Removed obsolete/deprecated stuff
[libdai.git] / include / dai / bipgraph.h
1 /* This file is part of libDAI - http://www.libdai.org/
2 *
3 * libDAI is licensed under the terms of the GNU General Public License version
4 * 2, or (at your option) any later version. libDAI is distributed without any
5 * warranty. See the file COPYING for more details.
6 *
7 * Copyright (C) 2006-2009 Joris Mooij [joris dot mooij at libdai dot org]
8 * Copyright (C) 2006-2007 Radboud University Nijmegen, The Netherlands
9 */
10
11
12 /// \file
13 /// \brief Defines the BipartiteGraph class, which represents a bipartite graph
14
15
16 #ifndef __defined_libdai_bipgraph_h
17 #define __defined_libdai_bipgraph_h
18
19
20 #include <ostream>
21 #include <vector>
22 #include <algorithm>
23 #include <dai/util.h>
24 #include <dai/exceptions.h>
25
26
27 namespace dai {
28
29
30 /// Represents the neighborhood structure of nodes in an undirected, bipartite graph.
31 /** A bipartite graph has two types of nodes: type 1 and type 2. Edges can occur only between
32 * nodes of different type. Nodes are indexed by an unsigned integer. If there are nr1()
33 * nodes of type 1 and nr2() nodes of type 2, the nodes of type 1 are numbered
34 * 0,1,2,...,nr1()-1 and the nodes of type 2 are numbered 0,1,2,...,nr2()-1. An edge
35 * between node \a n1 of type 1 and node \a n2 of type 2 is represented by a BipartiteGraph::Edge(\a n1,\a n2).
36 *
37 * A BipartiteGraph is implemented as a sparse adjacency list, i.e., it stores for each node a list of
38 * its neighboring nodes. More precisely: it stores for each node of type 1 a vector of Neighbor structures
39 * (accessible by the nb1() method) describing the neighboring nodes of type 2; similarly, for each node
40 * of type 2 it stores a vector of Neighbor structures (accessibly by the nb2() method) describing the
41 * neighboring nodes of type 1.
42 * Thus, each node has an associated variable of type BipartiteGraph::Neighbors, which is a vector of
43 * Neighbor structures, describing its neighboring nodes of the other type.
44 * \idea Cache second-order neighborhoods in BipartiteGraph.
45 */
46 class BipartiteGraph {
47 public:
48 /// Describes the neighbor relationship of two nodes in a BipartiteGraph.
49 /** Sometimes we want to do an action, such as sending a
50 * message, for all edges in a graph. However, most graphs
51 * will be sparse, so we need some way of storing a set of
52 * the neighbors of a node, which is both fast and
53 * memory-efficient. We also need to be able to go between
54 * viewing node \a a as a neighbor of node \a b, and node \a b
55 * as a neighbor of node \a a. The Neighbor struct solves
56 * both of these problems. Each node has a list of neighbors,
57 * stored as a std::vector<\link Neighbor \endlink>, and
58 * extra information is included in the Neighbor struct which
59 * allows us to access a node as a neighbor of its neighbor
60 * (the \c dual member).
61 *
62 * By convention, variable identifiers naming indices into a
63 * vector of neighbors are prefixed with an underscore ("_").
64 * The neighbor list which they point into is then understood
65 * from context. For example:
66 *
67 * \code
68 * void BP::calcNewMessage( size_t i, size_t _I )
69 * \endcode
70 *
71 * Here, \a i is the "absolute" index of node i, but \a _I is
72 * understood as a "relative" index, giving node \a I 's entry in
73 * <tt>nb1(i)</tt>. The corresponding Neighbor structure can be
74 * accessed as <tt>nb1(i,_I)</tt> or <tt>nb1(i)[_I]</tt>. The
75 * absolute index of \a _I, which would be called \a I, can be
76 * recovered from the \c node member: <tt>nb1(i,_I).node</tt>.
77 * The \c iter member gives the relative index \a _I, and the
78 * \c dual member gives the "dual" relative index, i.e., the
79 * index of \a i in \a I 's neighbor list.
80 *
81 * \code
82 * Neighbor n = nb1(i,_I);
83 * n.node == I &&
84 * n.iter == _I &&
85 * nb2(n.node,n.dual).node == i
86 * \endcode
87 *
88 * In a FactorGraph, the nodes of type 1 represent variables, and
89 * the nodes of type 2 represent factors. For convenience, nb1() is
90 * called FactorGraph::nbV(), and nb2() is called FactorGraph::nbF().
91 *
92 * There is no easy way to transform a pair of absolute node
93 * indices \a i and \a I into a Neighbor structure relative
94 * to one of the nodes. Such a feature has never yet been
95 * found to be necessary. Iteration over edges can always be
96 * accomplished using the Neighbor lists, and by writing
97 * functions that accept relative indices:
98 * \code
99 * for( size_t i = 0; i < nrVars(); ++i )
100 * foreach( const Neighbor &I, nbV(i) )
101 * calcNewMessage( i, I.iter );
102 * \endcode
103 */
104 struct Neighbor {
105 /// Corresponds to the index of this Neighbor entry in the vector of neighbors
106 size_t iter;
107 /// Contains the number of the neighboring node
108 size_t node;
109 /// Contains the "dual" iter
110 size_t dual;
111
112 /// Default constructor
113 Neighbor() {}
114 /// Constructor that sets the Neighbor members according to the parameters
115 Neighbor( size_t iter, size_t node, size_t dual ) : iter(iter), node(node), dual(dual) {}
116
117 /// Cast to \c size_t returns \c node member
118 operator size_t () const { return node; }
119 };
120
121 /// Describes the neighbors of some node.
122 typedef std::vector<Neighbor> Neighbors;
123
124 /// Represents an edge: an Edge(\a n1,\a n2) corresponds to the edge between node \a n1 of type 1 and node \a n2 of type 2.
125 typedef std::pair<size_t,size_t> Edge;
126
127 private:
128 /// Contains for each node of type 1 a vector of its neighbors
129 std::vector<Neighbors> _nb1;
130
131 /// Contains for each node of type 2 a vector of its neighbors
132 std::vector<Neighbors> _nb2;
133
134 /// Used internally by isTree()
135 struct levelType {
136 /// Indices of nodes of type 1
137 std::vector<size_t> ind1;
138 /// Indices of nodes of type 2
139 std::vector<size_t> ind2;
140 };
141
142 public:
143 /// \name Constructors and destructors
144 //@{
145 /// Default constructor (creates an empty bipartite graph)
146 BipartiteGraph() : _nb1(), _nb2() {}
147
148 /// Constructs BipartiteGraph from a range of edges.
149 /** \tparam EdgeInputIterator Iterator that iterates over instances of BipartiteGraph::Edge.
150 * \param nr1 The number of nodes of type 1.
151 * \param nr2 The number of nodes of type 2.
152 * \param begin Points to the first edge.
153 * \param end Points just beyond the last edge.
154 */
155 template<typename EdgeInputIterator>
156 BipartiteGraph( size_t nr1, size_t nr2, EdgeInputIterator begin, EdgeInputIterator end ) : _nb1( nr1 ), _nb2( nr2 ) {
157 construct( nr1, nr2, begin, end );
158 }
159 //@}
160
161 /// \name Accessors and mutators
162 //@{
163 /// Returns constant reference to the \a _i2 'th neighbor of node \a i1 of type 1
164 const Neighbor & nb1( size_t i1, size_t _i2 ) const {
165 DAI_DEBASSERT( i1 < _nb1.size() );
166 DAI_DEBASSERT( _i2 < _nb1[i1].size() );
167 return _nb1[i1][_i2];
168 }
169 /// Returns reference to the \a _i2 'th neighbor of node \a i1 of type 1
170 Neighbor & nb1( size_t i1, size_t _i2 ) {
171 DAI_DEBASSERT( i1 < _nb1.size() );
172 DAI_DEBASSERT( _i2 < _nb1[i1].size() );
173 return _nb1[i1][_i2];
174 }
175
176 /// Returns constant reference to the \a _i1 'th neighbor of node \a i2 of type 2
177 const Neighbor & nb2( size_t i2, size_t _i1 ) const {
178 DAI_DEBASSERT( i2 < _nb2.size() );
179 DAI_DEBASSERT( _i1 < _nb2[i2].size() );
180 return _nb2[i2][_i1];
181 }
182 /// Returns reference to the \a _i1 'th neighbor of node \a i2 of type 2
183 Neighbor & nb2( size_t i2, size_t _i1 ) {
184 DAI_DEBASSERT( i2 < _nb2.size() );
185 DAI_DEBASSERT( _i1 < _nb2[i2].size() );
186 return _nb2[i2][_i1];
187 }
188
189 /// Returns constant reference to all neighbors of node \a i1 of type 1
190 const Neighbors & nb1( size_t i1 ) const {
191 DAI_DEBASSERT( i1 < _nb1.size() );
192 return _nb1[i1];
193 }
194 /// Returns reference to all neighbors of node \a i1 of type 1
195 Neighbors & nb1( size_t i1 ) {
196 DAI_DEBASSERT( i1 < _nb1.size() );
197 return _nb1[i1];
198 }
199
200 /// Returns constant reference to all neighbors of node \a i2 of type 2
201 const Neighbors & nb2( size_t i2 ) const {
202 DAI_DEBASSERT( i2 < _nb2.size() );
203 return _nb2[i2];
204 }
205 /// Returns reference to all neighbors of node \a i2 of type 2
206 Neighbors & nb2( size_t i2 ) {
207 DAI_DEBASSERT( i2 < _nb2.size() );
208 return _nb2[i2];
209 }
210 //@}
211
212 /// \name Adding nodes and edges
213 //@{
214 /// (Re)constructs BipartiteGraph from a range of edges.
215 /** \tparam EdgeInputIterator Iterator that iterates over instances of BipartiteGraph::Edge.
216 * \param nr1 The number of nodes of type 1.
217 * \param nr2 The number of nodes of type 2.
218 * \param begin Points to the first edge.
219 * \param end Points just beyond the last edge.
220 */
221 template<typename EdgeInputIterator>
222 void construct( size_t nr1, size_t nr2, EdgeInputIterator begin, EdgeInputIterator end );
223
224 /// Adds a node of type 1 without neighbors and returns the index of the added node.
225 size_t add1() { _nb1.push_back( Neighbors() ); return _nb1.size() - 1; }
226
227 /// Adds a node of type 2 without neighbors and returns the index of the added node.
228 size_t add2() { _nb2.push_back( Neighbors() ); return _nb2.size() - 1; }
229
230 /// Adds a node of type 1, with neighbors specified by a range of nodes of type 2.
231 /** \tparam NodeInputIterator Iterator that iterates over instances of \c size_t.
232 * \param begin Points to the first index of the nodes of type 2 that should become neighbors of the added node.
233 * \param end Points just beyond the last index of the nodes of type 2 that should become neighbors of the added node.
234 * \param sizeHint For improved efficiency, the size of the range may be specified by \a sizeHint.
235 * \returns Index of the added node.
236 */
237 template <typename NodeInputIterator>
238 size_t add1( NodeInputIterator begin, NodeInputIterator end, size_t sizeHint = 0 ) {
239 Neighbors nbs1new;
240 nbs1new.reserve( sizeHint );
241 size_t iter = 0;
242 for( NodeInputIterator it = begin; it != end; ++it ) {
243 DAI_ASSERT( *it < nr2() );
244 Neighbor nb1new( iter, *it, nb2(*it).size() );
245 Neighbor nb2new( nb2(*it).size(), nr1(), iter++ );
246 nbs1new.push_back( nb1new );
247 nb2( *it ).push_back( nb2new );
248 }
249 _nb1.push_back( nbs1new );
250 return _nb1.size() - 1;
251 }
252
253 /// Adds a node of type 2, with neighbors specified by a range of nodes of type 1.
254 /** \tparam NodeInputIterator Iterator that iterates over instances of \c size_t.
255 * \param begin Points to the first index of the nodes of type 1 that should become neighbors of the added node.
256 * \param end Points just beyond the last index of the nodes of type 1 that should become neighbors of the added node.
257 * \param sizeHint For improved efficiency, the size of the range may be specified by \a sizeHint.
258 * \returns Index of the added node.
259 */
260 template <typename NodeInputIterator>
261 size_t add2( NodeInputIterator begin, NodeInputIterator end, size_t sizeHint = 0 ) {
262 Neighbors nbs2new;
263 nbs2new.reserve( sizeHint );
264 size_t iter = 0;
265 for( NodeInputIterator it = begin; it != end; ++it ) {
266 DAI_ASSERT( *it < nr1() );
267 Neighbor nb2new( iter, *it, nb1(*it).size() );
268 Neighbor nb1new( nb1(*it).size(), nr2(), iter++ );
269 nbs2new.push_back( nb2new );
270 nb1( *it ).push_back( nb1new );
271 }
272 _nb2.push_back( nbs2new );
273 return _nb2.size() - 1;
274 }
275
276 /// Adds an edge between node \a n1 of type 1 and node \a n2 of type 2.
277 /** If \a check == \c true, only adds the edge if it does not exist already.
278 */
279 void addEdge( size_t n1, size_t n2, bool check = true );
280 //@}
281
282 /// \name Erasing nodes and edges
283 //@{
284 /// Removes node \a n1 of type 1 and all incident edges; indices of other nodes are changed accordingly.
285 void erase1( size_t n1 );
286
287 /// Removes node \a n2 of type 2 and all incident edges; indices of other nodes are changed accordingly.
288 void erase2( size_t n2 );
289
290 /// Removes edge between node \a n1 of type 1 and node \a n2 of type 2.
291 void eraseEdge( size_t n1, size_t n2 );
292 //@}
293
294 /// \name Queries
295 //@{
296 /// Returns number of nodes of type 1
297 size_t nr1() const { return _nb1.size(); }
298 /// Returns number of nodes of type 2
299 size_t nr2() const { return _nb2.size(); }
300
301 /// Calculates the number of edges, time complexity: O(nr1())
302 size_t nrEdges() const {
303 size_t sum = 0;
304 for( size_t i1 = 0; i1 < nr1(); i1++ )
305 sum += nb1(i1).size();
306 return sum;
307 }
308
309 /// Calculates second-order neighbors (i.e., neighbors of neighbors) of node \a n1 of type 1.
310 /** If \a include == \c true, includes \a n1 itself, otherwise excludes \a n1.
311 */
312 std::vector<size_t> delta1( size_t n1, bool include = false ) const;
313
314 /// Calculates second-order neighbors (i.e., neighbors of neighbors) of node \a n2 of type 2.
315 /** If \a include == \c true, includes \a n2 itself, otherwise excludes \a n2.
316 */
317 std::vector<size_t> delta2( size_t n2, bool include = false ) const;
318
319 /// Returns true if the graph is connected
320 /** \todo Should be optimized by invoking boost::graph library
321 */
322 bool isConnected() const;
323
324 /// Returns true if the graph is a tree, i.e., if it is singly connected and connected.
325 bool isTree() const;
326
327 /// Checks internal consistency
328 void checkConsistency() const;
329 //@}
330
331 /// \name Input and output
332 //@{
333 /// Writes this BipartiteGraph to an output stream in GraphViz .dot syntax
334 void printDot( std::ostream& os ) const;
335 //@}
336 };
337
338
339 template<typename EdgeInputIterator>
340 void BipartiteGraph::construct( size_t nr1, size_t nr2, EdgeInputIterator begin, EdgeInputIterator end ) {
341 _nb1.clear();
342 _nb1.resize( nr1 );
343 _nb2.clear();
344 _nb2.resize( nr2 );
345
346 for( EdgeInputIterator e = begin; e != end; e++ ) {
347 #ifdef DAI_DEBUG
348 addEdge( e->first, e->second, true );
349 #else
350 addEdge( e->first, e->second, false );
351 #endif
352 }
353 }
354
355
356 } // end of namespace dai
357
358
359 /** \example example_bipgraph.cpp
360 * This example deals with the following bipartite graph:
361 * \dot
362 * graph example {
363 * ordering=out;
364 * subgraph cluster_type1 {
365 * node[shape=circle,width=0.4,fixedsize=true,style=filled];
366 * 12 [label="2"];
367 * 11 [label="1"];
368 * 10 [label="0"];
369 * }
370 * subgraph cluster_type2 {
371 * node[shape=polygon,regular=true,sides=4,width=0.4,fixedsize=true,style=filled];
372 * 21 [label="1"];
373 * 20 [label="0"];
374 * }
375 * 10 -- 20;
376 * 11 -- 20;
377 * 12 -- 20;
378 * 11 -- 21;
379 * 12 -- 21;
380 * }
381 * \enddot
382 * It has three nodes of type 1 (drawn as circles) and two nodes of type 2 (drawn as rectangles).
383 * Node 0 of type 1 has only one neighbor (node 0 of type 2), but node 0 of type 2 has three neighbors (nodes 0,1,2 of type 1).
384 * The example code shows how to construct a BipartiteGraph object representing this bipartite graph and
385 * how to iterate over nodes and their neighbors.
386 *
387 * \section Output
388 * \verbinclude examples/example_bipgraph.out
389 *
390 * \section Source
391 */
392
393
394 #endif