Ajout FDC

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1789 331e1502-861f-0410-8da2-ba01fb791d7f

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

@@ -36,7 +36,6 @@
 #define moDensityOfStatesSampling_h
 
 #include <eoInit.h>
-#include <eval/moEval.h>
 #include <eoEvalFunc.h>
 #include <algo/moRandomSearch.h>
 #include <continuator/moFitnessStat.h>
@@ -59,8 +58,8 @@ public:
   /**
    * Default Constructor
    * @param _init initialisation method of the solution
-   * @param _neighborhood neighborhood giving neighbor in random order
-   * @param _nbStep Number of steps of the random walk 
+   * @param _fullEval Fitness function, full evaluation function
+   * @param _nbSol Number of solutions in the sample
    */
   moDensityOfStatesSampling(eoInit<EOT> & _init, 
 			    eoEvalFunc<EOT>& _fullEval, 

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

@@ -0,0 +1,95 @@
+/*
+  <moFDCsampling.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 moFDCsampling_h
+#define moFDCsampling_h
+
+#include <eoInit.h>
+#include <eval/moEval.h>
+#include <eoEvalFunc.h>
+#include <algo/moRandomSearch.h>
+#include <continuator/moFitnessStat.h>
+#include <utils/eoDistance.h>
+#include <continuator/moDistanceStat.h>
+#include <sampling/moSampling.h>
+
+/**
+ * To compute the fitness distance correlation: 
+ *   Sample the fitness and the distance from a particular solution of random solution in the search space
+ *   The fitness values and distances of solutions are collected during the random search
+ *   Then the correlation between the fitness and the distance can be computed
+ *
+ */
+template <class Neighbor>
+class moFDCsampling : 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 giving neighbor in random order
+   * @param _dist the distance function between solution
+   * @param _refSol the reference solution to compute the distance (think of global optimum when possible)
+   * @param _nbSol Number of solutions of the sample
+   */
+  moFDCsampling(eoInit<EOT> & _init, 
+		eoEvalFunc<EOT>& _fullEval,
+		eoDistance<EOT>& _dist,
+		EOT& _refSol,
+		unsigned int _nbSol) : 
+    moSampling<Neighbor>(_init, * new moRandomSearch<Neighbor>(_init, _fullEval, _nbSol), fitnessStat),
+    distStat(_dist, _refSol)
+  {
+    add(distStat);
+  }
+
+  /** 
+   * default destructor
+   */
+  ~moFDCsampling() {
+    // delete the pointer on the local search which has been constructed in the constructor
+    delete &localSearch;
+  }
+
+protected:
+  moFitnessStat<EOT> fitnessStat;
+  moDistanceStat<EOT> distStat;
+};
+
+
+#endif

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

@@ -13,6 +13,7 @@ ADD_EXECUTABLE(sampling sampling.cpp)
 ADD_EXECUTABLE(densityOfStates densityOfStates.cpp) 
 ADD_EXECUTABLE(autocorrelation autocorrelation.cpp) 
 ADD_EXECUTABLE(adaptiveWalks adaptiveWalks.cpp) 
+ADD_EXECUTABLE(fdc fdc.cpp) 
 
 TARGET_LINK_LIBRARIES(testRandomWalk eoutils ga eo) 
 TARGET_LINK_LIBRARIES(testMetropolisHasting eoutils ga eo) 
@@ -21,3 +22,4 @@ TARGET_LINK_LIBRARIES(sampling eoutils ga eo)
 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)

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

@@ -0,0 +1,192 @@
+//-----------------------------------------------------------------------------
+/** fdc.cpp
+ *
+ * SV - 06/05/10
+ *
+ */
+//-----------------------------------------------------------------------------
+
+// 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/oneMaxEval.h>
+
+//-----------------------------------------------------------------------------
+// the distance defined over the search space
+#include <utils/eoDistance.h>
+
+//-----------------------------------------------------------------------------
+// the sampling class
+#include <sampling/moFDCsampling.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();
+  
+  // 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 just the number of 1 in the bit string
+  oneMaxEval<Indi> fullEval;
+
+  /* =========================================================
+   *
+   * The sampling of the search space
+   *
+   * ========================================================= */
+  
+  // Hamming distance to the global optimum
+  eoHammingDistance<Indi> distance; // Hamming distance
+  Indi bestSolution(vecSize, true); // global optimum
+
+  // sampling object : 
+  //    - random initialization
+  //    - fitness function
+  //    - number of solutions to sample
+  moFDCsampling<Neighbor> sampling(random, fullEval, distance, bestSolution, 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> & distValues    = sampling.getValues(1); 
+
+  std::cout << "First values:" << std::endl;
+  std::cout << "Fitness  " << fitnessValues[0] << std::endl;
+  std::cout << "Distance " << distValues[0] << std::endl;
+
+  std::cout << "Last values:" << std::endl;
+  std::cout << "Fitness  " << fitnessValues[fitnessValues.size() - 1] << std::endl;
+  std::cout << "Distance " << distValues[distValues.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;
+}