Ajout de la random neutral walk sampling, on tient le bon bout ;)

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1797 331e1502-861f-0410-8da2-ba01fb791d7f

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

@@ -0,0 +1,88 @@
+/*
+  <moAverageFitnessNeighborStat.h>
+  Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
+
+  Sébastien Verel, Arnaud Liefooghe, Jérémie 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 moAverageFitnessNeighborStat_h
+#define moAverageFitnessNeighborStat_h
+
+#include <continuator/moStat.h>
+#include <continuator/moNeighborhoodStat.h>
+
+/**
+ * From moNeighborhoodStat, to compute the average and the standard deviation of fitness in the neighborhood
+ */
+template< class Neighbor >
+class moAverageFitnessNeighborStat : public moStat<typename Neighbor::EOT, double >
+{
+public :
+    typedef typename Neighbor::EOT EOT ;
+    typedef typename EOT::Fitness Fitness ;
+
+    using moStat< EOT, double >::value;
+
+    /**
+     * Default Constructor
+     * @param _nhStat a neighborhoodStat
+     */
+    moAverageFitnessNeighborStat(moNeighborhoodStat<Neighbor> & _nhStat):
+            moStat<EOT, double >(0.0, "average"), nhStat(_nhStat) {}
+
+    /**
+     * Set the average and the standard deviation of fitness in the neighborhood
+     * @param _sol the first solution
+     */
+    virtual void init(EOT & _sol) {
+        value() = nhStat.getMean();
+    }
+
+    /**
+     * Set the average and the standard deviation of fitness in the neighborhood
+     * @param _sol the corresponding solution
+     */
+    virtual void operator()(EOT & _sol) {
+        value() = nhStat.getMean();
+    }
+
+    /**
+     * @return the class name
+     */
+    virtual std::string className(void) const {
+        return "moAverageFitnessNeighborStat";
+    }
+
+private:
+    /** moNeighborhoodStat */
+    moNeighborhoodStat<Neighbor> & nhStat;
+};
+
+#endif

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

@@ -0,0 +1,88 @@
+/*
+  <moStdFitnessNeighborStat.h>
+  Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
+
+  Sébastien Verel, Arnaud Liefooghe, Jérémie 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 moStdFitnessNeighborStat_h
+#define moStdFitnessNeighborStat_h
+
+#include <continuator/moStat.h>
+#include <continuator/moNeighborhoodStat.h>
+
+/**
+ * From moNeighborhoodStat, to compute the average and the standard deviation of fitness in the neighborhood
+ */
+template< class Neighbor >
+class moStdFitnessNeighborStat : public moStat<typename Neighbor::EOT, double >
+{
+public :
+    typedef typename Neighbor::EOT EOT ;
+    typedef typename EOT::Fitness Fitness ;
+
+    using moStat< EOT, double >::value;
+
+    /**
+     * Default Constructor
+     * @param _nhStat a neighborhoodStat
+     */
+    moStdFitnessNeighborStat(moNeighborhoodStat<Neighbor> & _nhStat):
+            moStat<EOT, double >(0.0, "stdev"), nhStat(_nhStat) {}
+
+    /**
+     * Set the average and the standard deviation of fitness in the neighborhood
+     * @param _sol the first solution
+     */
+    virtual void init(EOT & _sol) {
+        value() = nhStat.getSD();
+    }
+
+    /**
+     * Set the average and the standard deviation of fitness in the neighborhood
+     * @param _sol the corresponding solution
+     */
+    virtual void operator()(EOT & _sol) {
+        value() = nhStat.getSD();
+    }
+
+    /**
+     * @return the class name
+     */
+    virtual std::string className(void) const {
+        return "moStdFitnessNeighborStat";
+    }
+
+private:
+    /** moNeighborhoodStat */
+    moNeighborhoodStat<Neighbor> & nhStat;
+};
+
+#endif

trunk/paradiseo-mo/src/mo.h

@@ -45,6 +45,7 @@
 #include <algo/moRandomBestHC.h>
 #include <algo/moNeutralHC.h>
 #include <algo/moRandomWalk.h>
+#include <algo/moRandomNeutralWalk.h>
 #include <algo/moTS.h>
 #include <algo/moILS.h>
 
@@ -67,6 +68,8 @@
 #include <continuator/moNeighborhoodStat.h>
 #include <continuator/moNeutralDegreeNeighborStat.h>
 #include <continuator/moSecondMomentNeighborStat.h>
+#include <continuator/moAverageFitnessNeighborStat.h>
+#include <continuator/moStdFitnessNeighborStat.h>
 #include <continuator/moSizeNeighborStat.h>
 #include <continuator/moCounterStat.h>
 #include <continuator/moCounterMinusOneStat.h>
@@ -133,6 +136,7 @@
 #include <perturb/moRestartPerturb.h>
 #include <perturb/moNeighborhoodPerturb.h>
 #include <perturb/moLocalSearchInit.h>
+#include <perturb/moSolInit.h>
 
 #include <acceptCrit/moAcceptanceCriterion.h>
 #include <acceptCrit/moAlwaysAcceptCrit.h>
@@ -152,6 +156,7 @@
 #include <sampling/moRndBestFitnessCloudSampling.h>
 #include <sampling/moMHRndFitnessCloudSampling.h>
 #include <sampling/moMHBestFitnessCloudSampling.h>
+#include <sampling/moNeutralWalkSampling.h>
 
 #include <problems/bitString/moBitNeighbor.h>
 #include <problems/eval/moOneMaxIncrEval.h>

trunk/paradiseo-mo/src/perturb/moSolInit.h

@@ -0,0 +1,60 @@
+/*
+<moSolInit.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  ue,
+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".
+
+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 _moSolInit_h
+#define _moSolInit_h
+
+#include <eoInit.h>
+
+/**
+ * Initialization of the solution with the external solution
+ */
+template< class EOT >
+class moSolInit : public eoInit<EOT> {
+public:
+  /**
+   * Default Constructor
+   * @param _extSol external solution of the intiialization
+   */
+  moSolInit(EOT & _extSol) : extSol(_extSol) {
+  }
+  
+  /**
+   * Initialization on the externatl solution
+   * @param _solution to initialize
+   */
+  void operator()(EOT& _solution){
+    _solution = extSol;
+  }
+
+private:
+  EOT& extSol;
+};
+
+#endif

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

@@ -52,7 +52,7 @@
  *   Sample the fitness of solutions from Metropolis-Hasting sampling
  *   and the fitness of one random neighbor
  *
- *   The values are collected during the random search
+ *   The values are collected during the Metropolis-Hasting walk
  * 
  */
 template <class Neighbor>

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

@@ -0,0 +1,148 @@
+/*
+  <moNeutralWalkSampling.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 moNeutralWalkSampling_h
+#define moNeutralWalkSampling_h
+
+#include <eoInit.h>
+#include <eval/moEval.h>
+#include <eoEvalFunc.h>
+#include <algo/moRandomNeutralWalk.h>
+#include <sampling/moSampling.h>
+#include <perturb/moSolInit.h>
+#include <continuator/moSolutionStat.h>
+#include <utils/eoDistance.h>
+#include <continuator/moDistanceStat.h>
+#include <continuator/moNeighborhoodStat.h>
+#include <continuator/moMaxNeighborStat.h>
+#include <continuator/moMinNeighborStat.h>
+#include <continuator/moAverageFitnessNeighborStat.h>
+#include <continuator/moStdFitnessNeighborStat.h>
+#include <continuator/moSizeNeighborStat.h>
+#include <continuator/moNbInfNeighborStat.h>
+#include <continuator/moNbSupNeighborStat.h>
+#include <continuator/moNeutralDegreeNeighborStat.h>
+
+/**
+ * To explore the evolvability of solutions in a neutral networks:
+ *   Perform a random neutral walk based on the neighborhood,
+ *   The measures of evolvability of solutions are collected during the random neutral walk
+ *   The distribution and autocorrelation can be computed from the serie of values  
+ * 
+ *    Informations collected:
+ *         - the current solution of the walk
+ *         - the distance from the starting solution
+ *         - the minimal fitness in the neighborhood
+ *         - the average fitness
+ *         - the standard deviation of the fitness
+ *         - the maximal fitness
+ *         - the size of the neighborhood
+ *         - the number of neighbors with lower fitness
+ *         - the number of neighbors with equal fitness (neutral degree)
+ *         - the number of neighbors with higher fitness
+ */
+template <class Neighbor>
+class moNeutralWalkSampling : public moSampling<Neighbor>
+{
+public:
+  typedef typename Neighbor::EOT EOT ;
+  
+  using moSampling<Neighbor>::localSearch;
+
+  /**
+   * Default Constructor
+   * @param _initSol the first the solution of the walk
+   * @param _neighborhood neighborhood giving neighbor in random order
+   * @param _fullEval Fitness function, full evaluation function
+   * @param _eval neighbor evaluation, incremental evaluation function
+   * @param _distance the distance to measure the distance from the initial solution
+   * @param _nbStep Number of steps of the random walk 
+   */
+  moNeutralWalkSampling(EOT & _initSol, 
+			moNeighborhood<Neighbor> & _neighborhood, 
+			eoEvalFunc<EOT>& _fullEval, 
+			moEval<Neighbor>& _eval, 
+			eoDistance<EOT> & _distance,
+			unsigned int _nbStep) : 
+    moSampling<Neighbor>(init, * new moRandomNeutralWalk<Neighbor>(_neighborhood, _fullEval, _eval, _nbStep), solutionStat),
+    init(_initSol),
+    distStat(_distance, _initSol),
+    neighborhoodStat(_neighborhood, _eval),
+    minStat(neighborhoodStat),
+    averageStat(neighborhoodStat),
+    stdStat(neighborhoodStat),
+    maxStat(neighborhoodStat),
+    nbSupStat(neighborhoodStat),
+    nbInfStat(neighborhoodStat),
+    sizeStat(neighborhoodStat),
+    ndStat(neighborhoodStat)
+  {
+    add(neighborhoodStat, false);
+    add(distStat);
+    add(minStat);
+    add(averageStat);
+    add(stdStat);
+    add(maxStat);
+    add(sizeStat);
+    add(nbInfStat);
+    add(ndStat);
+    add(nbSupStat);
+  }
+
+  /** 
+   * default destructor
+   */
+  ~moNeutralWalkSampling() {
+    // delete the pointer on the local search which has been constructed in the constructor
+    delete localSearch;
+  }
+
+protected:
+  moSolInit<EOT> init;
+  moSolutionStat<EOT> solutionStat;
+  moDistanceStat<EOT> distStat;
+  moNeighborhoodStat< Neighbor > neighborhoodStat;
+  moMinNeighborStat< Neighbor > minStat;
+  moAverageFitnessNeighborStat< Neighbor > averageStat;
+  moStdFitnessNeighborStat< Neighbor > stdStat;
+  moMaxNeighborStat< Neighbor > maxStat;
+  moNbSupNeighborStat< Neighbor > nbSupStat;
+  moNbInfNeighborStat< Neighbor > nbInfStat;
+  moSizeNeighborStat< Neighbor > sizeStat;
+  moNeutralDegreeNeighborStat< Neighbor > ndStat;
+
+};
+
+
+#endif