Improved documentation of bipgraph.h and added example_bipgraph.cpp

diff --git a/example.cpp b/example.cpp
deleted file mode 100644 (file)
index 47c83f3..0000000
--- a/example.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-/*  Copyright (C) 2006-2008  Joris Mooij  [joris dot mooij at tuebingen dot mpg dot de]
-    Radboud University Nijmegen, The Netherlands /
-    Max Planck Institute for Biological Cybernetics, Germany
-
-    This file is part of libDAI.
-
-    libDAI is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    libDAI is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with libDAI; if not, write to the Free Software
-    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
-*/
-
-
-#include <iostream>
-#include <dai/alldai.h>
-
-
-using namespace dai;
-using namespace std;
-
-
-int main( int argc, char *argv[] ) {
-    if ( argc != 2 ) {
-        cout << "Usage: " << argv[0] << " <filename.fg>" << endl << endl;
-        cout << "Reads factor graph <filename.fg> and runs" << endl;
-        cout << "Belief Propagation and JunctionTree on it." << endl << endl;
-        return 1;
-    } else {
-        FactorGraph fg;
-        fg.ReadFromFile(argv[1]);
-
-        size_t  maxiter = 10000;
-        double  tol = 1e-9;
-        size_t  verb = 1;
-
-        PropertySet opts;
-        opts.Set("maxiter",maxiter);
-        opts.Set("tol",tol);
-        opts.Set("verbose",verb);
-
-        JTree jt( fg, opts("updates",string("HUGIN")) );
-        jt.init();
-        jt.run();
-
-        BP bp(fg, opts("updates",string("SEQFIX"))("logdomain",false));
-        bp.init();
-        bp.run();
-
-        cout << "Exact single node marginals:" << endl;
-        for( size_t i = 0; i < fg.nrVars(); i++ )
-            cout << jt.belief(fg.var(i)) << endl;
-
-        cout << "Approximate (loopy belief propagation) single node marginals:" << endl;
-        for( size_t i = 0; i < fg.nrVars(); i++ )
-            cout << bp.belief(fg.var(i)) << endl;
-
-        cout << "Exact factor marginals:" << endl;
-        for( size_t I = 0; I < fg.nrFactors(); I++ )
-            cout << jt.belief(fg.factor(I).vars()) << endl;
-
-        cout << "Approximate (loopy belief propagation) factor marginals:" << endl;
-        for( size_t I = 0; I < fg.nrFactors(); I++ )
-            cout << bp.belief(fg.factor(I).vars()) << "=" << bp.beliefF(I) << endl;
-
-        cout << "Exact log partition sum: " << jt.logZ() << endl;
-        cout << "Approximate (loopy belief propagation) log partition sum: " << bp.logZ() << endl;
-    }
-
-    return 0;
-}

diff --git a/examples/example.cpp b/examples/example.cpp
new file mode 100644 (file)
index 0000000..47c83f3
--- /dev/null
+++ b/examples/example.cpp
@@ -0,0 +1,79 @@
+/*  Copyright (C) 2006-2008  Joris Mooij  [joris dot mooij at tuebingen dot mpg dot de]
+    Radboud University Nijmegen, The Netherlands /
+    Max Planck Institute for Biological Cybernetics, Germany
+
+    This file is part of libDAI.
+
+    libDAI is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    libDAI is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with libDAI; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+*/
+
+
+#include <iostream>
+#include <dai/alldai.h>
+
+
+using namespace dai;
+using namespace std;
+
+
+int main( int argc, char *argv[] ) {
+    if ( argc != 2 ) {
+        cout << "Usage: " << argv[0] << " <filename.fg>" << endl << endl;
+        cout << "Reads factor graph <filename.fg> and runs" << endl;
+        cout << "Belief Propagation and JunctionTree on it." << endl << endl;
+        return 1;
+    } else {
+        FactorGraph fg;
+        fg.ReadFromFile(argv[1]);
+
+        size_t  maxiter = 10000;
+        double  tol = 1e-9;
+        size_t  verb = 1;
+
+        PropertySet opts;
+        opts.Set("maxiter",maxiter);
+        opts.Set("tol",tol);
+        opts.Set("verbose",verb);
+
+        JTree jt( fg, opts("updates",string("HUGIN")) );
+        jt.init();
+        jt.run();
+
+        BP bp(fg, opts("updates",string("SEQFIX"))("logdomain",false));
+        bp.init();
+        bp.run();
+
+        cout << "Exact single node marginals:" << endl;
+        for( size_t i = 0; i < fg.nrVars(); i++ )
+            cout << jt.belief(fg.var(i)) << endl;
+
+        cout << "Approximate (loopy belief propagation) single node marginals:" << endl;
+        for( size_t i = 0; i < fg.nrVars(); i++ )
+            cout << bp.belief(fg.var(i)) << endl;
+
+        cout << "Exact factor marginals:" << endl;
+        for( size_t I = 0; I < fg.nrFactors(); I++ )
+            cout << jt.belief(fg.factor(I).vars()) << endl;
+
+        cout << "Approximate (loopy belief propagation) factor marginals:" << endl;
+        for( size_t I = 0; I < fg.nrFactors(); I++ )
+            cout << bp.belief(fg.factor(I).vars()) << "=" << bp.beliefF(I) << endl;
+
+        cout << "Exact log partition sum: " << jt.logZ() << endl;
+        cout << "Approximate (loopy belief propagation) log partition sum: " << bp.logZ() << endl;
+    }
+
+    return 0;
+}

diff --git a/examples/example_bipgraph.cpp b/examples/example_bipgraph.cpp
new file mode 100644 (file)
index 0000000..beca451
--- /dev/null
+++ b/examples/example_bipgraph.cpp
@@ -0,0 +1,34 @@
+#include <dai/bipgraph.h>
+
+using namespace std;
+using namespace dai;
+
+int main() {
+    vector<BipartiteGraph::Edge> edges;
+    edges.reserve( 5 );
+    edges.push_back( BipartiteGraph::Edge(0, 0) );
+    edges.push_back( BipartiteGraph::Edge(1, 0) );
+    edges.push_back( BipartiteGraph::Edge(2, 0) );
+    edges.push_back( BipartiteGraph::Edge(1, 1) );
+    edges.push_back( BipartiteGraph::Edge(2, 1) );
+    BipartiteGraph G( 3, 2, edges.begin(), edges.end() );
+
+    cout << "G has " << G.nr1() << " nodes of type 1, " << G.nr2() << " nodes of type 2 and " << G.nrEdges() << " edges." << endl << endl;
+
+    for( size_t n1 = 0; n1 < G.nr1(); n1++ ) {
+        cout << "Node " << n1 << " of type 1 has " << G.nb1(n1).size() << " neighbors:" << endl;
+        foreach( const BipartiteGraph::Neighbor &n2, G.nb1(n1) ) {
+            size_t _n2 = n2.iter;
+            size_t _n1 = n2.dual;
+            cout << "  the " << n2.iter << "'th neighbor is node " << n2 << " of type 2" << endl;
+
+            // The _n2'th neighbor of n1 is n2:
+            assert( G.nb1(n1)[_n2] == n2 );
+            // The _n1'th neighbor of n2 is n1:
+            assert( G.nb2(n2)[_n1] == n1 );
+            // n2 can be used as an abbreviation of n2.node:
+            assert( static_cast<size_t>(n2) == n2.node );
+        }
+        cout << endl;
+    }
+}

diff --git a/examples/example_bipgraph.out b/examples/example_bipgraph.out
new file mode 100644 (file)
index 0000000..d49fca3
--- /dev/null
+++ b/examples/example_bipgraph.out
@@ -0,0 +1,13 @@
+G has 3 nodes of type 1, 2 nodes of type 2 and 5 edges.
+
+Node 0 of type 1 has 1 neighbors:
+  the 0'th neighbor is node 0 of type 2
+
+Node 1 of type 1 has 2 neighbors:
+  the 0'th neighbor is node 0 of type 2
+  the 1'th neighbor is node 1 of type 2
+
+Node 2 of type 1 has 2 neighbors:
+  the 0'th neighbor is node 0 of type 2
+  the 1'th neighbor is node 1 of type 2
+