Ajout du neutral degree, et correction Royal Road

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1790 331e1502-861f-0410-8da2-ba01fb791d7f

trunk/paradiseo-mo/src/algo/moRandomSearch.h

@@ -58,7 +58,7 @@ public:
    */
   moRandomSearch(eoInit<EOT> & _init, eoEvalFunc<EOT>& _fullEval, unsigned _nbSolMax):
     moLocalSearch<Neighbor>(explorer, trueCont, _fullEval),
-    explorer(_init, _fullEval, _nbSolMax - 1)
+      explorer(_init, _fullEval, _nbSolMax>0?_nbSolMax - 1:0)
   {}
   
   /**
@@ -69,7 +69,7 @@ public:
    */
   moRandomSearch(eoInit<EOT> & _init, eoEvalFunc<EOT>& _fullEval, unsigned _nbSolMax, moContinuator<Neighbor>& _cont):
     moLocalSearch<Neighbor>(explorer, _cont, _fullEval),
-    explorer(_init, _fullEval, _nbSolMax - 1)
+    explorer(_init, _fullEval, _nbSolMax>0?_nbSolMax - 1:0)
   {}
   
 private:

trunk/paradiseo-mo/src/continuator/moNeighborhoodStat.h

@@ -70,6 +70,20 @@ public :
             solNeighborComparator(_solNeighborComparator)
     {}
 
+    /**
+     * Default Constructor
+     * where the comparators are basic, there only compare the fitness values
+     *
+     * @param _neighborhood a neighborhood
+     * @param _eval an evaluation function
+     */
+    moNeighborhoodStat(Neighborhood& _neighborhood, moEval<Neighbor>& _eval):
+            moStat<EOT, bool>(true, "neighborhood"),
+            neighborhood(_neighborhood), eval(_eval),
+            neighborComparator(defaultNeighborComp),
+            solNeighborComparator(defaultSolNeighborComp)
+    {}
+
     /**
      * Compute classical statistics of the first solution's neighborhood
      * @param _solution the first solution
@@ -229,6 +243,12 @@ private:
     moNeighborComparator<Neighbor>& neighborComparator;
     moSolNeighborComparator<Neighbor>& solNeighborComparator;
 
+    // default comparators
+    // compare the fitness values of neighbors: true is strictly greater
+    moNeighborComparator<Neighbor> defaultNeighborComp;
+    // compare the fitness values of the solution and the neighbor: true if strictly greater 
+    moSolNeighborComparator<Neighbor> defaultSolNeighborComp;
+
     // the stastics of the fitness
     Fitness max, min;
     //mean and standard deviation

trunk/paradiseo-mo/src/continuator/moVectorMonitor.h

@@ -69,6 +69,16 @@ public:
   moVectorMonitor(eoValueParam<EOT> & _param) : doubleParam(NULL), intParam(NULL), eotParam(&_param)
   { }
 
+  /**
+   * Default Constructor
+   * @param _param the parameter of type EOT to save in the vector
+   */
+  template <class T>
+  moVectorMonitor(eoValueParam<T> & _param) : doubleParam(NULL), intParam(NULL), eotParam(NULL)
+  {
+    std::cerr << "Sorry the type can not be in a vector of moVectorMonitor" << std::endl;
+  }
+
   /**
    * To test if the value are basic type (double or unsigned int), or EOT type
    *

trunk/paradiseo-mo/src/mo.h

@@ -140,6 +140,8 @@
 #include <sampling/moDensityOfStatesSampling.h>
 #include <sampling/moAutocorrelationSampling.h>
 #include <sampling/moHillClimberSampling.h>
+#include <sampling/moFDCsampling.h>
+#include <sampling/moNeutralDegreeSampling.h>
 
 #include <problems/bitString/moBitNeighbor.h>
 #include <problems/eval/moOneMaxIncrEval.h>

trunk/paradiseo-mo/src/problems/eval/moRoyalRoadIncrEval.h

@@ -31,6 +31,7 @@ Contact: paradiseo-help@lists.gforge.inria.fr
 #define _moRoyalRoadIncrEval_H
 
 #include <eval/moEval.h>
+#include <eval/royalRoadEval.h>
 
 /**
  * Incremental evaluation Function for the Royal Road problem
@@ -45,7 +46,7 @@ public:
    * Default constructor
    * @param _k size of a block
    */
-  moRoyalRoadIncrEval(unsigned int _k) : k(_k) {}
+  moRoyalRoadIncrEval(RoyalRoadEval<EOT> & _rr) : k(_rr.blockSize()) {}
 
   /*
    * incremental evaluation of the neighbor for the Royal Road problem
@@ -53,13 +54,13 @@ public:
    * @param _neighbor the neighbor to consider (of type moBitNeigbor)
    */
   virtual void operator()(EOT & _solution, Neighbor & _neighbor) {
-    // which block can change?
+    // which block can be changed?
     unsigned int n = _neighbor.index() / k;
     
     // complete block?
-    offset = n * k;
+    unsigned int offset = n * k;
     
-    j = 0;
+    unsigned int j = 0;
     while (_solution[offset + j] && j < k) j++;
     
     if (j == k) // the block is complete, so the fitness decreases from one
@@ -71,9 +72,16 @@ public:
 
 	if (j == k) // the block can be filled, so the fitness increases from one
 	  _neighbor.fitness(_solution.fitness() + 1);
-      }
+	else
+	  _neighbor.fitness(_solution.fitness());
+      } else 
+	_neighbor.fitness(_solution.fitness());
     }
   }
+
+protected:
+  // size of the blocks
+  unsigned int k;
 };
 
 #endif

trunk/paradiseo-mo/src/sampling/moAutocorrelationSampling.h

@@ -61,6 +61,8 @@ public:
    * Default Constructor
    * @param _init initialisation method of the solution
    * @param _neighborhood neighborhood giving neighbor in random order
+   * @param _fullEval Fitness function, full evaluation function
+   * @param _eval neighbor evaluation, incremental evaluation function
    * @param _nbStep Number of steps of the random walk 
    */
   moAutocorrelationSampling(eoInit<EOT> & _init, 

trunk/paradiseo-mo/src/sampling/moNeutralDegreeSampling.h

@@ -0,0 +1,124 @@
+/*
+  <moNeutralDegreeSampling.h>
+  Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
+
+  Sebastien Verel, Arnaud Liefooghe, Jeremie Humeau
+
+  This software is governed by the CeCILL license under French law and
+  abiding by the rules of distribution of free software.  You can  use,
+  modify and/ or redistribute the software under the terms of the CeCILL
+  license as circulated by CEA, CNRS and INRIA at the following URL
+  "http://www.cecill.info".
+
+  As a counterpart to the access to the source code and  rights to copy,
+  modify and redistribute granted by the license, users are provided only
+  with a limited warranty  and the software's author,  the holder of the
+  economic rights,  and the successive licensors  have only  limited liability.
+
+  In this respect, the user's attention is drawn to the risks associated
+  with loading,  using,  modifying and/or developing or reproducing the
+  software by the user in light of its specific status of free software,
+  that may mean  that it is complicated to manipulate,  and  that  also
+  therefore means  that it is reserved for developers  and  experienced
+  professionals having in-depth computer knowledge. Users are therefore
+  encouraged to load and test the software's suitability as regards their
+  requirements in conditions enabling the security of their systems and/or
+  data to be ensured and,  more generally, to use and operate it in the
+  same conditions as regards security.
+  The fact that you are presently reading this means that you have had
+  knowledge of the CeCILL license and that you accept its terms.
+
+  ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+  Contact: paradiseo-help@lists.gforge.inria.fr
+*/
+
+#ifndef moNeutralDegreeSampling_h
+#define moNeutralDegreeSampling_h
+
+#include <eoInit.h>
+#include <neighborhood/moNeighborhood.h>
+#include <eval/moEval.h>
+#include <eoEvalFunc.h>
+#include <algo/moRandomSearch.h>
+#include <continuator/moFitnessStat.h>
+#include <continuator/moNeighborhoodStat.h>
+#include <continuator/moNeutralDegreeNeighborStat.h>
+#include <sampling/moSampling.h>
+
+/**
+ * To compute the density of states: 
+ *   Sample the fitness of random solution in the search space
+ *   The fitness values of solutions are collected during the random search
+ * 
+ */
+template <class Neighbor>
+class moNeutralDegreeSampling : public moSampling<Neighbor>
+{
+public:
+  typedef typename Neighbor::EOT EOT ;
+  
+  using moSampling<Neighbor>::localSearch;
+
+  /**
+   * Default Constructor
+   * @param _init initialisation method of the solution
+   * @param _neighborhood neighborhood to compute the neutral degree
+   * @param _fullEval Fitness function, full evaluation function
+   * @param _eval neighbor evaluation, incremental evaluation function
+   * @param _nbSol Number of solutions in the sample
+   */
+  moNeutralDegreeSampling(eoInit<EOT> & _init, 
+			  moNeighborhood<Neighbor> & _neighborhood, 
+			  eoEvalFunc<EOT>& _fullEval, 
+			  moEval<Neighbor>& _eval, 
+			  unsigned int _nbSol) : 
+    moSampling<Neighbor>(_init, * new moRandomSearch<Neighbor>(_init, _fullEval, _nbSol), fitnessStat),
+    neighborhoodStat(_neighborhood, _eval),
+    ndStat(neighborhoodStat)
+  {
+    add(neighborhoodStat, false);
+    add(ndStat);
+  }
+
+  /**
+   * Constructor with comparators
+   * @param _init initialisation method of the solution
+   * @param _neighborhood neighborhood to compute the neutral degree
+   * @param _fullEval Fitness function, full evaluation function
+   * @param _eval neighbor evaluation, incremental evaluation function
+   * @param _neighborComparator a neighbor Comparator
+   * @param _solNeighborComparator a comparator between a solution and a neighbor
+   * @param _nbSol Number of solutions in the sample
+   */
+  moNeutralDegreeSampling(eoInit<EOT> & _init, 
+			  moNeighborhood<Neighbor> & _neighborhood, 
+			  eoEvalFunc<EOT>& _fullEval, 
+			  moEval<Neighbor>& _eval, 
+			  moNeighborComparator<Neighbor>& _neighborComparator, 
+			  moSolNeighborComparator<Neighbor>& _solNeighborComparator,
+			  unsigned int _nbSol) : 
+    moSampling<Neighbor>(_init, * new moRandomSearch<Neighbor>(_init, _fullEval, _nbSol), fitnessStat),
+    neighborhoodStat(_neighborhood, _eval, _neighborComparator, _solNeighborComparator),
+    ndStat(neighborhoodStat)
+  {
+    add(neighborhoodStat, false);
+    add(ndStat);
+  }
+
+  /** 
+   * default destructor
+   */
+  ~moNeutralDegreeSampling() {
+    // delete the pointer on the local search which has been constructed in the constructor
+    delete &localSearch;
+  }
+
+protected:
+  moFitnessStat<EOT> fitnessStat;
+  moNeighborhoodStat< Neighbor > neighborhoodStat;
+  moNeutralDegreeNeighborStat< Neighbor > ndStat;
+
+};
+
+
+#endif

trunk/paradiseo-mo/src/sampling/moSampling.h

@@ -64,10 +64,10 @@ public:
    * @param _stat statistic to compute during the search
    */
   template <class ValueType>
-  moSampling(eoInit<EOT> & _init, moLocalSearch<Neighbor> & _localSearch, moStat<EOT,ValueType> & _stat) : init(_init), localSearch(_localSearch), continuator(_localSearch.getContinuator())
+  moSampling(eoInit<EOT> & _init, moLocalSearch<Neighbor> & _localSearch, moStat<EOT,ValueType> & _stat, bool _monitoring = true) : init(_init), localSearch(_localSearch), continuator(_localSearch.getContinuator())
   {
     checkpoint = new moCheckpoint<Neighbor>(*continuator);
-    add(_stat);
+    add(_stat, _monitoring);
   }
 
   /**
@@ -87,14 +87,14 @@ public:
    * @param _stat another statistic to compute during the search
    */
   template< class ValueType >
-  void add(moStat<EOT, ValueType> & _stat) {
-    //    statVec.push_back(&_stat);
-
-    moVectorMonitor<EOT> * monitor = new moVectorMonitor<EOT>(_stat);
-    monitorVec.push_back(monitor);
-
+  void add(moStat<EOT, ValueType> & _stat, bool _monitoring = true) {
     checkpoint->add(_stat);
-    checkpoint->add(*monitor);
+
+    if (_monitoring) {
+      moVectorMonitor<EOT> * monitor = new moVectorMonitor<EOT>(_stat);
+      monitorVec.push_back(monitor);
+      checkpoint->add(*monitor);
+    }
   }    
 
   /**

trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt

@@ -14,6 +14,7 @@ ADD_EXECUTABLE(densityOfStates densityOfStates.cpp)
 ADD_EXECUTABLE(autocorrelation autocorrelation.cpp) 
 ADD_EXECUTABLE(adaptiveWalks adaptiveWalks.cpp) 
 ADD_EXECUTABLE(fdc fdc.cpp) 
+ADD_EXECUTABLE(neutralDegree neutralDegree.cpp) 
 
 TARGET_LINK_LIBRARIES(testRandomWalk eoutils ga eo) 
 TARGET_LINK_LIBRARIES(testMetropolisHasting eoutils ga eo) 
@@ -23,3 +24,4 @@ TARGET_LINK_LIBRARIES(densityOfStates eoutils ga eo)
 TARGET_LINK_LIBRARIES(autocorrelation eoutils ga eo)
 TARGET_LINK_LIBRARIES(adaptiveWalks eoutils ga eo)
 TARGET_LINK_LIBRARIES(fdc eoutils ga eo)
+TARGET_LINK_LIBRARIES(neutralDegree eoutils ga eo)

trunk/paradiseo-mo/tutorial/Lesson6/autocorrelation.cpp

@@ -1,5 +1,5 @@
 //-----------------------------------------------------------------------------
-/** sampling.cpp
+/** autocorrelation.cpp
  *
  * SV - 03/05/10
  *

trunk/paradiseo-mo/tutorial/Lesson6/neutralDegree.cpp

@@ -0,0 +1,215 @@
+//-----------------------------------------------------------------------------
+/** neutralDegree.cpp
+ *
+ * SV - 03/05/10
+ *
+ */
+//-----------------------------------------------------------------------------
+
+// standard includes
+#define HAVE_SSTREAM
+
+#include <stdexcept>  // runtime_error 
+#include <iostream>   // cout
+#include <sstream>    // ostrstream, istrstream
+#include <fstream>
+#include <string.h>
+
+// the general include for eo
+#include <eo>
+
+// declaration of the namespace
+using namespace std;
+
+//-----------------------------------------------------------------------------
+// representation of solutions, and neighbors
+#include <ga/eoBit.h>                         // bit string : see also EO tutorial lesson 1: FirstBitGA.cpp
+#include <problems/bitString/moBitNeighbor.h> // neighbor of bit string
+
+//-----------------------------------------------------------------------------
+// fitness function, and evaluation of neighbors
+#include <eval/royalRoadEval.h>
+#include <problems/eval/moRoyalRoadIncrEval.h>
+
+//-----------------------------------------------------------------------------
+// neighborhood description
+#include <neighborhood/moOrderNeighborhood.h> // visit all neighbor in order of their bit-flip
+
+//-----------------------------------------------------------------------------
+// the sampling class
+#include <sampling/moNeutralDegreeSampling.h>
+
+// Declaration of types
+//-----------------------------------------------------------------------------
+// Indi is the typedef of the solution type like in paradisEO-eo
+typedef eoBit<unsigned int> Indi;                      // bit string with unsigned fitness type
+// Neighbor is the typedef of the neighbor type,
+// Neighbor = How to compute the neighbor from the solution + information on it (i.e. fitness)  
+// all classes from paradisEO-mo use this template type
+typedef moBitNeighbor<unsigned int> Neighbor ;         // bit string neighbor with unsigned fitness type
+
+
+void main_function(int argc, char **argv)
+{
+  /* =========================================================
+   *
+   * Parameters
+   *
+   * ========================================================= */
+  // more information on the input parameters: see EO tutorial lesson 3
+  // but don't care at first it just read the parameters of the bit string size and the random seed.
+
+  // First define a parser from the command-line arguments
+  eoParser parser(argc, argv);
+  
+  // For each parameter, define Parameter, read it through the parser,
+  // and assign the value to the variable
+
+  // random seed parameter
+  eoValueParam<uint32_t> seedParam(time(0), "seed", "Random number seed", 'S');
+  parser.processParam( seedParam );
+  unsigned seed = seedParam.value();
+  
+  // length of the bit string
+  eoValueParam<unsigned int> vecSizeParam(20, "vecSize", "Genotype size", 'V');
+  parser.processParam( vecSizeParam, "Representation" );
+  unsigned vecSize = vecSizeParam.value();
+  
+  // size of the block
+  eoValueParam<unsigned int> blockSizeParam(4, "blockSize", "Block size of the Royal Road", 'k');
+  parser.processParam( blockSizeParam, "Representation" );
+  unsigned blockSize = blockSizeParam.value();
+  
+  // the number of solution sampled
+  eoValueParam<unsigned int> solParam(100, "nbSol", "Number of random solution", 'n');
+  parser.processParam( solParam, "Representation" );
+  unsigned nbSol = solParam.value();
+  
+  // the name of the output file
+  string str_out = "out.dat"; // default value
+  eoValueParam<string> outParam(str_out.c_str(), "out", "Output file of the sampling", 'o');
+  parser.processParam(outParam, "Persistence" );
+  
+  // the name of the "status" file where all actual parameter values will be saved
+  string str_status = parser.ProgramName() + ".status"; // default value
+  eoValueParam<string> statusParam(str_status.c_str(), "status", "Status file");
+  parser.processParam( statusParam, "Persistence" );
+  
+  // do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED
+  // i.e. in case you need parameters somewhere else, postpone these
+  if (parser.userNeedsHelp()) {
+    parser.printHelp(cout);
+    exit(1);
+  }
+  if (statusParam.value() != "") {
+    ofstream os(statusParam.value().c_str());
+    os << parser;// and you can use that file as parameter file
+  }
+
+  /* =========================================================
+   *
+   * Random seed
+   *
+   * ========================================================= */
+
+  // reproducible random seed: if you don't change SEED above,
+  // you'll aways get the same result, NOT a random run
+  // more information: see EO tutorial lesson 1 (FirstBitGA.cpp)
+  rng.reseed(seed);
+
+  /* =========================================================
+   *
+   * Initialization of the solution
+   *
+   * ========================================================= */
+
+  // a Indi random initializer: each bit is random
+  // more information: see EO tutorial lesson 1 (FirstBitGA.cpp)
+  eoUniformGenerator<bool> uGen;
+  eoInitFixedLength<Indi> random(vecSize, uGen);
+
+  /* =========================================================
+   *
+   * Eval fitness function (full evaluation)
+   *
+   * ========================================================= */
+
+  // the fitness function is the royal function (oneMax is a Royal Road with block of 1)
+  RoyalRoadEval<Indi> fullEval(blockSize);
+
+  /* =========================================================
+   *
+   * evaluation of a neighbor solution
+   *
+   * ========================================================= */
+
+  // Incremental evaluation of the neighbor: fitness is modified by +1 , 0 or -1
+  moRoyalRoadIncrEval<Neighbor> neighborEval(fullEval);
+
+  /* =========================================================
+   *
+   * the neighborhood of a solution
+   *
+   * ========================================================= */
+
+  // Exploration of the neighborhood in increasing order of the neigbor's index:
+  // bit-flip from bit 0 to bit (vecSize - 1)
+  moOrderNeighborhood<Neighbor> neighborhood(vecSize);
+
+  /* =========================================================
+   *
+   * The sampling of the search space
+   *
+   * ========================================================= */
+  
+  // sampling object : 
+  //    - random initialization
+  //    - neighborhood to compute the neutral degree
+  //    - fitness function
+  //    - neighbor evaluation
+  //    - number of solutions to sample
+  moNeutralDegreeSampling<Neighbor> sampling(random, neighborhood, fullEval, neighborEval, nbSol);
+  
+  /* =========================================================
+   *
+   * execute the sampling
+   *
+   * ========================================================= */
+  
+  sampling();
+  
+  /* =========================================================
+   *
+   * export the sampling
+   *
+   * ========================================================= */
+  
+  // to export the statistics into file
+  sampling.fileExport(str_out);
+
+  // to get the values of statistics 
+  // so, you can compute some statistics in c++ from the data
+  const std::vector<double> & fitnessValues = sampling.getValues(0); 
+  const std::vector<double> & ndValues = sampling.getValues(1); 
+
+  std::cout << "First values:" << std::endl;
+  std::cout << "Fitness   " << fitnessValues[0] << std::endl;
+  std::cout << "N. Degree " << ndValues[0] << std::endl;
+
+  std::cout << "Last values:" << std::endl;
+  std::cout << "Fitness  " << fitnessValues[fitnessValues.size() - 1] << std::endl;
+  std::cout << "N. Degree " << ndValues[fitnessValues.size() - 1] << std::endl;
+}
+
+// A main that catches the exceptions
+
+int main(int argc, char **argv)
+{
+    try {
+        main_function(argc, argv);
+    }
+    catch (exception& e) {
+        cout << "Exception: " << e.what() << '\n';
+    }
+    return 1;
+}

trunk/problems/eval/royalRoadEval.h

@@ -43,7 +43,7 @@ public:
    * Default constructor
    * @param _k size of a block
    */
-  RoyalRoad(unsigned int _k) : k(_k) {}
+  RoyalRoadEval(unsigned int _k) : k(_k) {}
 
   /**
    * Count the number of complete blocks in the bit string
@@ -70,6 +70,14 @@ public:
     _solution.fitness(sum);
   }
 
+  /**
+   * get the size of a block
+   * @return block size
+   */
+  unsigned int blockSize() {
+    return k;
+  }
+
 private:
   // size of a block
   unsigned int k;