Misc small changes:

* Renamed DEBUG to DAI_DEBUG to avoid conflicts
* Renamed variable _N in mr.* for compatibility with g++ under cygwin

diff --git a/ChangeLog b/ChangeLog
index c352fd0..396f393 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,7 +1,15 @@
 libDAI-0.2.2 (2008-??-??)
 -------------------------
-
-* Contributions by Christian, resulting in vast speed and memory improvements
+ 
+- Renamed DEBUG to DAI_DEBUG to avoid conflicts
+* Contributions by ???:
+  - Renamed variable _N in mr.* for compatibility with g++ under cygwin
+* Contributions by Giuseppe Passino:
+  - removed "using namespace std;" from header files - bad practice
+  - moved header files in include/dai and sources in src
+  - changed #ifndefs to GNU style
+  - added extra warning checks (-W -Wextra) and fixed resulting warnings
+* Contributions by Christian Wojek, resulting in vast speed and memory improvements
   for large factor graphs:
   - Sparse implementation of nodes->edge conversion table _E12ind in bipgraph.h
   - New FactorGraph constructor that constructs from given ranges of factors

diff --git a/Makefile b/Makefile
index f68a0f6..ea849fb 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -30,7 +30,7 @@ BOOSTFLAGS = -lboost_program_options
 CC = g++
 
 # Flags for the C++ compiler
-CCFLAGS = -Wall -W -Wextra -fpic -g -DDEBUG -I./include -Llib -O3 #-static #-pg #-DVERBOSE
+CCFLAGS = -Wall -W -Wextra -fpic -g -DDAI_DEBUG -I./include -Llib -O3 #-static #-pg #-DVERBOSE
 
 # To enable the Matlab interface, define WITH_MATLAB = yes
 WITH_MATLAB = 
@@ -38,7 +38,7 @@ ifdef WITH_MATLAB
 # Replace the following by the directory where Matlab has been installed
 MATLABDIR = /opt/matlab/bin
 MEX = $(MATLABDIR)/mex
-MEXFLAGS = -g -I. -DDEBUG -largeArrayDims #-g means debugging
+MEXFLAGS = -g -I. -DDAI_DEBUG -largeArrayDims #-g means debugging
 endif
 
 # Replace the following with the extension of compiled MEX files on this platform, e.g. .mexglx for x86

diff --git a/include/dai/factor.h b/include/dai/factor.h
index 5978943..5f13988 100644 (file)
--- a/include/dai/factor.h
+++ b/include/dai/factor.h
@@ -65,7 +65,7 @@ template <typename T> class TFactor {
 
         // Construct Factor from VarSet and TProb<T>
         TFactor( const VarSet& ns, const TProb<T> p ) : _vs(ns), _p(p) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( _vs.stateSpace() == _p.size() );
 #endif
         }
@@ -89,7 +89,7 @@ template <typename T> class TFactor {
         TProb<T> & p() { return _p; }
         const VarSet & vars() const { return _vs; }
         size_t stateSpace() const { 
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( _vs.stateSpace() == _p.size() );
 #endif
             return _p.size();
@@ -122,7 +122,7 @@ template <typename T> class TFactor {
         TFactor<T> operator* (const TFactor<T>& Q) const;
         TFactor<T>& operator*= (const TFactor<T>& Q) { return( *this = (*this * Q) ); }
         TFactor<T> operator+ (const TFactor<T>& Q) const {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( Q._vs == _vs );
 #endif
             TFactor<T> sum(*this); 
@@ -130,7 +130,7 @@ template <typename T> class TFactor {
             return sum; 
         }
         TFactor<T> operator- (const TFactor<T>& Q) const {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( Q._vs == _vs );
 #endif
             TFactor<T> sum(*this); 
@@ -138,14 +138,14 @@ template <typename T> class TFactor {
             return sum; 
         }
         TFactor<T>& operator+= (const TFactor<T>& Q) { 
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( Q._vs == _vs );
 #endif
             _p += Q._p;
             return *this;
         }
         TFactor<T>& operator-= (const TFactor<T>& Q) { 
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( Q._vs == _vs );
 #endif
             _p -= Q._p;
@@ -168,7 +168,7 @@ template <typename T> class TFactor {
         }
 
         TFactor<T> divided_by( const TFactor<T>& denom ) const { 
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( denom._vs == _vs );
 #endif
             TFactor<T> quot(*this); 
@@ -177,7 +177,7 @@ template <typename T> class TFactor {
         }
 
         TFactor<T>& divide( const TFactor<T>& denom ) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( denom._vs == _vs );
 #endif
             _p /= denom._p;
@@ -253,7 +253,7 @@ template <typename T> class TFactor {
             if( x._vs.empty() || y._vs.empty() )
                 return -1;
             else {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
                 assert( x._vs == y._vs );
 #endif
                 return dist( x._p, y._p, dt );
@@ -265,7 +265,7 @@ template <typename T> class TFactor {
 
 
 template<typename T> TFactor<T> TFactor<T>::part_sum(const VarSet & ns) const {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
     assert( ns << _vs );
 #endif
 
@@ -305,7 +305,7 @@ template<typename T> Complex KL_dist(const TFactor<T> & P, const TFactor<T> & Q)
     if( P._vs.empty() || Q._vs.empty() )
         return -1;
     else {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
         assert( P._vs == Q._vs );
 #endif
         return KL_dist( P._p, Q._p );
@@ -315,7 +315,7 @@ template<typename T> Complex KL_dist(const TFactor<T> & P, const TFactor<T> & Q)
 
 // calculate N(psi, i, j)
 template<typename T> T TFactor<T>::strength( const Var &i, const Var &j ) const {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
     assert( _vs && i );
     assert( _vs && j );
     assert( i != j );

diff --git a/include/dai/mr.h b/include/dai/mr.h
index 707d4f6..153b83a 100644 (file)
--- a/include/dai/mr.h
+++ b/include/dai/mr.h
@@ -62,7 +62,7 @@ class MR : public DAIAlgFG {
         InitType Inits() const { return GetPropertyAs<InitType>("inits"); }
 
         MR( const FactorGraph & fg, const Properties &opts );
-        void init(size_t _N, double *_w, double *_th);
+        void init(size_t Nin, double *_w, double *_th);
         void makekindex();
         void read_files();
         void init_cor();
@@ -106,7 +106,7 @@ class sub_nb {
     public:
         // construct full subset containing nr_elmt elements
         sub_nb(size_t nr_elmt) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( nr_elmt < sizeof(size_t) / sizeof(char) * 8 );
 #endif
             bits = nr_elmt;
@@ -152,7 +152,7 @@ class sub_nb {
                     else
                         i--;
                 }
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( bit < bits );
 #endif
             return bit;

diff --git a/include/dai/prob.h b/include/dai/prob.h
index 1291242..65d86de 100644 (file)
--- a/include/dai/prob.h
+++ b/include/dai/prob.h
@@ -145,7 +145,7 @@ template <typename T> class TProb {
 
         /// Division by T x
         TProb<T>& operator/= (T x) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( x != 0.0 );
 #endif
             for( size_t i = 0; i < size(); i++ )
@@ -162,7 +162,7 @@ template <typename T> class TProb {
 
         /// Pointwise multiplication with q
         TProb<T>& operator*= (const TProb<T> & q) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             for( size_t i = 0; i < size(); i++ )
@@ -172,7 +172,7 @@ template <typename T> class TProb {
         
         /// Return product of *this with q
         TProb<T> operator* (const TProb<T> & q) const {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             TProb<T> prod( *this );
@@ -182,7 +182,7 @@ template <typename T> class TProb {
 
         /// Pointwise addition with q
         TProb<T>& operator+= (const TProb<T> & q) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             for( size_t i = 0; i < size(); i++ )
@@ -192,7 +192,7 @@ template <typename T> class TProb {
         
         /// Pointwise subtraction of q
         TProb<T>& operator-= (const TProb<T> & q) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             for( size_t i = 0; i < size(); i++ )
@@ -202,7 +202,7 @@ template <typename T> class TProb {
         
         /// Return sum of *this and q
         TProb<T> operator+ (const TProb<T> & q) const {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             TProb<T> sum( *this );
@@ -212,7 +212,7 @@ template <typename T> class TProb {
         
         /// Return *this minus q
         TProb<T> operator- (const TProb<T> & q) const {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             TProb<T> sum( *this );
@@ -222,11 +222,11 @@ template <typename T> class TProb {
 
         /// Pointwise division by q
         TProb<T>& operator/= (const TProb<T> & q) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             for( size_t i = 0; i < size(); i++ ) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
 //              assert( q[i] != 0.0 );
 #endif
                 if( q[i] == 0.0 )       // FIXME
@@ -239,7 +239,7 @@ template <typename T> class TProb {
         
         /// Pointwise division by q, division by zero yields infinity
         TProb<T>& divide (const TProb<T> & q) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             for( size_t i = 0; i < size(); i++ )
@@ -249,7 +249,7 @@ template <typename T> class TProb {
         
         /// Return quotient of *this with q
         TProb<T> operator/ (const TProb<T> & q) const {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( size() == q.size() );
 #endif
             TProb<T> quot( *this );
@@ -266,7 +266,7 @@ template <typename T> class TProb {
                     inv._p.push_back( _p[i] == 0.0 ? 0.0 : 1.0 / _p[i] );
             else
                 for( size_t i = 0; i < size(); i++ ) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
                     assert( _p[i] != 0.0 );
 #endif
                     inv._p.push_back( 1.0 / _p[i] );
@@ -333,7 +333,7 @@ template <typename T> class TProb {
 
         /// Return distance of p and q
         friend Real dist( const TProb<T> & p, const TProb<T> & q, DistType dt ) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( p.size() == q.size() );
 #endif
             Real result = 0.0;
@@ -362,7 +362,7 @@ template <typename T> class TProb {
 
         /// Return (complex) Kullback-Leibler distance with q
         friend Complex KL_dist( const TProb<T> & p, const TProb<T> & q ) {
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( p.size() == q.size() );
 #endif
             Complex result = 0.0;
@@ -412,7 +412,7 @@ template <typename T> class TProb {
                 Z = totalSum();
             else if( norm == NORMLINF )
                 Z = maxAbs();
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( Z != 0.0 );
 #endif
             T Zi = 1.0 / Z;
@@ -428,7 +428,7 @@ template <typename T> class TProb {
                 Z = totalSum();
             else if( norm == NORMLINF )
                 Z = maxAbs();
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             assert( Z != 0.0 );
 #endif
             Z = 1.0 / Z;

diff --git a/include/dai/properties.h b/include/dai/properties.h
index f871d62..a235a70 100644 (file)
--- a/include/dai/properties.h
+++ b/include/dai/properties.h
@@ -49,7 +49,7 @@ class Properties : public std::map<PropertyKey, PropertyValue> {
         /// Gets a property
         const PropertyValue & Get(const PropertyKey &key) const { 
             Properties::const_iterator x = find(key); 
-#ifdef DEBUG            
+#ifdef DAI_DEBUG            
             if( x == this->end() )
                 std::cerr << "Get cannot find property " << key << std::endl;
 #endif

diff --git a/include/dai/varset.h b/include/dai/varset.h
index 7c6cf61..d60d4dd 100644 (file)
--- a/include/dai/varset.h
+++ b/include/dai/varset.h
@@ -92,7 +92,7 @@ class VarSet : private std::set<Var> {
 
         /// Return statespace, i.e. the product of the number of states of each variable
         size_t stateSpace() const { 
-#ifdef DEBUG
+#ifdef DAI_DEBUG
             size_t x = 1;
             for( const_iterator i = begin(); i != end(); ++i )
                 x *= i->states();

diff --git a/src/mr.cpp b/src/mr.cpp
index 78ba6ab..5c6efee 100644 (file)
--- a/src/mr.cpp
+++ b/src/mr.cpp
@@ -59,10 +59,10 @@ bool MR::checkProperties() {
 
 
 // init N, con, nb, tJ, theta
-void MR::init(size_t _N, double *_w, double *_th) {
+void MR::init(size_t Nin, double *_w, double *_th) {
     size_t i,j;
     
-    N = _N;
+    N = Nin;
 
     con.resize(N);
     nb.resize(N);
@@ -624,15 +624,15 @@ MR::MR( const FactorGraph &fg, const Properties &opts ) : DAIAlgFG(fg, opts), su
         return;
 
     // create w and th
-    size_t _N = fg.nrVars();
+    size_t Nin = fg.nrVars();
 
-    double *w = new double[_N*_N];
-    double *th = new double[_N];
+    double *w = new double[Nin*Nin];
+    double *th = new double[Nin];
     
-    for( size_t i = 0; i < _N; i++ ) {
+    for( size_t i = 0; i < Nin; i++ ) {
         th[i] = 0.0;
-        for( size_t j = 0; j < _N; j++ )
-            w[i*_N+j] = 0.0;
+        for( size_t j = 0; j < Nin; j++ )
+            w[i*Nin+j] = 0.0;
     }
 
     for( size_t I = 0; I < fg.nrFactors(); I++ ) {
@@ -645,15 +645,15 @@ MR::MR( const FactorGraph &fg, const Properties &opts ) : DAIAlgFG(fg, opts), su
             VarSet::const_iterator jit = psi.vars().begin();
             size_t j = fg.findVar( *(++jit) );
 
-            w[i*_N+j] += 0.25 * log(psi[3] * psi[0] / (psi[2] * psi[1])); 
-            w[j*_N+i] += 0.25 * log(psi[3] * psi[0] / (psi[2] * psi[1])); 
+            w[i*Nin+j] += 0.25 * log(psi[3] * psi[0] / (psi[2] * psi[1])); 
+            w[j*Nin+i] += 0.25 * log(psi[3] * psi[0] / (psi[2] * psi[1])); 
 
             th[i] += 0.25 * log(psi[3] / psi[2] * psi[1] / psi[0]);
             th[j] += 0.25 * log(psi[3] / psi[1] * psi[2] / psi[0]);
         }
     }
     
-    init(_N, w, th);
+    init(Nin, w, th);
 
     delete th;
     delete w;