This file is indexed.

/usr/include/opengm/inference/auxiliary/planar_maxcut_graph.hxx is in libopengm-dev 2.3.6-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
#pragma once
#ifndef OPENGM_PLANAR_MAXCUT_GRAPH_HXX
#define OPENGM_PLANAR_MAXCUT_GRAPH_HXX


#include <queue> 
#include <cassert>
#include <iostream>
#include <list>
#include <stack>
#include "opengm/opengm.hxx"

//TODO: Fix include path
#include <planarity.src-patched/graph.h>
#include <planarity.src-patched/listcoll.h>
#include <planarity.src-patched/stack.h>
#include <planarity.src-patched/appconst.h>

#include <blossom5.src-patched/PerfectMatching.h>
#include <blossom5.src-patched/PMimplementation.h>
#include <blossom5.src-patched/MinCost/MinCost.h>

namespace opengm {
   namespace external{
      namespace pmc{

         typedef double DataType;
         typedef size_t IDType;


//////////////////////////////////////////////////////
// Graph components
//////////////////////////////////////////////////////

         struct Node;
         struct Edge;
         struct Face;
         struct DualNode;
         struct DualEdge;


         struct Node
         {
            Node(IDType id_) : id(id_), weight(0.0), adj(0), label(-1) {};
            Node(IDType id_, DataType weight_) : id(id_), weight(weight_), adj(0), label(-1) {};

            IDType id;
            DataType weight;
            std::list<Edge*> adj; // List of adjacent edges
            int label;
         };

         struct Face
         {
            Face() : edges(0), dual_nodes(0) {};

            std::list<Edge*> edges; // List of edges surrounding the face
            std::list<DualNode*> dual_nodes; // Clique of dual nodes for this face
         };

         struct Edge
         {
            Edge(Node* tail_, Node* head_, DataType weight_) : tail(tail_), head(head_), weight(weight_), left_face(NULL), right_face(NULL), in_cut(false) {};

            Node* tail;
            Node* head;
            DataType weight;

            Face* left_face; // pointers to the left and right face as seen from
            Face* right_face; // formal head to tail

            bool in_cut; // true iff edge is in the cut set
         };

         struct DualNode
         {
            DualNode(IDType id_) : id(id_), adj(0) {};

            IDType id;
            std::list<DualEdge*> adj; // List of adjacent dual edges
         };

         struct DualEdge
         {
            DualEdge(DualNode* tail_, DualNode* head_, DataType weight_, Edge* original_cross_edge_) :
               tail(tail_), head(head_), weight(weight_), original_cross_edge(original_cross_edge_), in_matching(false) {};

            DualNode* tail;
            DualNode* head;
            DataType weight;

            Edge* original_cross_edge; // Pointer to the original edge crossed by this dual edge, NULL if its a face clique edge

            bool in_matching; // true iff dual edge is in the matching
         };


         Node* get_dest(Node* v, Edge* e)
         // Returns a pointer to the destination node of Edge e as seen from node v. NULL if e is not incident on v.
         {
            if(v == e->tail)
               return e->head;
            else if (v == e->head)
               return e->tail;
            else
               return NULL;
         }

         DualNode* get_dest(DualNode* v, DualEdge* e)
         // Returns a pointer to the destination node of Edge e as seen from node v. NULL if e is not incident on v.
         {
            if(v == e->tail)
               return e->head;
            else if (v == e->head)
               return e->tail;
            else
               return NULL;
         }

         Edge* get_following_edge(Edge* e, Node* v)
         // Returns edge that succeeds e in v's adjacency list (NULL if e is not incident on v).
         {
            std::list<Edge*>::iterator it = v->adj.begin();
            while( (*it!=e) && (it!=v->adj.end()) ) ++it;

            if(it==v->adj.end()) // e is not in v's adj list
            {
               return NULL;
            }
            else // e is in v's adj list
            {
               ++it; // Make one more step
               if(it==v->adj.end()) // e is the last element in v's adj list
                  return v->adj.front();
               else
                  return *(it);
            }
         }


//////////////////////////////////////////////////////
// Graph class definition
//////////////////////////////////////////////////////

         class Graph
         {
         public:
            Graph() : nodes(0), edges(0), faces(0), dual_nodes(0), dual_edges(0) {};
            ~Graph() {};

            size_t num_nodes() const { return nodes.size(); };
            size_t num_edges() const { return edges.size(); };
            size_t num_faces() const { return faces.size(); };
            size_t num_dual_nodes() const { return dual_nodes.size(); };
            size_t num_dual_edges() const { return dual_edges.size(); };

            void print();

            Node* add_node(IDType id_, DataType weight_);
            Edge* add_edge(Node* tail_, Node* head_, DataType weight_);

            DualNode* add_dual_node(IDType id_);
            DualEdge* add_dual_edge(DualNode* tail_, DualNode* head_, DataType weight_, Edge* original_cross_edge_);

            Edge* find_edge(Node* v1, Node* v2);

            void planarize();

            void construct_dual();

            void mcpm();
            void assign_labels();
    
            template<class VEC> void read_labels(VEC& sol) const;
            std::vector<int> read_labels();

         private:
            std::list<Node*> nodes;
            std::list<Edge*> edges;
            std::list<Face*> faces;

            std::list<DualNode*> dual_nodes;
            std::list<DualEdge*> dual_edges;
         };



//////////////////////////////////////////////////////
// Basic functionality
//////////////////////////////////////////////////////

         inline Node* Graph::add_node(IDType id_, DataType weight_)
         {
            // Create new node and add to graph's list of nodes
            Node* v = new Node(id_, weight_);
            nodes.push_back(v);

            // Return pointer to the new node
            return v;
         }

         inline Edge* Graph::add_edge(Node* tail_, Node* head_, DataType weight_)
         {
            // Create new edge and add to graph's list of edges
            Edge* e = new Edge(tail_, head_, weight_);
            edges.push_back(e);

            // Add edge to both nodes' adjacency lists
            tail_->adj.push_back(e);
            head_->adj.push_back(e);

            // Return pointer to the new edge
            return e;
         }

         inline DualNode* Graph::add_dual_node(IDType id_)
         {
            // Create new dual node and add to graph's list of dual nodes
            DualNode* v = new DualNode(id_);
            dual_nodes.push_back(v);

            // Return pointer to the new dual node
            return v;
         }

         inline DualEdge* Graph::add_dual_edge(DualNode* tail_, DualNode* head_, DataType weight_, Edge* original_cross_edge_)
         {
            // Create new dual edge and add to graph's list of dual edges
            DualEdge* e = new DualEdge(tail_, head_, weight_, original_cross_edge_);
            dual_edges.push_back(e);

            // Add dual edge to both dual nodes' adjacency lists
            tail_->adj.push_back(e);
            head_->adj.push_back(e);

            // Return pointer to the new edge
            return e;
         }

         inline Edge* Graph::find_edge(Node* v1, Node* v2)
         // Returns edge connecting nodes v1 and v2 (NULL if it does not exist).
         {
            // Search v1's adjacency list for an edge connecting it to v2. Return that edge.
            for(std::list<Edge*>::iterator it=v1->adj.begin(); it!=v1->adj.end(); ++it)
            {
               if( (*it)->tail==v2 || (*it)->head==v2 )
               {
                  return *it;
               }
            }

            // Return NULL if the loop did not find one.
            return NULL;
         }


         inline void Graph::print()
         // Simple output of graph for debugging
         {
            std::cout << "Graph with " << num_nodes() << " nodes and "
                      << num_edges() << " edges. It has " << num_faces() << " faces.\n";

            // Iterate through the nodes of the graph
            for(std::list<Node*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
            {
               // Print current node's id and weight
               std::cout << (*it)->id << "\t[weight "<< (*it)->weight << ";\tlabel "
                         << (*it)->label << "]:\t";

               // For all edges in current node's adjacency list
               for(std::list<Edge*>::iterator jt = (*it)->adj.begin(); jt != (*it)->adj.end(); ++jt)
               {
                  // Get the destination of the current edge as seen from current node.
                  // Print destination id and weight of the edge
                  Node* v = get_dest(*it, *jt);
                  std::cout << v->id << " (" << (*jt)->weight << "), ";
               }
               std::cout << "\n";
            }
         }


//////////////////////////////////////////////////////
// Construction of planar embedding
//////////////////////////////////////////////////////

         inline void Graph::planarize()
         // Planarizes the graph. Sorts the adjacency lists of all nodes,
         // constructs faces and assigns the edges their faces
         {
            // Important:
            // The nodes need to have ids from 0 to num_nodes()-1
            // The graph needs to be biconnected
            // ToDo: Check for those conditions!

            //// Keep pointers to nodes in a vector
            std::vector<Node*> nodes_ptr (num_nodes());
            for(std::list<Node*>::iterator it=nodes.begin(); it!=nodes.end(); ++it)
            {
               nodes_ptr[(*it)->id] = *it;
            }

            //// Intiliaze graph in planarity code graph data structure.
            graphP g = gp_New();
            gp_InitGraph(g, num_nodes());
            for(std::list<Edge*>::iterator it=edges.begin(); it!=edges.end(); ++it)
            {
               Node* u = (*it)->tail;
               Node* v = (*it)->head;

               gp_AddEdge(g, u->id, 0, v->id, 0);
            }

            //// Invoke code that finds a planar embedding, i.e. sorts the adjacency lists
            if (gp_Embed(g, EMBEDFLAGS_PLANAR) == OK)
               gp_SortVertices(g);
            else
               std::cout << "Graph not planar\n"; // ToDo: Runtime error einfügen!

            //// Repopulate edges in the embedding order
            for (size_t i = 0; i < g->N; ++i)
            {
               Node* u = nodes_ptr[i];

               size_t j = g->G[i].link[1];
               while (j >= g->N)
               {
                  OPENGM_ASSERT(i != g->G[j].v); // ToDo: Was machen asserts?
                  OPENGM_ASSERT(g->G[j].v < g->N);

                  // Find the node and the connecting edge
                  Node* v = nodes_ptr[g->G[j].v];
                  std::list<Edge*>::iterator it = u->adj.begin();
                  while( (*it)->tail!=v && (*it)->head!=v && it!=u->adj.end())
                     ++it;
                  Edge* e = *it;
                  OPENGM_ASSERT(it != u->adj.end());

                  // Remove the edge from its current position, and insert at the back
                  u->adj.erase(it);
                  u->adj.push_back(e);

                  j = g->G[j].link[1];
               }
            }

            //// Clear faces
            // Pop all elements from the graph's list of faces and delete them
            while(!faces.empty())
            {
               delete faces.back();
               faces.pop_back();
            }

            // Set the face pointer of all edges to NULL
            for(std::list<Edge*>::iterator it=edges.begin(); it!=edges.end(); ++it)
            {
               (*it)->left_face = NULL;
               (*it)->right_face = NULL;
            }

            //// Construct faces
            for(std::list<Edge*>::iterator it=edges.begin(); it!=edges.end(); ++it) // Loop over all edges
            {
               Edge* e = (*it); // Current edge

               // Check if the left face of e has already been dealt with.
               // If not, construct it!
               Face* f = e->left_face;
               if(f==NULL)
               {
                  f = new Face(); // Create new face object
                  faces.push_back(f); // Add it to the graph's list of faces
                  e->left_face = f; // Set it as left face of current edge
                  f->edges.push_back(e); // Add e to f's list of edges

                  // Follow the orbit in FORWARD direction (i.e. starting with e's head)
                  Node* v = e->head;
                  Edge* ee = get_following_edge(e, v);
                  while(ee!=e) // If ee==e, we went the full circle
                  {
                     // Set f as face of ee, left or right depends on the formal direction of ee
                     if(v==ee->tail)
                        ee->left_face = f;
                     if(v==ee->head)
                        ee->right_face = f;
                     f->edges.push_back(ee); // add e to f's list of edges
                     v = get_dest(v, ee);
                     ee = get_following_edge(ee,v);
                  }
               }

               // Check if the right_face of e has already been dealt with.
               // If not, construct it!
               f = e->right_face;
               if (f==NULL)
               {
                  f = new Face(); // Create new face object
                  faces.push_back(f); // Add it to the graph's list of faces
                  e->right_face = f; // Set it as left face of current edge e
                  f->edges.push_back(e); // Add e to f's list of edges

                  // Follow the orbit in BACKWARD direction (i.e. starting with e's tail)
                  Node* v = e->tail;
                  Edge* ee = get_following_edge(e, v);
                  while(ee!=e) // If ee==e, we went the full circle
                  {
                     // Set f as face of ee, left or right depends on the formal direction of ee
                     if(v==ee->tail)
                        ee->left_face = f;
                     if(v==ee->head)
                        ee->right_face = f;
                     f->edges.push_back(ee); // add e to f's list of edges
                     v = get_dest(v, ee);
                     ee = get_following_edge(ee,v);
                  }
               }
            }

            //// Check: Do all edges have a left and a right face?
            for(std::list<Edge*>::iterator it=edges.begin(); it!=edges.end(); ++it)
            {
               OPENGM_ASSERT((*it)->left_face != NULL); // ToDo: Was machen asserts?
               OPENGM_ASSERT((*it)->right_face != NULL);
            }

            //// Check if genus = 0, i.e graph is planar
            std::cout<<num_nodes()<<" "<<num_edges()<< " "<<num_faces()<<std::endl;
            OPENGM_ASSERT(num_nodes()-num_edges()+num_faces() == 2);
            if(num_nodes()-num_edges()+num_faces() != 2)
               std::cout << "Genus not equal to zero\n"; // ToDO: Runtime error einfügen!

            //// Delete planarity code graph
            gp_Free(&g);
         }


//////////////////////////////////////////////////////
// Construction of planar embedding
//////////////////////////////////////////////////////

         inline void Graph::construct_dual()
         // Constructs the expanded dual of the graph
         {
            // Important:
            // G needs to be planarized in the sense that faces have to
            // be constructed and edges have to have faces assigned correclty
            // (it is not necessary that the adjacency lists are sorted)

            size_t cnt_dual_nodes = 0;

            // Loop over all edges
            for(std::list<Edge*>::iterator it=edges.begin(); it!=edges.end(); ++it)
            {
               // For the current edge of G, add two dual nodes, one for each face
               DualNode* u = add_dual_node(cnt_dual_nodes);
               DualNode* v = add_dual_node(cnt_dual_nodes + 1);
               cnt_dual_nodes += 2;

               // "Integrate" u into the left face: Connect it to all dual nodes already in that face and add
               // it to the face's list of dual nodes
               Face* lf = (*it)->left_face;
               for(std::list<DualNode*>::iterator jt=lf->dual_nodes.begin(); jt!=lf->dual_nodes.end(); ++jt)
               {
                  add_dual_edge(u, *jt, 0.0, NULL);
               }
               lf->dual_nodes.push_back(u);

               // "Integrate" u into the left face: Connect it to all dual nodes already in that face and add
               // it to the face's list of dual nodes
               Face* rf = (*it)->right_face;
               for(std::list<DualNode*>::iterator jt=rf->dual_nodes.begin(); jt!=rf->dual_nodes.end(); ++jt)
               {
                  add_dual_edge(v, *jt, 0.0, NULL);
               }
               rf->dual_nodes.push_back(v);

               // Connect the two nodes by a dual edge with weight=negative of the crossed edge's weight
               add_dual_edge(u, v, (-1.)*(*it)->weight, *it);
            }
         }


//////////////////////////////////////////////////////
// Max-Cut via a perfect matching
//////////////////////////////////////////////////////

         inline void Graph::mcpm()
         // Perform perfect matching in the dual graph
         {
            // Important:
            // Dual graph has to be constructed first
            // Dual nodes need to have id's from 0 to num_nodes()-1

            //// Read dual graph into Blossom V code
            // Note: Blossom V AddEdge assigns automatically edgeids 0,...,num_dual_edges()-1
            PerfectMatching PM(num_dual_nodes(), num_dual_edges());
            PerfectMatching::Options options;
            options.verbose = false;
            for(std::list<DualEdge*>::iterator it=dual_edges.begin(); it!=dual_edges.end(); ++it)
            {
               DualEdge* e = *it;
               PM.AddEdge(e->tail->id, e->head->id, e->weight);
            }

            //// Invoke perfect matching solver

            PM.options = options;
            PM.Solve();

            //// Read out solution, one dual edge at a time
            size_t i=0;
            for(std::list<DualEdge*>::iterator it=dual_edges.begin(); it!=dual_edges.end(); ++it)
            {
               DualEdge* e = *it;

               if(PM.GetSolution(i)==1) // Check solution from blossom v code
               {
                  // If dual edge is in the matching, tell it. If it crosses an original edge,
                  // tell the original edge that it is in the cut.
                  e->in_matching = true;
                  if(e->original_cross_edge != NULL)
                  {
                     e->original_cross_edge->in_cut = true;
                  }
               }
               else
               {
                  // If dual edge is NOT in the matching, tell it. If it crosses an original edge,
                  // tell the original edge that it is NOT in the cut
                  e->in_matching = false;
                  if(e->original_cross_edge != NULL)
                  {
                     e->original_cross_edge->in_cut = false;
                  }
               }

               ++i;
            }
         }

         inline void Graph::assign_labels()
         // Given a cut (i.e. edges have bool in_cut assigned), assign a labeling to the nodes
         {
            // Important:
            // A cut has to be given first, i.e. edges need to have the boolean in_cut set correctly

            //// Set all labels to -1 (meaning unassigned)
            for(std::list<Node*>::iterator it = nodes.begin(); it!=nodes.end(); ++it)
            {
               (*it)->label = -1;
            }

            // For a start, put an arbitrary node on a stack and label it arbitrarily
            std::stack<Node*> s;
            Node* u = nodes.front();
            u->label = 0;
            s.push(u);


            while(!s.empty()) // As long as stack is not empty
            {
               // Take top element from stack
               u = s.top();
               s.pop();

               // Go through all incident edges
               for(std::list<Edge*>::iterator it = u->adj.begin(); it!=u->adj.end(); ++it)
               {
                  Edge* e = *it; // Edge and...
                  Node* v = get_dest(u, e); // its destination (i.e. the neighbor)

                  // If the neighbor has not yet been seen, assign the respective label
                  // and put it on the stack.
                  if(v->label==-1)
                  {
                     s.push(v);

                     if(e->in_cut)
                        v->label = !(u->label);
                     else
                        v->label = u->label;
                  }
               }
            }
         }

         template<class VEC>
         void Graph::read_labels(VEC& sol) const
         {
            if(sol.size()<num_nodes())
                sol.resize(num_nodes(), -1);
            for(std::list<Node*>::const_iterator it = nodes.begin(); it!=nodes.end(); ++it){
               sol[(*it)->id] = (*it)->label;
            }
            return;
         }


         std::vector<int> Graph::read_labels()
         {
            // Important: Nodes need to have id's from 0 to num_nodes()-1, corresponding to the
            // openGM variable id

            std::vector<int> sol(num_nodes(), -1);

            for(std::list<Node*>::iterator it = nodes.begin(); it!=nodes.end(); ++it)
            {
               sol[(*it)->id] = (*it)->label;
            }

            return sol;
         }

      }
   }
} 

#endif // #ifndef OPENGM_PLANAR_MAXCUT_GRAPH_HXX