Paradiseo-eo sources added

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@40 331e1502-861f-0410-8da2-ba01fb791d7f

trunk/paradiseo-eo/tutorial/Lesson4/.cvsignore

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+Makefile.in

trunk/paradiseo-eo/tutorial/Lesson4/BitEA.cpp

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+#include <iostream>
+
+#include <ga/make_ga.h>
+#include <apply.h>
+
+// EVAL
+#include "binary_value.h"
+
+// GENERAL
+using namespace std;
+
+int main(int argc, char* argv[])
+{     
+
+  try
+  {
+// REPRESENTATION
+//-----------------------------------------------------------------------------
+// define your genotype and fitness types
+  typedef eoBit<double> EOT;
+
+// PARAMETRES
+  eoParser parser(argc, argv);  // for user-parameter reading
+
+// GENERAL
+  eoState state;    // keeps all things allocated
+
+  ///// FIRST, problem or representation dependent stuff
+  //////////////////////////////////////////////////////
+
+// EVAL
+  // The evaluation fn - encapsulated into an eval counter for output 
+  eoEvalFuncPtr<EOT, double> mainEval( binary_value<EOT> );
+  eoEvalFuncCounter<EOT> eval(mainEval);
+
+// REPRESENTATION
+  // the genotype - through a genotype initializer
+  eoInit<EOT>& init = make_genotype(parser, state, EOT());
+
+  // if you want to do sharing, you'll need a distance.
+  // here Hamming distance 
+  eoHammingDistance<EOT> dist;
+
+// OPERATORS
+  // Build the variation operator (any seq/prop construct)
+  eoGenOp<EOT>& op = make_op(parser, state, init);
+
+// GENERAL
+  //// Now the representation-independent things
+  //////////////////////////////////////////////
+
+  // initialize the population - and evaluate
+  // yes, this is representation indepedent once you have an eoInit
+  eoPop<EOT>& pop   = make_pop(parser, state, init);
+
+// STOP
+  // stopping criteria
+  eoContinue<EOT> & term = make_continue(parser, state, eval);
+  // output
+  eoCheckPoint<EOT> & checkpoint = make_checkpoint(parser, state, eval, term);
+// GENERATION
+  // algorithm (need the operator!)
+  eoAlgo<EOT>& ga = make_algo_scalar(parser, state, eval, checkpoint, op, &dist);
+
+  ///// End of construction of the algorith
+  /////////////////////////////////////////
+// PARAMETRES
+  // to be called AFTER all parameters have been read!!!
+  make_help(parser);
+
+  //// GO
+  ///////
+// EVAL
+  // evaluate intial population AFTER help and status in case it takes time
+  apply<EOT>(eval, pop);
+// STOP
+  // print it out (sort witout modifying) 
+  cout << "Initial Population\n";
+  pop.sortedPrintOn(cout);
+  cout << endl;
+
+// GENERATION
+  run_ea(ga, pop); // run the ga
+// STOP
+  // print it out (sort witout modifying) 
+  cout << "Final Population\n";
+  pop.sortedPrintOn(cout);
+  cout << endl;
+// GENERAL
+  }
+  catch(exception& e)
+  {
+    cout << e.what() << endl;
+  }
+}

trunk/paradiseo-eo/tutorial/Lesson4/CVS/Entries

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+/.cvsignore/1.1/Fri Sep 17 16:53:13 2004//
+/BitEA.cpp/1.4/Tue May 25 08:03:30 2004//
+/ESEA.cpp/1.4/Thu Jan 17 17:51:58 2002//
+/ESEA.param/1.1/Mon Dec 27 07:59:58 2004//
+/Makefile.am/1.4/Wed Sep 28 21:49:25 2005//
+/Makefile.simple/1.1/Fri Sep 17 15:20:18 2004//
+/RealEA.cpp/1.2/Thu Jan 17 17:51:58 2002//
+/RealEA.param/1.1/Mon Dec 27 07:59:58 2004//
+/binary_value.h/1.3/Tue May 25 08:03:30 2004//
+/real_value.h/1.1/Thu May  3 13:06:34 2001//
+D

trunk/paradiseo-eo/tutorial/Lesson4/CVS/Repository

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+eo/tutorial/Lesson4

trunk/paradiseo-eo/tutorial/Lesson4/CVS/Root

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+:ext:evomarc@eodev.cvs.sourceforge.net:/cvsroot/eodev

trunk/paradiseo-eo/tutorial/Lesson4/ESEA.cpp

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+// Program to test several EO-ES features
+
+#ifdef _MSC_VER
+#pragma warning(disable:4786)
+#endif
+
+#include <algorithm>
+#include <string>
+#include <iostream>
+#include <iterator>
+#include <stdexcept>
+#include <time.h>
+
+using namespace std;
+
+#include <eo>
+
+// representation specific
+#include <es/make_es.h>
+
+#include "real_value.h"		// the sphere fitness
+
+// Now the main 
+/////////////// 
+typedef eoMinimizingFitness  FitT;
+
+template <class EOT>
+void runAlgorithm(EOT, eoParser& _parser, eoState& _state);
+  
+int main_function(int argc, char *argv[]) 
+{
+  // Create the command-line parser
+  eoParser parser(argc, argv);  // for user-parameter reading
+
+  eoState state;    // keeps all things allocated
+
+
+  eoValueParam<bool>& simpleParam = parser.createParam(true, "Isotropic", "Isotropic self-adaptive mutation", 'i', "ES mutation");
+  eoValueParam<bool>& stdevsParam = parser.createParam(false, "Stdev", "One self-adaptive stDev per variable", 's', "ES mutation");
+  eoValueParam<bool>& corrParam = parser.createParam(false, "Correl", "Use correlated mutations", 'c', "ES mutation");
+
+    // Run the appropriate algorithm
+    if (simpleParam.value() == false)
+    {
+      cout << "Using eoReal" << endl;
+      runAlgorithm(eoReal<FitT>(), parser, state);
+    }
+    else if (stdevsParam.value() == false)
+    {
+      cout << "Using eoEsSimple" << endl;
+      runAlgorithm(eoEsSimple<FitT>(), parser, state);
+    }
+    else if (corrParam.value() == false)
+    {
+      cout << "Using eoEsStdev" << endl;
+      runAlgorithm(eoEsStdev<FitT>(), parser, state);
+    }
+    else 
+    {
+      cout << "Using eoEsFull" << endl;
+      runAlgorithm(eoEsFull<FitT>(), parser, state);
+    }
+
+	return 0;  
+}
+
+// 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;
+}
+
+/** The templatized main (sort of)
+ *  quite similar to the main of other genotypes 
+ *  (e.g. t-eoReal and t-eoGA in test dir)
+ */
+template <class EOT>
+void runAlgorithm(EOT, eoParser& _parser, eoState& _state)
+{
+  typedef typename EOT::Fitness FitT;
+
+  ///// FIRST, problem or representation dependent stuff
+  //////////////////////////////////////////////////////
+
+  // The evaluation fn - encapsulated into an eval counter for output 
+  eoEvalFuncPtr<EOT, double, const std::vector<double>&> 
+               mainEval( real_value );
+  eoEvalFuncCounter<EOT> eval(mainEval);
+
+  // the genotype - through a genotype initializer
+  eoRealInitBounded<EOT>& init = make_genotype(_parser, _state, EOT());
+
+  // Build the variation operator (any seq/prop construct)
+  eoGenOp<EOT>& op = make_op(_parser, _state, init);
+
+  //// Now the representation-independent things
+  //////////////////////////////////////////////
+
+  // initialize the population - and evaluate
+  // yes, this is representation indepedent once you have an eoInit
+  eoPop<EOT>& pop   = make_pop(_parser, _state, init);
+  apply<EOT>(eval, pop);
+
+  // stopping criteria
+  eoContinue<EOT> & term = make_continue(_parser, _state, eval);
+  // output
+  eoCheckPoint<EOT> & checkpoint = make_checkpoint(_parser, _state, eval, term);
+  // algorithm (need the operator!)
+  eoAlgo<EOT>& ga = make_algo_scalar(_parser, _state, eval, checkpoint, op);
+
+  ///// End of construction of the algorith
+  /////////////////////////////////////////
+  // to be called AFTER all parameters have been read!!!
+  make_help(_parser);
+
+  //// GO
+  ///////
+  cout << "Initial Population\n";
+  pop.sortedPrintOn(cout);
+  cout << endl;
+
+  run_ea(ga, pop); // run the ga
+
+  cout << "Final Population\n";
+  pop.sortedPrintOn(cout);
+  cout << endl;
+}

trunk/paradiseo-eo/tutorial/Lesson4/ESEA.param

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+
+######                 General    ######
+# --help=0                                 # -h : Prints this message
+# --stopOnUnknownParam=1                   # Stop if unkown param entered
+# --seed=1104133126                        # -S : Random number seed
+
+######    ES mutation             ######
+# --Isotropic=1                            # -i : Isotropic self-adaptive mutation
+# --Stdev=0                                # -s : One self-adaptive stDev per variable
+# --Correl=0                               # -c : Use correlated mutations
+
+######    Evolution Engine        ######
+--popSize=1                             # -P : Population Size
+--selection=Sequential                   # -S : Selection: DetTour(T), StochTour(t), Roulette, Ranking(p,e) or Sequential(ordered/unordered)
+--nbOffspring=700%                       # -O : Nb of offspring (percentage or absolute)
+--replacement=Comma                      # -R : Replacement: Comma, Plus or EPTour(T), SSGAWorst, SSGADet(T), SSGAStoch(t)
+--weakElitism=0                          # -w : Old best parent replaces new worst offspring *if necessary*
+
+######    Genotype Initialization    ######
+# --vecSize=10                             # -n : The number of variables 
+# --initBounds=10[-1,1]                    # -B : Bounds for initialization (MUST be bounded)
+--sigmaInit=0.3%                          # -s : Initial value for Sigmas (with a '%' -> scaled by the range of each variable)
+
+######    Output                  ######
+# --useEval=1                              # Use nb of eval. as counter (vs nb of gen.)
+# --useTime=1                              # Display time (s) every generation
+# --printBestStat=1                        # Print Best/avg/stdev every gen.
+# --printPop=0                             # Print sorted pop. every gen.
+
+######    Output - Disk           ######
+# --resDir=Res                             # Directory to store DISK outputs
+# --eraseDir=1                             # erase files in dirName if any
+# --fileBestStat=0                         # Output bes/avg/std to file
+
+######    Output - Graphical      ######
+# --plotBestStat=0                         # Plot Best/avg Stat
+# --plotHisto=0                            # Plot histogram of fitnesses
+
+######    Persistence             ######
+# --Load=                                  # -L : A save file to restart from
+# --recomputeFitness=0                     # -r : Recompute the fitness after re-loading the pop.?
+# --saveFrequency=0                        # Save every F generation (0 = only final state, absent = never)
+# --saveTimeInterval=0                     # Save every T seconds (0 or absent = never)
+# --status=t-eoESAll.status                # Status file
+
+######    Stopping criterion      ######
+# --maxGen=100                             # -G : Maximum number of generations () = none)
+# --steadyGen=100                          # -s : Number of generations with no improvement
+# --minGen=0                               # -g : Minimum number of generations
+# --maxEval=0                              # -E : Maximum number of evaluations (0 = none)
+# --targetFitness=0                        # -T : Stop when fitness reaches
+# --CtrlC=0                                # -C : Terminate current generation upon Ctrl C
+
+######    Variation Operators     ######
+# --objectBounds=10[-inf,+inf]             # -B : Bounds for variables
+# --operator=SGA                           # -o : Description of the operator (SGA only now)
+# --pCross=1                               # -C : Probability of Crossover
+# --pMut=1                                 # -M : Probability of Mutation
+# --crossType=global                       # -C : Type of ES recombination (global or standard)
+# --crossObj=discrete                      # -O : Recombination of object variables (discrete, intermediate or none)
+# --crossStdev=intermediate                # -S : Recombination of mutation strategy parameters (intermediate, discrete or none)
+# --TauLoc=1                               # -l : Local Tau (before normalization)

trunk/paradiseo-eo/tutorial/Lesson4/Makefile.am

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+noinst_PROGRAMS		= BitEA RealEA ESEA
+
+
+BitEA_SOURCES		= BitEA.cpp
+
+RealEA_SOURCES		= RealEA.cpp
+
+ESEA_SOURCES		= ESEA.cpp
+
+
+noinst_HEADERS		= binary_value.h \
+			real_value.h
+
+extra_DIST		= Makefile.simple
+
+
+AM_CXXFLAGS		= -I$(top_srcdir)/src
+
+LIBEO			= $(top_builddir)/src/libeo.a
+LIBES			= $(top_builddir)/src/es/libes.a
+LIBGA			= $(top_builddir)/src/ga/libga.a
+LIBUTILS		= $(top_builddir)/src/utils/libeoutils.a
+
+DEPS			= $(LIBEO) $(LIBUTILS) $(LIBES) $(LIBGA)
+
+LIBS			= $(LIBES) $(LIBGA) $(LIBEO) $(LIBUTILS)

trunk/paradiseo-eo/tutorial/Lesson4/Makefile.simple

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+### This Makefile is part of the tutorial of the EO library
+# Unlike other Makefiles in EO, it is not using the automake/autoconf 
+# so that it stays easy to understant (you are in the tutorial, remember!)
+# MS, Oct. 2002
+
+# if you use this Makefile as a starting point for another application
+# you might need to modify the following
+DIR_EO = ../../src
+
+.SUFFIXES: .cpp
+
+# Warning: $(CXX) in Linux (RedHat and Mandrake at least) is g++
+# However, if you are using this Makefile within xemacs, 
+# and have problems with the interpretation of the output (and its colors)
+# then you should use c++ instead (make CXX=c++ will do)
+
+.cpp: ; $(CXX)  -DPACKAGE=\"eo\" -DVERSION=\"0.9.3\" -I. -I$(DIR_EO) -Wall -g -o $@  $*.cpp $(DIR_EO)/utils/libeoutils.a $(DIR_EO)/libeo.a 
+
+.cpp.o: ; $(CXX) -DPACKAGE=\"eo\" -DVERSION=\"0.9.3\" -I. -I$(DIR_EO) -Wall -g -c $*.cpp
+
+ALL = BitEA RealEA ESEA
+
+all : $(ALL)
+
+BitEA : BitEA.o ; 
+	$(CXX)  -DPACKAGE=\"eo\" -DVERSION=\"0.9.2\" -Wall -g  -o $@  $<  $(DIR_EO)/ga/libga.a $(DIR_EO)/utils/libeoutils.a $(DIR_EO)/libeo.a 
+
+RealEA : RealEA.o ; $(CXX)  -DPACKAGE=\"eo\" -DVERSION=\"0.9.2\" -Wall -g  -o $@  $< $(DIR_EO)/es/libes.a $(DIR_EO)/utils/libeoutils.a $(DIR_EO)/libeo.a
+
+ESEA : ESEA.o ; $(CXX)  -DPACKAGE=\"eo\" -DVERSION=\"0.9.2\" -Wall -g  -o $@  $< $(DIR_EO)/es/libes.a $(DIR_EO)/utils/libeoutils.a $(DIR_EO)/libeo.a
+
+clean : 
+	@/bin/rm $(ALL) *.o *.sav *.xg *.status *~

trunk/paradiseo-eo/tutorial/Lesson4/RealEA.cpp

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+#include <iostream>
+
+#include <es/make_real.h>
+#include "real_value.h"
+#include <apply.h>
+
+using namespace std;
+
+int main(int argc, char* argv[])
+{
+
+  try
+  {
+  typedef eoReal<eoMinimizingFitness> EOT;
+
+  eoParser parser(argc, argv);  // for user-parameter reading
+
+  eoState state;    // keeps all things allocated
+
+  ///// FIRST, problem or representation dependent stuff
+  //////////////////////////////////////////////////////
+
+  // The evaluation fn - encapsulated into an eval counter for output 
+  eoEvalFuncPtr<EOT, double, const std::vector<double>&> 
+               mainEval( real_value );
+  eoEvalFuncCounter<EOT> eval(mainEval);
+
+  // the genotype - through a genotype initializer
+  eoRealInitBounded<EOT>& init = make_genotype(parser, state, EOT());
+
+  // Build the variation operator (any seq/prop construct)
+  eoGenOp<EOT>& op = make_op(parser, state, init);
+
+  //// Now the representation-independent things
+  //////////////////////////////////////////////
+
+  // initialize the population - and evaluate
+  // yes, this is representation indepedent once you have an eoInit
+  eoPop<EOT>& pop   = make_pop(parser, state, init);
+
+  // stopping criteria
+  eoContinue<EOT> & term = make_continue(parser, state, eval);
+  // output
+  eoCheckPoint<EOT> & checkpoint = make_checkpoint(parser, state, eval, term);
+  // algorithm (need the operator!)
+  eoAlgo<EOT>& ea = make_algo_scalar(parser, state, eval, checkpoint, op);
+
+  ///// End of construction of the algorith
+  /////////////////////////////////////////
+  // to be called AFTER all parameters have been read!!!
+  make_help(parser);
+
+  //// GO
+  ///////
+  // evaluate intial population AFTER help and status in case it takes time
+  apply<EOT>(eval, pop);
+  // print it out
+  cout << "Initial Population\n";
+  pop.sortedPrintOn(cout);
+  cout << endl;
+
+  run_ea(ea, pop); // run the ea
+
+  cout << "Final Population\n";
+  pop.sortedPrintOn(cout);
+  cout << endl;
+  }
+  catch(exception& e)
+  {
+    cout << e.what() << endl;
+  }
+}

trunk/paradiseo-eo/tutorial/Lesson4/RealEA.param

@@ -0,0 +1,57 @@
+
+######                 General    ######
+# --help=0                                 # -h : Prints this message
+# --stopOnUnknownParam=1                   # Stop if unkown param entered
+# --seed=1104133126                        # -S : Random number seed
+
+######    Evolution Engine        ######
+--popSize=10                             # -P : Population Size
+--selection=Sequential                   # -S : Selection: DetTour(T), StochTour(t), Roulette, Ranking(p,e) or Sequential(ordered/unordered)
+--nbOffspring=700%                       # -O : Nb of offspring (percentage or absolute)
+--replacement=Plus                      # -R : Replacement: Comma, Plus or EPTour(T), SSGAWorst, SSGADet(T), SSGAStoch(t)
+--weakElitism=0                          # -w : Old best parent replaces new worst offspring *if necessary*
+
+######    Genotype Initialization    ######
+# --vecSize=10                             # -n : The number of variables 
+# --initBounds=10[-1,1]                    # -B : Bounds for initialization (MUST be bounded)
+--sigmaInit=0.3%                          # -s : Initial value for Sigmas (with a '%' -> scaled by the range of each variable)
+
+######    Output                  ######
+# --useEval=1                              # Use nb of eval. as counter (vs nb of gen.)
+# --useTime=1                              # Display time (s) every generation
+# --printBestStat=1                        # Print Best/avg/stdev every gen.
+# --printPop=0                             # Print sorted pop. every gen.
+
+######    Output - Disk           ######
+# --resDir=Res                             # Directory to store DISK outputs
+# --eraseDir=1                             # erase files in dirName if any
+# --fileBestStat=0                         # Output bes/avg/std to file
+
+######    Output - Graphical      ######
+# --plotBestStat=0                         # Plot Best/avg Stat
+# --plotHisto=0                            # Plot histogram of fitnesses
+
+######    Persistence             ######
+# --Load=                                  # -L : A save file to restart from
+# --recomputeFitness=0                     # -r : Recompute the fitness after re-loading the pop.?
+# --saveFrequency=0                        # Save every F generation (0 = only final state, absent = never)
+# --saveTimeInterval=0                     # Save every T seconds (0 or absent = never)
+# --status=t-eoESAll.status                # Status file
+
+######    Stopping criterion      ######
+# --maxGen=100                             # -G : Maximum number of generations () = none)
+# --steadyGen=100                          # -s : Number of generations with no improvement
+# --minGen=0                               # -g : Minimum number of generations
+# --maxEval=0                              # -E : Maximum number of evaluations (0 = none)
+# --targetFitness=0                        # -T : Stop when fitness reaches
+# --CtrlC=0                                # -C : Terminate current generation upon Ctrl C
+
+######    Variation Operators     ######
+# --objectBounds=10[-inf,+inf]             # -B : Bounds for variables
+# --operator=SGA                           # -o : Description of the operator (SGA only now)
+# --pCross=1                               # -C : Probability of Crossover
+# --pMut=1                                 # -M : Probability of Mutation
+# --crossType=global                       # -C : Type of ES recombination (global or standard)
+# --crossObj=discrete                      # -O : Recombination of object variables (discrete, intermediate or none)
+# --crossStdev=intermediate                # -S : Recombination of mutation strategy parameters (intermediate, discrete or none)
+# --TauLoc=1                               # -l : Local Tau (before normalization)

trunk/paradiseo-eo/tutorial/Lesson4/binary_value.h

@@ -0,0 +1,25 @@
+#include <eo>
+
+//-----------------------------------------------------------------------------
+
+/** Just a simple function that takes binary value of a chromosome and sets
+    the fitnes.
+    @param _chrom A binary chromosome 
+*/
+
+template <class Chrom> double binary_value(const Chrom& _chrom)
+{
+  double sum = 0;
+  for (unsigned i = 0; i < _chrom.size(); i++)
+    if (_chrom[i])
+	sum += _chrom[i];
+  return sum;
+}
+
+struct BinaryValue
+{
+  template <class Chrom> void operator()(Chrom& _chrom)
+  {
+    _chrom.fitness(binary_value(_chrom));
+  }
+};

trunk/paradiseo-eo/tutorial/Lesson4/real_value.h

@@ -0,0 +1,19 @@
+#include <vector>
+//-----------------------------------------------------------------------------
+
+
+/** Just a simple function that takes an eoEsBase<double> and sets the fitnes 
+    to sphere 
+    @param _ind  vector<double>
+*/
+
+double real_value(const std::vector<double>& _ind)
+{
+  double sum = 0;
+  for (unsigned i = 0; i < _ind.size(); i++)
+      sum += _ind[i] * _ind[i];
+  return sqrt(sum);
+}
+
+
+