Migration from SVN

mo/tutorial/Lesson6/neutralWalk.cpp

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+//-----------------------------------------------------------------------------
+/** neutralWalk.cpp
+ *
+ * SV - 07/05/10
+ *
+ */
+//-----------------------------------------------------------------------------
+
+// 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/moRndWithoutReplNeighborhood.h> // visit one random neighbor possibly the same one several times
+
+//-----------------------------------------------------------------------------
+// the sampling class
+#include <utils/eoDistance.h>
+#include <sampling/moNeutralWalkSampling.h>
+
+//-----------------------------------------------------------------------------
+// the statistics class
+#include <sampling/moStatistics.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 steps of the random walk
+    eoValueParam<unsigned int> stepParam(100, "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
+    // more information: see EO tutorial lesson 1 (FirstBitGA.cpp)
+    rng.reseed(seed);
+
+    /* =========================================================
+     *
+     * 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 random order
+    // at each step one bit is randomly generated
+    moRndWithoutReplNeighborhood<Neighbor> neighborhood(vecSize);
+
+    /* =========================================================
+     *
+     * The sampling of the search space
+     *
+     * ========================================================= */
+
+    // Initial Solution of the random neutral walk
+    Indi initialSol(vecSize, false);
+
+    //          nearly 2 blocks are complete
+    for (unsigned i = 0; i < blockSize - 1; i++) {
+        initialSol[i] = true;
+        initialSol[blockSize + i] = true;
+        initialSol[2 * blockSize + i] = true;
+    }
+    //          first block is complete
+    initialSol[blockSize - 1] = true;
+
+    //          evaluation of the initial solution
+    fullEval(initialSol);
+
+    // Hamming distance
+    eoHammingDistance<Indi> distance;
+
+    // sampling object :
+    //    - random initialization
+    //    - neighborhood to compute the next step
+    //    - fitness function
+    //    - neighbor evaluation
+    //    - number of steps of the walk
+    moNeutralWalkSampling<Neighbor> sampling(initialSol, neighborhood, fullEval, neighborEval, distance, nbStep);
+
+    /* =========================================================
+     *
+     * execute the sampling
+     *
+     * ========================================================= */
+
+    std::cout << "Initial Solution: " << initialSol << std::endl;
+
+    // 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<Indi> & solutions = sampling.getSolutions(0);
+
+    std::cout << "First values:" << std::endl;
+    std::cout << "Solution  " << solutions[0] << std::endl;
+
+    std::cout << "Last values:" << std::endl;
+    std::cout << "Solution  " << solutions[solutions.size() - 1] << std::endl;
+
+    // export only the solution into file
+    sampling.fileExport(0, str_out + "_sol");
+
+    // more basic statistics on the distribution:
+    moStatistics statistics;
+
+    vector< vector<double> > dist;
+    vector<double> v;
+
+    statistics.distances(solutions, distance, dist);
+
+    for (unsigned i = 0; i < dist.size(); i++) {
+        for (unsigned j = 0; j < dist.size(); j++) {
+            std::cout << dist[i][j] << " " ;
+            if (j < i)
+                v.push_back(dist[i][j]);
+        }
+        std::cout << std::endl;
+    }
+
+    double min, max, avg, std;
+    statistics.basic(v, min, max, avg, std);
+    std::cout << "min=" << min << ", max=" << max << ", average=" << avg << ", std dev=" << std << 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;
+}