ex5.c

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/* ----------------------------------------------------------------------------
  ex5.C
  mbwall 10dec94
  Copyright 1995-1996  Massachusetts Institute of Technology

 DESCRIPTION:
   Example program for a composite genome derived from the GAGenome and
containing a 2DBinStr genome and a Bin2Dec genome.  This program uses
a steady-state GA to match a 2D pattern in the 2DBinStr part of the genome
and a sequence of numbers in the Bin2Dec part.
   In this example we derive a new genome and a new crossover object to be
used with it.  All of the operators (initialization, mutation, crossover, 
comparison, and objective) are defined as member functions but are also
override-able on any instance of the new genome.
---------------------------------------------------------------------------- */
#include <stdio.h>
#include <stdlib.h>
#include <iostream.h>
#include <fstream.h>
#include <math.h>
#include <ga/GABin2DecGenome.h>
#include <ga/GA2DBinStrGenome.h>
#include <ga/GASStateGA.h>




// This is the class definition for the new genome.  The default operators are
// defined as static member functions.  They can be overridden if necessary by
// anyone making an instance of this class - you don't need to derive a new
// class to change the behaviour of one or two of its operators.
class CompositeGenome : public GAGenome {
public:
  GADefineIdentity("CompositeGenome", 201);

  static void CompositeInitializer(GAGenome&);
  static int CompositeMutator(GAGenome&, float);
  static float CompositeComparator(const GAGenome&, const GAGenome&);
  static int CompositeCrossover(const GAGenome&, const GAGenome&,
				GAGenome*, GAGenome*);
public:
  CompositeGenome(int, int, GABin2DecPhenotype&, 
		  GAGenome::Evaluator f=NULL, void* u=NULL);
  CompositeGenome(const CompositeGenome & orig);
  CompositeGenome& operator=(const GAGenome& g);
  virtual ~CompositeGenome();
  virtual GAGenome* clone(GAGenome::CloneMethod) const ;
  virtual void copy(const GAGenome & c);
  virtual int equal(const GAGenome& g) const;
  virtual int read(istream & is);
  virtual int write(ostream & os) const;

  GA2DBinaryStringGenome & binstr() const {return *str;}
  GABin2DecGenome & bin2dec() const {return *b2d;}

protected:
  GA2DBinaryStringGenome *str;
  GABin2DecGenome *b2d;
};







// Member functions for the composite genome object
CompositeGenome::
CompositeGenome(int element, int bond, GABin2DecPhenotype& p, 
		GAGenome::Evaluator f, void* u) :
		GAGenome(  CompositeInitializer,
			 CompositeMutator,
			 CompositeComparator) {
		  evaluator(f); userData(u); crossover(CompositeCrossover);
		  str = new GA2DBinaryStringGenome(element, bond, f, u);
		  b2d = new GABin2DecGenome(p, f, u);
		}

CompositeGenome::CompositeGenome(const CompositeGenome & orig) {
  str = new GA2DBinaryStringGenome(orig.binstr());
  b2d = new GABin2DecGenome(orig.bin2dec());
  copy(orig);
}
  
CompositeGenome& 
CompositeGenome::operator=(const GAGenome& g) { copy(g); return *this; }

CompositeGenome::~CompositeGenome() { delete str; delete b2d; }

GAGenome* 
CompositeGenome::clone(GAGenome::CloneMethod) const {
  return new CompositeGenome(*this);
}

void 
CompositeGenome::copy(const GAGenome & c){
  if(&c != this && sameClass(c)){
    GAGenome::copy(c);
    CompositeGenome & bc = (CompositeGenome &)c;
    str->copy(*(bc.str));
    b2d->copy(*(bc.b2d));
  }
}

int 
CompositeGenome::equal(const GAGenome& g) const {
  CompositeGenome& genome = (CompositeGenome&)g;
  return ((*str == *genome.str) && (*b2d == *genome.b2d));
}

int 
CompositeGenome::read(istream & is) {
  is >> *str >> *b2d; 
  return is.fail() ? 1 : 0; 
}

int 
CompositeGenome::write(ostream & os) const {
  int i,j;
  for(j=0; j<str->height(); j++){
    for(i=0; i<str->width(); i++)
      os << (str->gene(i,j) == 1 ? '*' : ' ') << " ";
    os << "\n";
  }
  os << "\n" << *b2d << "\n";
  return os.fail() ? 1 : 0;
}



// These are the default initialization, mutation, and comparator operators for
// this genome class.  They are defined as static functions of the composite
// genome class and they're defaults for the class.  But they can be overridden
// on any instance of the genome.

// The initializer just calls the initializer for each of the genomes that are
// in the composite genome.

// I would have used simply 'Initializer', 'Mutator', etc rather than
// 'CompositeInitializer' but old versions of g++ are brain-dead and don't
// get the encapsulation properly.
void 
CompositeGenome::CompositeInitializer(GAGenome & c) {
  CompositeGenome & child = (CompositeGenome &)c;
  child.binstr().initialize();
  child.bin2dec().initialize();
  child._evaluated = gaFalse;
}


// The mutator just calls the mutator for each of the component genomes.
int 
CompositeGenome::CompositeMutator(GAGenome & c, float pmut) {
  CompositeGenome & child = (CompositeGenome &)c;
  int nmut = child.binstr().mutate(pmut) + child.bin2dec().mutate(pmut);
  if(nmut) child._evaluated = gaFalse;
  return nmut;
}

// The comparator just calls the comparators for each of the component genomes,
// then averages the score.
float 
CompositeGenome::CompositeComparator(const GAGenome& a, const GAGenome& b) {
  CompositeGenome& sis = (CompositeGenome &)a;
  CompositeGenome& bro = (CompositeGenome &)b;
  return 0.5 * (sis.binstr().compare(bro) + sis.bin2dec().compare(bro));
}

// The crossover operator invokes the crossover for each of the genomes in the
// composite genome.  We use sexual crossover only, and we do not test to see
// if no crossover has been assigned.
int
CompositeGenome::
CompositeCrossover(const GAGenome& a, const GAGenome& b,
		   GAGenome* c, GAGenome* d){ 
  CompositeGenome& mom = (CompositeGenome&)a;
  CompositeGenome& dad = (CompositeGenome&)b;
  int n=0;

  GAGenome::SexualCrossover strcross = mom.str->sexual();
  GAGenome::SexualCrossover b2dcross = mom.b2d->sexual();

  if(c && d){
    CompositeGenome& sis = (CompositeGenome&)*c;
    CompositeGenome& bro = (CompositeGenome&)*d;
    (*strcross)(mom.binstr(), dad.binstr(), &sis.binstr(), &bro.binstr());
    (*b2dcross)(mom.bin2dec(),dad.bin2dec(), &sis.bin2dec(), &bro.bin2dec());
    sis._evaluated = gaFalse;
    bro._evaluated = gaFalse;
    n = 2;
  }
  else if(c){
    CompositeGenome& sis = (CompositeGenome&)*c;
    (*strcross)(mom.binstr(), dad.binstr(), &sis.binstr(), 0);
    (*b2dcross)(mom.bin2dec(), dad.bin2dec(), &sis.bin2dec(), 0);
    sis._evaluated = gaFalse;
    n = 1;
  }
  else if(d){
    CompositeGenome& bro = (CompositeGenome&)*d;
    (*strcross)(mom.binstr(), dad.binstr(), 0, &bro.binstr());
    (*b2dcross)(mom.bin2dec(), dad.bin2dec(), 0, &bro.bin2dec());
    bro._evaluated = gaFalse;
    n = 1;
  }

  return n;
}

















// This object is a container for the data that we are supposed to match in 
// our objective function.
typedef struct _CompositeData {
  short ** str;
  float * b2d;
} CompositeData;

// In this objective function we try to match the pattern in the 2D part of the
// genome and match the sequence of values in the binary-to-decimal part of the
// genome.  The overall score is the sum of both parts.
float
Objective(GAGenome & g) {
  CompositeGenome & genome = (CompositeGenome &)g;
  GA2DBinaryStringGenome & str = genome.binstr();
  GABin2DecGenome & b2d = genome.bin2dec();

  int i;

  short **pattern = ((CompositeData *)g.userData())->str;

  float val1=0.0;
  for(i=0; i<str.width(); i++)
    for(int j=0; j<str.height(); j++)
      val1 += (float)(str.gene(i,j) == pattern[i][j]);

  float *sequence = ((CompositeData *)g.userData())->b2d;

  float val2=b2d.nPhenotypes();
  for(i=0; i<b2d.nPhenotypes(); i++)
    val2 += 1.0 / (1.0 + fabs(b2d.phenotype(i) - sequence[i]));

  return(val1 + val2);
}











int
main(int argc, char *argv[])
{
  cout << "Example 5\n\n";
  cout << "This program shows how to use a composite genome.  It reads\n";
  cout << "a matrix from a data file and a set of values to be matched in\n";
  cout << "a binary-to-decimal genome then uses a steady-state GA to\n";
  cout << "match the pattern and value set.\n\n";

// See if we've been given a seed to use (for testing purposes).  When you
// specify a random seed, the evolution will be exactly the same each time
// you use that seed number.

  for(int ii=1; ii<argc; ii++) {
    if(strcmp(argv[ii++],"seed") == 0) {
      GARandomSeed((unsigned int)atoi(argv[ii]));
    }
  }

  GAParameterList params;
  GASteadyStateGA::registerDefaultParameters(params);
  params.set(gaNpReplacement, 0.5);
  params.set(gaNscoreFilename, "bog.dat");
  params.set(gaNflushFrequency, 10);
  params.set(gaNnGenerations, 800);
  params.parse(argc, argv, gaFalse);

  int i,j, n;
  char filename1[128] = "smiley.txt";
  char filename2[128] = "values.txt";

  for(i=1; i<argc; i++){
    if(strcmp("graph", argv[i]) == 0){
      if(++i >= argc){
        cerr << argv[0] << ": you must specify a filename.\n";
        exit(1);
      }
      else{
        sprintf(filename1, argv[i]);
        continue;
      }
    }
    else if(strcmp("values", argv[i]) == 0){
      if(++i >= argc){
        cerr << argv[0] << ": you must specify a filename.\n";
        exit(1);
      }
      else{
        sprintf(filename2, argv[i]);
        continue;
      }
    }
    else if(strcmp("seed", argv[i]) == 0){
      if(++i < argc) continue;
      continue;
    }
    else {
      cerr << argv[0] << ":  unrecognized arguement: " << argv[i] << "\n\n";
      cerr << "valid arguements include standard GAlib flags plus:\n";
      cerr << "  graph\tname of graph filename (" << filename1 << ")\n";
      cerr << "  values\tname of values filename (" << filename2 << ")\n";
      cerr << "\n";
      exit(1);
    }
  }

  ifstream infile;

// First we read in the pattern for the 2DBinStr genome.
// File format is pretty simple:
//   two integers that give the height then width of the matrix,
//   then the matrix of 1's and 0's (with whitespace inbetween).

  infile.open(filename1, ios :: in);
  if(!infile){
    cerr << "Cannot open " << filename1 << " for input.\n";
    exit(1);
  }

  int height, width;
  infile >> height;
  infile >> width;

  short **target = new short*[width];
  for(i=0; i<width; i++)
    target[i] = new short[height];

  for(j=0; j<height; j++)
    for(i=0; i<width; i++)
      infile >> target[i][j];

  infile.close();

// Now we read in a sequence of numbers that the Bin2Dec genome is supposed
// to match for its objective.  File format is
// pretty simple:  a single integer that tells how many numbers will follow,
// then the sequence of numbers.

  infile.open(filename2, ios :: in);
  if(!infile){
    cerr << "Cannot open " << filename2 << " for input.\n";
    exit(1);
  }
  infile >> n;
  float *sequence = new float[n];
  for(i=0; i<n; i++)
      infile >> sequence[i];
  infile.close();

// Print out the pattern and sequence.

  cout << "input pattern:\n";
  for(j=0; j<height; j++){
    for(i=0; i<width; i++)
      cout << (target[i][j] == 1 ? '*' : ' ') << " ";
    cout << "\n";
  }
  cout << "\n"; cout.flush();

  cout << "input sequence:\n";
  for(i=0; i<n; i++)
    cout << sequence[i] << " ";
  cout << "\n"; cout.flush();

// Create a phenotype then fill it with the phenotypes we will need to map to
// the values we read from the file.  The arguments to the add() method of a
// Bin2Dec phenotype are (1) number of bits, (2) min value, and (3) max value.
// The phenotype maps a floating-point number onto the number of bits that
// you designate.  Here we just make everything use 8 bits and pick a min and
// max based upon the number we read in from the file.  You can experiment with
// the number of bits and max/min values in order to make the GA work better
// or worse.

  GABin2DecPhenotype map;
  for(i=0; i<n; i++)
    map.add(12, 0.5*sequence[i], 2.0*sequence[i]);

// Create an instance of our user data structure and stuff it with the values
// that we read in from the files.

  CompositeData mydata;
  mydata.str = target;
  mydata.b2d = sequence;

// Now create the GA and run it.  First a genome, then the GA.
  CompositeGenome genome(width, height, map, Objective, (void *)&mydata);
  GASteadyStateGA ga(genome);
  ga.parameters(params);
  ga.parameters(argc,argv);
  ga.evolve();

  genome = ga.statistics().bestIndividual();
  cout << "\nthe ga generated:\n" << genome << "\n";

// Don't forget to free up the memory we allocated.

  for(i=0; i<width; i++)
    delete target[i];
  delete [] target;
  delete [] sequence;

  return 0;
}