add sampling, add moVectorMonitor

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1774 331e1502-861f-0410-8da2-ba01fb791d7f

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

@@ -48,14 +48,14 @@ template<class Neighbor>
 class moLocalSearch: public eoMonOp<typename Neighbor::EOT>
 {
 public:
-	typedef moNeighborhood<Neighbor> Neighborhood;
-	typedef moNeighborhoodExplorer<Neighbor> NeighborhoodExplorer;
-    typedef typename Neighbor::EOT EOT ;
+  typedef moNeighborhood<Neighbor> Neighborhood;
+  typedef moNeighborhoodExplorer<Neighbor> NeighborhoodExplorer;
+  typedef typename Neighbor::EOT EOT ;
 
     /**
      * Constructor of a moLocalSearch needs a NeighborhooExplorer and a Continuator
      */
-    moLocalSearch(NeighborhoodExplorer& _searchExpl, moContinuator<Neighbor> & _continuator, eoEvalFunc<EOT>& _fullEval) : searchExplorer(_searchExpl), continuator(_continuator), fullEval(_fullEval) { } ;
+    moLocalSearch(NeighborhoodExplorer& _searchExpl, moContinuator<Neighbor> & _cont, eoEvalFunc<EOT>& _fullEval) : searchExplorer(_searchExpl), cont(&_cont), fullEval(_fullEval) { } ;
 
     /**
      * Run the local search on a solution
@@ -70,9 +70,9 @@ public:
         searchExplorer.initParam(_solution);
 
         // initialization of the external continuator (for example the time, or the number of generations)
-        continuator.init(_solution);
+        cont->init(_solution);
 
-        bool b=continuator(_solution);
+        bool b= (*cont)(_solution);
 
         do {
             // explore the neighborhood of the solution
@@ -88,22 +88,40 @@ public:
             // update the parameter of the search (for ex. Temperature of the SA)
             searchExplorer.updateParam(_solution);
 
-            b=continuator(_solution);
+            b=(*cont)(_solution);
         } while (b && searchExplorer.isContinue(_solution));
 
         searchExplorer.terminate(_solution);
 
-        continuator.lastCall(_solution);
+        cont->lastCall(_solution);
 
         return true;
     };
 
+    /** 
+     * external continuator object
+     * @return the external continuator 
+    */
+  void setContinuator(moContinuator<Neighbor> & _cont) {
+    cont = &_cont ;
+  }
+
+    /** 
+     * external continuator object
+     * 
+     * @overload
+     * @return the external continuator 
+    */
+  moContinuator<Neighbor>* getContinuator() const {
+    return cont ;
+  }
+
 protected:
     // make the exploration of the neighborhood according to a local search heuristic
     moNeighborhoodExplorer<Neighbor>& searchExplorer ;
 
     // external continuator
-    moContinuator<Neighbor>& continuator ;
+    moContinuator<Neighbor> * cont ;
 
     //full evaluation function
     eoEvalFunc<EOT>& fullEval;

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

@@ -0,0 +1,135 @@
+/*
+  <moVectorMonitor.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 moVectorMonitor_h
+#define moVectorMonitor_h
+
+#include <utils/eoMonitor.h>
+#include <utils/eoParam.h>
+
+/**
+ * To save the values of the same type in a vector
+ * It is similar to eoFileMonitor
+ * 
+ */
+class moVectorMonitor : public eoMonitor
+{
+public:
+  
+  /**
+   * Default Constructor
+   * @param _param the parameter of type double to save in the vector
+   */
+  moVectorMonitor(eoValueParam<double> & _param) : doubleParam(&_param), intParam(NULL)
+  { }
+
+  /**
+   * Default Constructor
+   * @param _param the parameter of type unsigned int to save in the vector
+   */
+  moVectorMonitor(eoValueParam<unsigned int> & _param) : doubleParam(NULL), intParam(&_param)
+  { }
+
+  /**
+   * Pure virtual function to have all the values
+   *
+   * @return the vector of values
+   */
+  //  template <class ValueType>
+  //  const std::vector<ValueType>& getVector() const  ;
+
+  /**
+   * To "print" the value of the parameter in the vector
+   *
+   * @return this monitor (sorry I don't why, but it is like this in EO)
+   */
+  eoMonitor& operator()(void) {
+    if (doubleParam != NULL)
+      valueVec.push_back(doubleParam->value());
+    else
+      valueVec.push_back((double) intParam->value());
+    
+    return *this ;
+  }
+
+  /**
+   * To have all the values
+   *
+   * @return the vector of values
+   */
+  const std::vector<double>& getVector() const {
+    return valueVec ;
+  } 
+
+  /**
+   * to get the value out.
+   * @return the string of the value
+   */
+  std::string getValue(unsigned int i) const {
+    std::ostringstream os;
+    os << (valueVec[i]) ;
+    return os.str();
+  }
+
+  /**
+   * clear the vector
+   */
+  void clear() {
+    valueVec.clear();
+  }
+
+  /**
+   * number of value
+   * @return size of the vector
+   */
+  unsigned int size() {
+    return valueVec.size();
+  }
+
+  /**
+   * @return name of the class
+   */
+  virtual std::string className(void) const {
+    return "moVectorMonitor";
+  }
+  
+protected:
+  eoValueParam<double> * doubleParam ;
+  eoValueParam<unsigned int> * intParam ;
+
+  std::vector<double> valueVec;
+};
+
+
+#endif

trunk/paradiseo-mo/src/mo.h

@@ -71,6 +71,7 @@
 #include <continuator/moFullEvalContinuator.h>
 #include <continuator/moNeighborEvalContinuator.h>
 #include <continuator/moTimeContinuator.h>
+#include <continuator/moVectorMonitor.h>
 
 #include <eval/moEval.h>
 #include <eval/moFullEvalByCopy.h>
@@ -128,6 +129,8 @@
 #include <coolingSchedule/moCoolingSchedule.h>
 #include <coolingSchedule/moSimpleCoolingSchedule.h>
 
+#include <sampling/moSampling.h>
+
 #include <problems/bitString/moBitNeighbor.h>
 #include <problems/eval/moOneMaxIncrEval.h>
 #include <problems/permutation/moShiftNeighbor.h>

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

@@ -0,0 +1,168 @@
+/*
+  <moSampling.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 moSampling_h
+#define moSampling_h
+
+#include <vector>
+#include <eoFunctor.h>
+#include <utils/eoMonitor.h>
+#include <continuator/moStat.h>
+#include <continuator/moCheckpoint.h>
+#include <continuator/moVectorMonitor.h>
+#include <eoInit.h>
+
+/**
+ * To sample the search space:
+ * A local search is used to sample the search space
+ * Some statistics are computed at each step of the local search
+ * 
+ * Can be used to study the fitness landscape
+ */
+template <class Neighbor>
+class moSampling : public eoF<void>
+{
+public:
+  typedef typename Neighbor::EOT EOT ;
+  
+  /**
+   * Default Constructor
+   * @param _init initialisation method of the solution
+   * @param _localSearch  local search to sample the search space
+   * @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())
+  {
+    checkpoint = new moCheckpoint<Neighbor>(*continuator);
+    add(_stat);
+  }
+
+  ~moSampling() {
+    for(unsigned i = 0; i < monitorVec.size(); i++)
+      delete monitorVec[i];
+
+    delete checkpoint ;
+  }
+
+  /**
+   * Add a statistic
+   * @param _stat another statistic to compute during the search
+   */
+  template< class ValueType >
+  void add(moStat<EOT, ValueType> & _stat) {
+    //    statVec.push_back(&_stat);
+
+    moVectorMonitor * monitor = new moVectorMonitor(_stat);
+    monitorVec.push_back(monitor);
+
+    checkpoint->add(_stat);
+    checkpoint->add(*monitor);
+  }    
+
+  /**
+   * To sample the search and get the statistics
+   */
+  void operator()(void) {
+    // clear all statisic vectors
+    for(unsigned i = 0; i < monitorVec.size(); i++)
+      monitorVec[i]->clear();
+
+    // change the checkpoint to compute the statistics
+    localSearch.setContinuator(*checkpoint);
+
+    // the initial solution
+    EOT solution;
+
+    // initialisation of the solution
+    init(solution);
+
+    // compute the sampling
+    localSearch(solution);
+
+    // set to initial continuator
+    localSearch.setContinuator(*continuator);
+  }
+
+  /**
+   * to export the vector of values into one file
+   */
+  void exportFile(std::string _filename, std::string _delim = " ") {
+    // create file
+    ofstream os(_filename.c_str()); 
+
+    if (!os) {
+      string str = "moSampling: Could not open " + _filename;
+      throw runtime_error(str);
+    }
+    
+    // all vector have the same size
+    unsigned vecSize = monitorVec[0]->size();
+
+    for(unsigned int i = 0; i < vecSize; i++) {
+      std::vector<moVectorMonitor*>::iterator it = monitorVec.begin();
+
+      os << (*it)->getValue(i);
+      
+      for(++it; it != monitorVec.end(); ++it)
+	{
+	  os << _delim.c_str() << (*it)->getValue(i);
+	}
+      
+      os << std::endl ;
+    }
+    
+  }
+
+  /**
+   * @return name of the class
+   */
+  virtual std::string className(void) const {
+    return "moSampling";
+  }
+  
+protected:
+  eoInit<EOT> & init;
+  moLocalSearch<Neighbor> & localSearch;
+
+  moContinuator<Neighbor> * continuator;
+  moCheckpoint<Neighbor> * checkpoint;
+
+  //  std::vector<moStatBase<EOT>*> statVec;
+  std::vector<moVectorMonitor*> monitorVec;
+
+};
+
+
+#endif

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

@@ -9,7 +9,9 @@ LINK_DIRECTORIES(${EO_BIN_DIR}/lib)
 ADD_EXECUTABLE(testRandomWalk testRandomWalk.cpp) 
 ADD_EXECUTABLE(testMetropolisHasting testMetropolisHasting.cpp) 
 ADD_EXECUTABLE(testRandomNeutralWalk testRandomNeutralWalk.cpp) 
+ADD_EXECUTABLE(sampling sampling.cpp) 
 
 TARGET_LINK_LIBRARIES(testRandomWalk eoutils ga eo) 
 TARGET_LINK_LIBRARIES(testMetropolisHasting eoutils ga eo) 
 TARGET_LINK_LIBRARIES(testRandomNeutralWalk eoutils ga eo)
+TARGET_LINK_LIBRARIES(sampling eoutils ga eo)

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

@@ -0,0 +1,214 @@
+//-----------------------------------------------------------------------------
+/** sampling.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>
+#include <ga.h>
+
+using namespace std;
+
+//-----------------------------------------------------------------------------
+// fitness function
+#include <eval/oneMaxEval.h>
+#include <problems/bitString/moBitNeighbor.h>
+#include <eoInt.h>
+#include <neighborhood/moRndWithReplNeighborhood.h>
+
+#include <eval/moFullEvalByModif.h>
+#include <eval/moFullEvalByCopy.h>
+#include <continuator/moTrueContinuator.h>
+#include <algo/moLocalSearch.h>
+#include <explorer/moRandomWalkExplorer.h>
+#include <continuator/moCheckpoint.h>
+#include <continuator/moFitnessStat.h>
+#include <continuator/moSolutionStat.h>
+#include <utils/eoDistance.h>
+#include <continuator/moDistanceStat.h>
+
+#include <utils/eoFileMonitor.h>
+#include <utils/eoUpdater.h>
+
+#include <sampling/moSampling.h>
+
+// REPRESENTATION
+//-----------------------------------------------------------------------------
+typedef eoBit<unsigned> Indi;
+typedef moBitNeighbor<unsigned int> Neighbor ; // incremental evaluation
+typedef moRndWithReplNeighborhood<Neighbor> Neighborhood ;
+
+void main_function(int argc, char **argv)
+{
+    /* =========================================================
+    *
+    * Parameters
+    *
+    * ========================================================= */
+
+    // 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
+
+    eoValueParam<uint32_t> seedParam(time(0), "seed", "Random number seed", 'S');
+    parser.processParam( seedParam );
+    unsigned seed = seedParam.value();
+
+    // description of genotype
+    eoValueParam<unsigned int> vecSizeParam(8, "vecSize", "Genotype size", 'V');
+    parser.processParam( vecSizeParam, "Representation" );
+    unsigned vecSize = vecSizeParam.value();
+
+    eoValueParam<unsigned int> stepParam(10, "nbStep", "Number of steps of the random walk", 'n');
+    parser.processParam( stepParam, "Representation" );
+    unsigned nbStep = stepParam.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
+    rng.reseed(seed);
+
+
+    /* =========================================================
+     *
+     * Eval fitness function
+     *
+     * ========================================================= */
+
+    oneMaxEval<Indi> eval;
+
+
+    /* =========================================================
+     *
+     * Initilisation of the solution
+     *
+     * ========================================================= */
+
+    // a Indi random initializer
+    eoUniformGenerator<bool> uGen;
+    eoInitFixedLength<Indi> random(vecSize, uGen);
+
+
+    /* =========================================================
+     *
+     * evaluation of a neighbor solution
+     *
+     * ========================================================= */
+
+    moFullEvalByModif<Neighbor> nhEval(eval);
+
+    //An eval by copy can be used instead of the eval by modif
+    //moFullEvalByCopy<Neighbor> nhEval(eval);
+
+
+    /* =========================================================
+     *
+     * the neighborhood of a solution
+     *
+     * ========================================================= */
+
+    Neighborhood neighborhood(vecSize);
+
+
+    /* =========================================================
+     *
+     * a neighborhood explorer solution
+     *
+     * ========================================================= */
+
+    moRandomWalkExplorer<Neighbor> explorer(neighborhood, nhEval, nbStep);
+
+
+    /* =========================================================
+     *
+     * the continuator and the checkpoint
+     *
+     * ========================================================= */
+
+    moTrueContinuator<Neighbor> continuator;//always continue
+
+    moFitnessStat<Indi, unsigned> fStat;
+    eoHammingDistance<Indi> distance;
+    Indi bestSolution(vecSize, true);
+    moDistanceStat<Indi, unsigned> distStat(distance, bestSolution);
+
+    /* =========================================================
+     *
+     * the local search algorithm
+     *
+     * ========================================================= */
+
+    moLocalSearch<Neighbor> localSearch(explorer, continuator, eval);
+
+    /* =========================================================
+     *
+     * The sampling of the search space
+     *
+     * ========================================================= */
+    
+    moSampling<Neighbor> sampling(random, localSearch, fStat);
+
+    /* =========================================================
+     *
+     * execute the sampling
+     *
+     * ========================================================= */
+
+    sampling();
+
+    sampling.exportFile(str_out);
+
+}
+
+// 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;
+}