eoCounter?

eoEasyEA -- made it copyable again
eoEvalFunc -- added specialized eoEvalFuncCounter
eoEvolutionStrategy -- nothing much
eoGenContinue -- nothing
eoPop -- fixed nth_element_fitness
eoBitOp -- fixed error in xover
eoFileMonitor -- now appends always
eoParam -- worked around memory leak in MSC's strstream
eoParser -- changed -pconfig_file to @config_file
eoParser -- added messages instead of exception when required param is missing
eoStat -- added eoDistanceStat
t-eoFunctor -- don't know

eo/src/eo

@@ -109,6 +109,8 @@
 
 // aliens
 //#include <eoNonUniform.h>
+#include <eoCounter.h>
+#include <utils/eoParser.h>
 
 //-----------------------------------------------------------------------------
 // to be continued ...

eo/src/eoEasyEA.h

@@ -55,9 +55,9 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
          eoReplacement<EOT>& _replace     
      ) : continuator(_continuator), 
          eval(_eval),
-         selectTransform(0),
+         selectTransform(dummySelect, dummyTransform),
          breed(_breed),
-         mergeReduce(0),
+         mergeReduce(dummyMerge, dummyReduce),
          replace(_replace)
          {}
 
@@ -70,9 +70,9 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
          eoReduce<EOT>& _reduce
      ) : continuator(_continuator), 
          eval(_eval),
-         selectTransform(0),
+         selectTransform(dummySelect, dummyTransform),
          breed(_breed),
-         mergeReduce(new eoMergeReduce<EOT>(_merge, _reduce)),
+         mergeReduce(_merge, _reduce),
          replace(mergeReduce)
          {}
 
@@ -85,9 +85,9 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
          eoReplacement<EOT>& _replace     
      ) : continuator(_continuator), 
          eval(_eval),
-         selectTransform(new eoSelectTransform<EOT>(_select, _transform)),
+         selectTransform(_select, _transform),
          breed(selectTransform),
-         mergeReduce(0),
+         mergeReduce(dummyMerge, dummyReduce),
          replace(_replace)
          {}
 
@@ -101,17 +101,15 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
          eoReduce<EOT>&    _reduce
      ) : continuator(_continuator), 
          eval(_eval),
-         selectTransform(new eoSelectTransform<EOT>(_select, _transform)),
+         selectTransform(_select, _transform),
-         breed(*selectTransform),
+         breed(selectTransform),
-         mergeReduce(new eoMergeReduce<EOT>(_merge, _reduce)),
+         mergeReduce(_merge, _reduce),
-         replace(*mergeReduce)
+         replace(mergeReduce)
          {}
 
 
 
         
-     ~eoEasyEA() { delete selectTransform; delete mergeReduce; }
-
   /// Apply a few generation of evolution to the population.
   virtual void operator()(eoPop<EOT>& _pop) 
   {
@@ -146,16 +144,27 @@ template<class EOT> class eoEasyEA: public eoAlgo<EOT>
   
  private:
 
-     /// dissallow copying cuz of pointer stuff
+  // If selectTransform needs not be used, dummySelect and dummyTransform are used
-     eoEasyEA(const eoEasyEA&);
+  // to instantiate it.
-     /// dissallow copying cuz of pointer stuff
+     class eoDummySelect : public eoSelect<EOT>
-     const eoEasyEA& operator=(const eoEasyEA&);
+     { public : void operator()(const eoPop<EOT>&, eoPop<EOT>&) {} } dummySelect;
+
+     class eoDummyTransform : public eoTransform<EOT>
+     { public : void operator()(eoPop<EOT>&) {} } dummyTransform;
+
 
   eoContinue<EOT>&          continuator;
   eoEvalFunc<EOT>&          eval;
-  eoSelectTransform<EOT>*   selectTransform;
+  
+  eoSelectTransform<EOT>    selectTransform;
   eoBreed<EOT>&             breed;
-  eoMergeReduce<EOT>*       mergeReduce;
+  
+  // If mergeReduce needs not be used, dummyMerge and dummyReduce are used
+  // to instantiate it.
+  eoNoElitism<EOT>          dummyMerge;
+  eoTruncate<EOT>           dummyReduce;
+
+  eoMergeReduce<EOT>        mergeReduce;
   eoReplacement<EOT>&       replace;
 };
 

eo/src/eoEvalFunc.h

@@ -44,4 +44,30 @@ template<class EOT> class eoEvalFunc : public eoUnaryFunctor<void, EOT&>
 	typedef typename EOT::Fitness EOFitT;
 };
 
+/** 
+Counts the number of evaluations actually performed, thus checks first
+if it has to evaluate.. etc.
+*/
+
+#include <utils/eoParam.h>
+template<class EOT> class eoEvalFuncCounter : public eoEvalFunc<EOT>, public eoValueParam<unsigned long>
+{
+    public :
+        eoEvalFuncCounter(eoEvalFunc<EOT>& _func, std::string _name = "eval_counter") 
+            : func(_func), eoValueParam<unsigned long>(0, _name) {}
+
+        void operator()(EOT& _eo)
+        {
+            if (_eo.invalid())
+            {
+                value()++;
+                func(_eo);
+            }
+        }
+
+    private :
+        eoEvalFunc<EOT>& func;
+};
+
+
 #endif

eo/src/eoEvolutionStrategy.h

@@ -81,6 +81,20 @@ class eoEvolutionStrategy: public eoAlgo<EOT>
      eoEasyEA<EOT> easyEA;
 };
 
+template <class EOT>
+eoEvolutionStrategy<EOT> make_es(eoContinue<EOT>& _continuator,
+         eoEvalFunc<EOT>& _eval, 
+         eoGOpSelector<EOT>&  _opSel,
+         float _lambdaRate,
+         bool _comma)
+
+{
+    if (_comma)
+        return eoEvolutionStrategy<EOT>(_continuator, _eval, _opSel, _lambdaRate, eoEvolutionStrategy<EOT>::comma_strategy());
+    //else
+    return eoEvolutionStrategy<EOT>(_continuator, _eval, _opSel, _lambdaRate, eoEvolutionStrategy<EOT>::plus_strategy());
+}
+
 //-----------------------------------------------------------------------------
 
 #endif eoSelectTransformReduce_h

eo/src/eoGenContinue.h

@@ -36,13 +36,13 @@ class eoGenContinue: public eoContinue<EOT>
 public:
 
 	/// Ctor for setting a
-	eoGenContinue( unsigned _totalGens)
+	eoGenContinue( unsigned long _totalGens)
 	  : repTotalGenerations( _totalGens ), 
       thisGenerationPlaceHolder(0),
 	  thisGeneration(thisGenerationPlaceHolder){};
 	
     /// Ctor for enabling the save/load the no. of generations counted
-	eoGenContinue( unsigned _totalGens, unsigned& _currentGen)
+	eoGenContinue( unsigned long _totalGens, unsigned long& _currentGen)
 	  : repTotalGenerations( _totalGens ), 
       thisGenerationPlaceHolder(0),
 	  thisGeneration(_currentGen){};
@@ -57,21 +57,21 @@ public:
 
 	/** Sets the number of generations to reach 
 	    and sets the current generation to 0 (the begin)*/
-	virtual void totalGenerations( unsigned _tg ) { 
+	virtual void totalGenerations( unsigned long _tg ) { 
 	  repTotalGenerations = _tg; 
 	  thisGeneration = 0;
 	};
 
 	/** Returns the number of generations to reach*/
-	virtual unsigned totalGenerations( ) 
+	virtual unsigned long totalGenerations( ) 
     {  
 	  return repTotalGenerations; 
 	};
     
 private:
-	unsigned repTotalGenerations;
+	unsigned long repTotalGenerations;
-    unsigned thisGenerationPlaceHolder;
+    unsigned long thisGenerationPlaceHolder;
-    unsigned& thisGeneration;
+    unsigned long& thisGeneration;
 };
 
 #endif

eo/src/eoPop.h

@@ -113,11 +113,12 @@ class eoPop: public vector<EOT>, public eoObject, public eoPersistent
   struct GetFitness { Fitness operator()(const EOT& _eo) const { return _eo.fitness(); } };
   
   Fitness nth_element_fitness(int which) const
-  {
+  { // probably not the fastest way to do this, but what the heck
+
       vector<Fitness> fitness(size());
       std::transform(begin(), end(), fitness.begin(), GetFitness());
 
-      vector<Fitness>::iterator it = fitness.begin();
+      vector<Fitness>::iterator it = fitness.begin() + which;
       std::nth_element(fitness.begin(), it, fitness.end(), greater<Fitness>());
       return *it;
   }

eo/src/ga/eoBitOp.h

@@ -192,7 +192,7 @@ template<class Chrom> class eoBinCrossover: public eoQuadraticOp<Chrom>
     {
       unsigned site = rng.random(min(chrom1.size(), chrom2.size()));
 
-      if (std::equal(chrom1.begin(), chrom1.begin()+site, chrom2.begin()))
+      if (!std::equal(chrom1.begin(), chrom1.begin()+site, chrom2.begin()))
       {
 
         swap_ranges(chrom1.begin(), chrom1.begin() + site, chrom2.begin());
@@ -267,6 +267,7 @@ template<class Chrom> class eoBinNxOver: public eoQuadraticOp<Chrom>
 };
 
 
+
 /** eoBinGxOver --> gene crossover 
 \class eoBinGxOver eoBitOp.h ga/eoBitOp.h
 \ingroup bitstring

eo/src/utils/eoFileMonitor.cpp

@@ -8,21 +8,8 @@
 
 using namespace std;
 
-eoMonitor& eoFileMonitor::operator()(void)
+void eoFileMonitor::printHeader(std::ostream& os)
 {
-    if (firsttime)
-    {
-        firsttime = false;
-
-        // create file
-        ofstream os(filename.c_str()); 
-
-        if (!os)
-        {
-            string str = "eoFileMonitor: Could not open " + filename;
-            throw runtime_error(str);
-        }
-
     iterator it = vec.begin();
 
     os << (*it)->longName();
@@ -33,9 +20,25 @@ eoMonitor& eoFileMonitor::operator()(void)
     {
         os << ',' << (*it)->longName();
     }
+    os << '\n';
 }
-    // ok, now the real saving. append to file
 
+void eoFileMonitor::printHeader()
+{
+    // create file
+    ofstream os(filename.c_str()); 
+
+    if (!os)
+    {
+        string str = "eoFileMonitor: Could not open " + filename;
+        throw runtime_error(str);
+    }
+    
+    printHeader(os);
+}
+
+eoMonitor& eoFileMonitor::operator()(void)
+{
     ofstream os(filename.c_str(), ios_base::app);
 
     if (!os)
@@ -44,15 +47,21 @@ eoMonitor& eoFileMonitor::operator()(void)
         throw runtime_error(str);
     }
 
+    return operator()(os);
+}
+
+eoMonitor& eoFileMonitor::operator()(std::ostream& os)
+{
     iterator it = vec.begin();
 
-    os << '\n' << (*it)->getValue();
+    os << (*it)->getValue();
     
     for(++it; it != vec.end(); ++it)
     {
         os << ',' << (*it)->getValue();
     }
 
+    os << '\n';
     return *this;
 }
 

eo/src/utils/eoFileMonitor.h

@@ -38,13 +38,17 @@
 class eoFileMonitor : public eoMonitor
 {
 public :
-    eoFileMonitor(std::string _filename, std::string _delim = ",") : filename(_filename), delim(_delim), firsttime(true) {}
+    eoFileMonitor(std::string _filename, std::string _delim = ",") : filename(_filename), delim(_delim) {}
     eoMonitor& operator()(void);
 
+    eoMonitor& operator()(std::ostream& os);
+
+    void printHeader(void);
+    virtual void printHeader(std::ostream& os);
+
 private :
-    std::string filename;
     std::string delim;
-    bool firsttime;
+    std::string filename;
 };
 
 #endif

eo/src/utils/eoParam.h

@@ -153,7 +153,8 @@ public :
 
     std::string getValue(void) const
     {
-        std::ostrstream os;
+        char buf[1024];
+        std::ostrstream os(buf, 1023);
         os << repValue;
         os << std::ends;
         return os.str(); 

eo/src/utils/eoParser.cpp

@@ -39,7 +39,6 @@ eoParameterLoader::~eoParameterLoader()
 eoParser::eoParser ( int _argc, char **_argv , string _programDescription, string _lFileParamName, char _shortHand) : 
     programName( _argv[0]),  
     programDescription( _programDescription), 
-    parameterFile("", _lFileParamName, "Load using a configuration file", _shortHand),
     needHelp(false, "help", "Prints this message", 'h')
 {
     strstream stream;
@@ -51,15 +50,7 @@ eoParser::eoParser ( int _argc, char **_argv , string _programDescription, strin
 
     readFrom(stream);
 
-    processParam(parameterFile);
     processParam(needHelp);
-
-    if (parameterFile.getValue() != parameterFile.defValue())
-    {
-        ifstream is (parameterFile.getValue().c_str());
-
-        readFrom(is);
-    }
 }
 
 void eoParser::processParam(eoParam& param, std::string section)
@@ -72,7 +63,8 @@ void eoParser::doRegisterParam(eoParam& param) const
 {
     if (param.required() && !isItThere(param))
     {
-        throw std::runtime_error("required parameter missing");
+        string msg = "required parameter: " + param.longName() + " missing";
+        messages.push_back(msg);
     }
 
     pair<bool, string> value = getValue(param);
@@ -165,6 +157,24 @@ void eoParser::readFrom(istream& is)
               shortNameMap[str[1]] = value;
           }
       }
+      if (str[0] == '@')
+      { // read response file
+         string filename(str.begin() + 1, str.end());
+        
+        ifstream ifs (filename.c_str());
+
+        ifs.peek(); // check if it exists
+
+        if (!ifs)
+        {
+            string msg = "Could not open response file: " + filename;
+            throw runtime_error(msg);
+        }
+
+        // read and overwrite
+        readFrom(ifs);
+        break; // stop reading command line
+      }
   }
 
   updateParameters();
@@ -214,6 +224,13 @@ void eoParser::printOn(ostream& os) const
 
 void eoParser::printHelp(ostream& os) 
 {
+    if (needHelp.value() == false && !messages.empty())
+    {
+        std::copy(messages.begin(), messages.end(), ostream_iterator<string>(os, "\n"));
+        messages.clear();
+        return;
+    }
+
     // print program name and description
     os << this->programName <<": "<< programDescription << "\n\n";
 
@@ -253,6 +270,7 @@ void eoParser::printHelp(ostream& os)
       os <<". By default: "<<p->second->defValue() << '\n';
     } // for p
 
+    os << "\n@param_file \t defines a file where the parameters are stored\n";
     os << '\n';
 
 }

eo/src/utils/eoParser.h

@@ -127,7 +127,7 @@ public:
   std::string className(void) const { return "Parser"; }
 
   /// true if the user made an error or asked for help
-  bool userNeedsHelp(void) const { return needHelp.value(); }
+  bool userNeedsHelp(void) const { return needHelp.value() || !messages.empty(); }
 
   /**
    * Prints an automatic help in the specified output using the information
@@ -157,8 +157,9 @@ private:
   map<char, string>   shortNameMap;
   map<string, string> longNameMap;
 
-  eoValueParam<string> parameterFile;
   eoValueParam<bool>   needHelp;
+
+  mutable std::vector<std::string> messages;
 };
 
 

eo/src/utils/eoStat.h

@@ -104,19 +104,76 @@ public :
 };
 
 template <class EOT>
-class eoBestFitnessStat : public eoStat<EOT, typename EOT::Fitness >
+class eoNthElementFitnessStat : public eoStat<EOT, typename EOT::Fitness >
 {
 public :
     typedef typename EOT::Fitness Fitness;
 
-    eoBestFitnessStat(std::string _description = "Best Fitness") : eoStat<EOT, Fitness>(Fitness(), _description) {}
+    eoNthElementFitnessStat(int _which, std::string _description = "nth element fitness") : which(_which), eoStat<EOT, Fitness>(Fitness(), _description) {}
 
     virtual void operator()(const eoPop<EOT>& _pop)
     {
-        value() = _pop.nth_element_fitness(0);
+        if (which > _pop.size())
+            throw logic_error("fitness requested of element outside of pop");
+
+        value() = _pop.nth_element_fitness(which);
+    }
+
+private :
+    unsigned which;
+};
+
+
+template <class EOT>
+class eoBestFitnessStat : public eoNthElementFitnessStat<EOT>
+{
+public :
+    typedef typename EOT::Fitness Fitness;
+
+    eoBestFitnessStat(std::string _description = "Best Fitness") : eoNthElementFitnessStat<EOT>(0, _description) {}
+};
+
+template <class EOT>
+class eoDistanceStat : public eoStat<EOT, double>
+{
+public :
+    eoDistanceStat(std::string _name = "distance") : eoStat<EOT, double>(0.0, _name) {}
+
+    template <class T>
+    double distance(T a, T b)
+    {
+        T res = a-b;
+        return res < 0? -res : res;
+    }
+
+    double distance(bool a, bool b)
+    {
+        return (a==b)? 0 : 1;
+    }
+
+    void operator()(const eoPop<EOT>& _pop)
+    {
+        double& v = value();
+        v = 0.0;
+
+        for (unsigned i = 0; i < _pop.size(); ++i)
+        {
+            for (unsigned j = 0; j < _pop.size(); ++j)
+            {
+                for (unsigned k = 0; k < _pop[i].size(); ++k)
+                {
+                    v += distance(_pop[i][k], _pop[j][k]);
+                }
+            }
+        }
+
+        double sz = _pop.size();
+        v /= sz * sz * _pop[0].size();
     }
 };
 
+
+
 /*
 template <class EOT>
 class eoStdevStat : public eoStat<EOT, double >

eo/test/t-eoFunctor.cpp

@@ -18,7 +18,6 @@ public :
 };
 
 #include <iostream>
-#include <eoTranspose.h>
 #include <eoFixedLength.h>
 #include <eoVariableLength.h>
 
@@ -46,8 +45,5 @@ int main(void)
     eo.push_back(1);
     eo.push_back(2);
 
-    eoTranspose<EoType> transpose;
-    transpose(eo);
-
     return 1;
 }

eo/win/eo.dsp

@@ -41,7 +41,7 @@ RSC=rc.exe
 # PROP Intermediate_Dir "Release"
 # PROP Target_Dir ""
 # ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_MBCS" /D "_LIB" /YX /FD /c
-# ADD CPP /nologo /W3 /GR /GX /O2 /I "../src" /D "WIN32" /D "NDEBUG" /D "_MBCS" /D "_LIB" /FD /c
+# ADD CPP /nologo /W3 /GR /GX /O2 /I "../src" /I "eo/src" /D "WIN32" /D "NDEBUG" /D "_MBCS" /D "_LIB" /FD /c
 # SUBTRACT CPP /YX
 # ADD BASE RSC /l 0xc0a /d "NDEBUG"
 # ADD RSC /l 0xc0a /d "NDEBUG"

eo/win/t_eoFunctor.dsp

@@ -41,7 +41,7 @@ RSC=rc.exe
 # PROP Intermediate_Dir "t_eoFunctor___Win32_Release"
 # PROP Target_Dir ""
 # ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
-# ADD CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
+# ADD CPP /nologo /W3 /GX /O2 /I "../src" /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
 # ADD BASE RSC /l 0x409 /d "NDEBUG"
 # ADD RSC /l 0x409 /d "NDEBUG"
 BSC32=bscmake.exe