            degree[u_node] = deg; //update degree
            degreelists[deg].push(u_node);
            //u_id has been pushed back into degreelists
            degree_lists_marker.unmark(u_node);
            if (min_degree > deg) 
              min_degree = deg;
            q2list.pop();
          } // while (!q2list.empty())

while (!qxlist.empty()) {
            const size_type u_id = qxlist.top();
            const vertex_t u_node = get(index_vertex_map, u_id);

// if u_id is outmatched by others, no need to update degree
            if (degree_lists_marker.outmatched_or_done(u_node)) {
              qxlist.pop();
              continue;
            }
            marker.increment_tag();
            deg = deg0;
            adj_iter i, ie;
            for (boost::tie(i, ie) = adjacent_vertices(u_node, G); i != ie; ++i) {
              vertex_t i_node = *i;
              if (marker.is_tagged(i_node)) 
                continue;
              marker.mark_tagged(i_node);

if (numbering.is_numbered(i_node)) {
                adj_iter j, je;
                for (boost::tie(j, je) = adjacent_vertices(i_node, G); j != je; ++j) {
                  const vertex_t j_node = *j;
                  if (marker.is_not_tagged(j_node)) {
                    marker.mark_tagged(j_node);
                    deg += supernode_size[j_node];
                  }
                }
              } else
                deg += supernode_size[i_node];
            } // for adjacent vertices of u_node
            deg -= supernode_size[u_node];
            degree[u_node] = deg;
            degreelists[deg].push(u_node);
            // u_id has been pushed back into degreelists
            degree_lists_marker.unmark(u_node); 
            if (min_degree > deg)
              min_degree = deg;
            qxlist.pop();
          } // while (!qxlist.empty()) {

marker.set_tag_as_multiple_tag();
          llist.pop();
        } // while (! llist.empty())

} // update()

void build_permutation(InversePermutationMap next,
                             PermutationMap prev) 
      {
        // collect the permutation info
        size_type i;
        for (i = 0; i < n; ++i) {
          diff_t size = supernode_size[get(index_vertex_map, i)];
          if ( size <= 0 ) {
            prev[i] = next[i];
            supernode_size[get(index_vertex_map, i)]
              = next[i] + 1;  // record the supernode info
          } else
            prev[i] = - next[i];
        }
        for (i = 1; i < n + 1; ++i) {
          if ( prev[i-1] > 0 )
            continue;
          diff_t parent = i;
          while ( prev[parent - 1] < 0 ) {
            parent = - prev[parent - 1];
          }

diff_t root = parent;
          diff_t num = prev[root - 1] + 1;
          next[i-1] = - num;
          prev[root-1] = num;

parent = i;
          diff_t next_node = - prev[parent - 1];
          while (next_node > 0) {
            prev[parent-1] = - root;
            parent = next_node;
            next_node = - prev[parent - 1];
          }
        }
        for (i = 0; i < n; i++) {
          diff_t num = - next[i] - 1;
          next[i] = num;
          prev[num] = i;
        }
      } // build_permutation()
    };

} //namespace detail

// MMD algorithm
  // 
  //The implementation presently includes the enhancements for mass
  //elimination, incomplete degree update, multiple elimination, and
  //external degree.
  //
  //Important Note: This implementation requires the BGL graph to be
  //directed.  Therefore, nonzero entry (i, j) in a symmetrical matrix
  //A coresponds to two directed edges (i->j and j->i).
  //
  //see Alan George and Joseph W. H. Liu, The Evolution of the Minimum
  //Degree Ordering Algorithm, SIAM Review, 31, 1989, Page 1-19
  template<class Graph, class DegreeMap, 
           class InversePermutationMap, 
           class PermutationMap,
           class SuperNodeMap, class VertexIndexMap>
  void minimum_degree_ordering
    (Graph& G, 
     DegreeMap degree, 
     InversePermutationMap inverse_perm, 
     PermutationMap perm, 
     SuperNodeMap supernode_size, 
     int delta, 
     VertexIndexMap vertex_index_map)
  {
    detail::mmd_impl<Graph,DegreeMap,InversePermutationMap,
      PermutationMap, SuperNodeMap, VertexIndexMap> 
      impl(G, num_vertices(G), delta, degree, inverse_perm, 
           perm, supernode_size, vertex_index_map);
    impl.do_mmd();
    impl.build_permutation(inverse_perm, perm);
  }

} // namespace boost

#endif // MINIMUM_DEGREE_ORDERING_HPP