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109
eo/src/eoAged.h
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// eoAged.h
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoAge.h
// (c) GeNeura Team, 1998
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef EOAGED_H
#define EOAGED_H
//-----------------------------------------------------------------------------
#include <iostream> // istream, ostream
#include <string> // para string
using namespace std;
//-----------------------------------------------------------------------------
// eoAge
//-----------------------------------------------------------------------------
/** eoAge is a template class that adds an age to an object.\\
Requisites for template instantiation are that the object must admit a default ctor
and a copy ctor. The Object must be an eoObject, thus, it must have its methods: className,
printOn, readFrom.
@see eoObject
*/
template <class Object>
class eoAged: public Object
{
public:
/// Main ctor from an already built Object.
eoAged( const Object& _o): Object( _o ), age(0) {};
/// Copy constructor.
eoAged( const eoAged& _a): Object( _a ), age( _a.age ) {};
/// Virtual dtor. They are needed in virtual class hierarchies
virtual ~eoAged() {};
///returns the age of the object
unsigned long Age() const {return age;}
/// Increments age
const eoAged& operator ++ () { age++; return *this;}
/** @name Methods from eoObject
readFrom and printOn are directly inherited from eo1d
*/
//@{
/** Return the class id. This should be redefined in each class; but
it's got code as an example of implementation. Only "leaf" classes
can be non-virtual.
*/
virtual string className() const { return string("eoAged")+Object::className(); };
/**
* Read object.
* @param _is A istream.
* @throw runtime_exception If a valid object can't be read.
*/
virtual void readFrom(istream& _is) {
Object::readFrom( _is );
_is >> age;
}
/**
* Write object. It's called printOn since it prints the object _on_ a stream.
* @param _os A ostream.
*/
virtual void printOn(ostream& _os) const{
Object::printOn( _os );
_os << age;
}
//@}
private:
/** Default Constructor. \\
It´s private so that it is not used anywhere; the right way of using this object
is to create an Object and passing it to an aged by means of the copy ctor; that way
it´s turned into an Aged object*/
eoAged(): Object(), age(0) {};
unsigned long age;
};
#endif EOAGE_H

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eo/src/eoBin.h
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/*
eoBin.h
(c) GeNeura Team 1998
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
#ifndef eoBin_h
#define eoBin_h
//-----------------------------------------------------------------------------
#include <iostream> // ostream, istream
#include <functional> // bind2nd
#include <string> // string
#include <eoVector.h> // EO
/** eoBin: implementation of binary chromosome.
* based on STL's bit_vector (vector<bool>).
*/
template <class F> class eoBin: public eoVector<bool, F>
{
public:
/**
* (Default) Constructor.
* @param size Size of the binary string.
*/
eoBin(unsigned size = 0, bool value = false):
eoVector<bool,F>(size, value) {}
/**
* Constructor.
* @param size Size of the binary string.
*/
eoBin(unsigned size, const eoRnd<bool>& rnd): eoVector<bool,F>(size)
{
generate(begin(), end(), rnd);
}
/** Constructor from istream.
@param is The istream to read from.*/
eoBin(istream& _is):eoVector<bool,F>(_is){};
/// My class name.
string className() const
{
return "eoBin";
}
/**
* To print me on a stream.
* @param os The ostream.
*/
void printOn(ostream& os) const
{
copy(begin(), end(), ostream_iterator<bool>(os));
}
/**
* To read me from a stream.
* @param is The istream.
*/
void readFrom(istream& is)
{
string bits;
is >> bits;
if (is)
{
resize(bits.size());
transform(bits.begin(), bits.end(), begin(),
bind2nd(equal_to<char>(), '1'));
}
}
};
//-----------------------------------------------------------------------------
#endif eoBin_h

325
eo/src/eoBitOp.h
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//-----------------------------------------------------------------------------
// eoBitOp.h
//-----------------------------------------------------------------------------
#ifndef eoBitOp_h
#define eoBitOp_h
//-----------------------------------------------------------------------------
#include <algorithm> // swap_ranges
#include <eoUniform.h> // eoUniform
#include <eoBin.h> // eoBin
#include <eoOp.h> // eoMonOp
/** @name BitWise Genetic operators
Even as these operators might seem general, they are particular versions of genetic
operators useful only for binary operators. As any set of genetic operators, it must
have a factory that knows how to build them from a description
@author GeNeura Team
@version 0.1
@see eoBin
@see eoBitOpFactory
*/
//@{
/** eoBinRandom --> mofify a chromosome in a random way */
template<class Chrom> class eoBinRandom: public eoMonOp<Chrom>
{
public:
/// The class name.
string className() const { return "eoBinRandom"; }
/**
* Randomizes a cromosome.
* @param chrom The cromosome to be randomize.
*/
void operator()(Chrom& chrom) const
{
eoUniform<float> uniform(0.0, 1.0);
for (unsigned i = 0; i < chrom.size(); i++)
chrom[i] = (uniform() < 0.5) ? false : true;
}
};
/** eoBinBitFlip --> chages a bit */
template<class Chrom> class eoBinBitFlip: public eoMonOp<Chrom>
{
public:
/// The class name.
string className() const { return "eoBinBitFlip"; }
/**
* Change one bit.
* @param chrom The cromosome which one bit is going to be changed.
*/
void operator()(Chrom& chrom) const
{
eoUniform<int> uniform(0, chrom.size());
unsigned i = uniform();
chrom[i] = (chrom[i]) ? false : true;
}
};
/** eoBinMutation --> classical mutation */
template<class Chrom> class eoBinMutation: public eoMonOp<Chrom>
{
public:
/**
* (Default) Constructor.
* @param _rate Rate of mutation.
*/
eoBinMutation(const double& _rate = 0.01): rate(_rate), uniform(0.0, 1.0) {}
/// The class name.
string className() const { return "eoBinMutation"; }
/**
* Mutate a chromosome.
* @param chrom The chromosome to be mutated.
*/
void operator()(Chrom& chrom) const
{
for (unsigned i = 0; i < chrom.size(); i++)
if (uniform() < rate)
chrom[i] = !chrom[i];
}
private:
double rate;
mutable eoUniform<float> uniform;
};
/** eoBinInversion: inverts the bits of the chromosome between an interval */
template<class Chrom> class eoBinInversion: public eoMonOp<Chrom>
{
public:
/// The class name.
string className() const { return "eoBinInversion"; }
/**
* Inverts a range of bits in a binary chromosome.
* @param chrom The chromosome whos bits are going to be inverted (a range).
*/
void operator()(Chrom& chrom) const
{
eoUniform<unsigned> uniform(0, chrom.size() + 1);
unsigned u1 = uniform(), u2;
do u2 = uniform(); while (u1 == u2);
unsigned r1 = min(u1, u2), r2 = max(u1, u2);
reverse(chrom.begin() + r1, chrom.begin() + r2);
}
};
/** eoBinNext --> next binary value */
template<class Chrom> class eoBinNext: public eoMonOp<Chrom>
{
public:
/// The class name.
string className() const { return "eoBinNext"; }
/**
* Change the bit string x to be x+1.
* @param chrom The chromosome to be added one.
*/
void operator()(Chrom& chrom) const
{
for (int i = chrom.size() - 1; i >= 0; i--)
if (chrom[i])
{
chrom[i] = 0;
continue;
}
else
{
chrom[i] = 1;
break;
}
}
};
/** eoBinPrev --> previos binary value */
template<class Chrom> class eoBinPrev: public eoMonOp<Chrom>
{
public:
/// The class name.
string className() const { return "eoBinPrev"; }
/**
* Change the bit string x to be x-1.
* @param chrom The chromosome to be substracted one.
*/
void operator()(Chrom& chrom) const
{
for (int i = chrom.size() - 1; i >= 0; i--)
if (chrom[i])
{
chrom[i] = 0;
break;
}
else
{
chrom[i] = 1;
continue;
}
}
};
/** eoBinCrossover --> classic crossover */
template<class Chrom> class eoBinCrossover: public eoQuadraticOp<Chrom>
{
public:
/// The class name.
string className() const { return "eoBinCrossover"; }
/**
* 2-point crossover for binary chromosomes.
* @param chrom1 The first chromosome.
* @param chrom2 The first chromosome.
*/
void operator()(Chrom& chrom1, Chrom& chrom2) const
{
eoUniform<unsigned> uniform(1, min(chrom1.size(), chrom2.size()));
swap_ranges(chrom1.begin(), chrom1.begin() + uniform(), chrom2.begin());
}
};
/** eoBinNxOver --> n-point crossover */
template<class Chrom> class eoBinNxOver: public eoQuadraticOp<Chrom>
{
public:
/// (Defualt) Constructor.
eoBinNxOver(const unsigned& _num_points = 2): num_points(_num_points)
{
if (num_points < 1)
runtime_error("NxOver --> invalid number of points");
}
/// The class name.
string className() const { return "eoBinNxOver"; }
/**
* n-point crossover for binary chromosomes.
* @param chrom1 The first chromosome.
* @param chrom2 The first chromosome.
*/
void operator()(Chrom& chrom1, Chrom& chrom2) const
{
unsigned max_size = min(chrom1.size(), chrom2.size());
unsigned max_points = min(max_size - 1, num_points);
vector<bool> points(max_size, false);
eoUniform<unsigned> uniform(1, max_size);
// select ranges of bits to swap
do {
unsigned bit = uniform();
if (points[bit])
continue;
else
{
points[bit] = true;
max_points--;
}
} while (max_points);
// swap bits between chromosomes
bool change = false;
for (unsigned bit = 1; bit < points.size(); bit++)
{
if (points[bit])
change = !change;
if (change)
swap(chrom1[bit], chrom2[bit]);
}
}
private:
unsigned num_points;
};
/** eoBinGxOver --> gene crossover */
template<class Chrom> class eoBinGxOver: public eoQuadraticOp<Chrom>
{
public:
/// Constructor.
eoBinGxOver(const unsigned _gene_size, const unsigned _num_points = 2):
gene_size(_gene_size), num_points(_num_points)
{
if (gene_size < 1)
runtime_error("GxOver --> invalid gene size");
if (num_points < 1)
runtime_error("GxOver --> invalid number of points");
}
/// The class name
string className() const { return "eoBinGxOver"; }
/**
* Gene crossover for binary chromosomes.
* @param chrom1 The first chromosome.
* @param chrom2 The first chromosome.
*/
void operator()(Chrom& chrom1, Chrom& chrom2) const
{
unsigned max_genes = min(chrom1.size(), chrom2.size()) / gene_size;
unsigned cut_genes = min(max_genes, num_points);
vector<bool> points(max_genes, false);
eoUniform<unsigned> uniform(0, max_genes);
// selects genes to swap
do {
unsigned bit = uniform();
if (points[bit])
continue;
else
{
points[bit] = true;
cut_genes--;
}
} while (cut_genes);
// swaps genes
for (unsigned i = 0; i < points.size(); i++)
if (points[i])
swap_ranges(chrom1.begin() + i * gene_size,
chrom1.begin() + i * gene_size + gene_size,
chrom2.begin() + i * gene_size);
}
private:
unsigned gene_size;
unsigned num_points;
};
//-----------------------------------------------------------------------------
//@}
#endif eoBitOp_h

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eo/src/eoBitOpFactory.h
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// eoBitOpFactory.h
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoOpFactory.h
// (c) GeNeura Team, 1998
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef _EOBITOPFACTORY_H
#define _EOBITOPFACTORY_H
#include <eoOpFactory.h>
#include <eoBitOp.h>
//-----------------------------------------------------------------------------
/** EO Factory. An instance of the factory class to create operators that act
on bitstring chromosomes. Only those chromosomes can instantiate the operators
that are created here
@see eoSelect*/
template< class EOT>
class eoBitOpFactory: public eoOpFactory<EOT> {
public:
/// @name ctors and dtors
//{@
/// constructor
eoBitOpFactory( ) {};
/// destructor
virtual ~eoBitOpFactory() {};
//@}
/** Another factory method: creates an object from an istream, reading from
it whatever is needed to create the object. Usually, the format for the istream will be\\
objectType parameter1 parameter2 ... parametern\\
If there are problems, an exception is raised; it should be caught at the
upper level, because it might be something for that level\\
At the same time, it catches exceptions thrown at a lower level, which will
indicate that whatever is in the stream is for this method to process
@param _is an stream from where a single line will be read
@throw runtime_exception if the object type is not known
*/
virtual eoOp<EOT>* make(istream& _is) {
eoOp<EOT> * opPtr = NULL;
try {
opPtr = eoOpFactory<EOT>::make( _is );
} catch ( const string& objectTypeStr ) {
if ( objectTypeStr == "eoBinRandom") {
opPtr = new eoBinRandom<EOT>();
}
if ( objectTypeStr == "eoBinBitFlip" ) {
opPtr = new eoBinBitFlip<EOT>( );
}
if ( objectTypeStr == "eoBinMutation" ) {
float rate;
_is >> rate;
opPtr = new eoBinMutation<EOT>( rate );
}
if ( objectTypeStr == "eoBinInversion" ) {
opPtr = new eoBinInversion<EOT>( );
}
if ( objectTypeStr == "eoBinNext" ) {
opPtr = new eoBinNext<EOT>( );
}
if ( objectTypeStr == "eoBinPrev" ) {
opPtr = new eoBinPrev<EOT>( );
}
if ( objectTypeStr == "eoBinNext" ) {
opPtr = new eoBinNext<EOT>( );
}
if ( objectTypeStr == "eoBinCrossover" ) {
opPtr = new eoBinCrossover<EOT>( );
}
if ( objectTypeStr == "eoBinNxOver" ) {
unsigned nPoints;
_is >> nPoints;
opPtr = new eoBinNxOver<EOT>( nPoints );
}
if ( objectTypeStr == "eoBinGxOver" ) {
unsigned geneSize, nPoints;
_is >> geneSize >> nPoints;
opPtr = new eoBinGxOver<EOT>( geneSize, nPoints );
}
if ( objectTypeStr == "eoBinUxOver" ) {
float rate;
_is >> rate;
opPtr = new eoBinUxOver<EOT>( rate );
}
if ( !opPtr ) { // to be caught by the upper level
throw objectTypeStr;
}
}
return opPtr;
};
};
#endif _EOBITOPFACTORY_H

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eo/src/eoData.h
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/** -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
-----------------------------------------------------------------------------
eoData.h
Some numeric limits and types and things like that; with #ifdefs to keep
compatibility
(c) GeNeura Team & Maarten Keijzer, 1998, 1999, 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
#ifndef EODATA_H
#define EODATA_H
//-----------------------------------------------------------------------------
#include <vector> // vector
#include <set> // set
#include <string> // string
using namespace std;
#ifdef _MSC_VER
#include <limits> // MAXDOUBLE
#define MAXFLOAT numeric_limits<float>::max()
#define MINFLOAT numeric_limits<float>::min()
#define MAXDOUBLE numeric_limits<double>::max()
#define MAXINT numeric_limits<int>::max()
#else
#include <float.h>
#include <limits.h>
#ifndef _WIN32 // should be the define for UN*X flavours: _POSIX??
#include <values.h>
#endif
#ifndef MAXFLOAT
#define MAXFLOAT (float)1e127
#define MAXDOUBLE (double)1.79769313486231570e+308
#define MAXINT 2147483647
#endif
#endif
#ifndef _MSC_VER
#include <math.h>
#define _isnan isnan
#endif
//-----------------------------------------------------------------------------
#endif EODATA_H

64
eo/src/eoDrawable.h
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoDrawable.h
// (c) GeNeura Team, 1999
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef EODRAWABLE_H
#define EODRAWABLE_H
//-----------------------------------------------------------------------------
using namespace std;
//-----------------------------------------------------------------------------
// eoDrawable
//-----------------------------------------------------------------------------
/** eoDrawable is a template class that adds a drawing interface to an object.\\
Requisites for template instantiation are that the object must admit a default ctor
and a copy ctor. The Object must be an eoObject, thus, it must have its methods: className,
eoDrawables can be drawn on any two-dimensional surface; it can be added to any
object with above characteristics.
@see eoObject
*/
template <class Object>
class eoDrawable
{
public:
/// Main ctor from an already built Object.
eoDrawable( const Object& _o): Object( _o ){};
/// Copy constructor.
eoDrawable( const eoDrawable& _d): Object( _d ){};
/// Virtual dtor. They are needed in virtual class hierarchies
virtual ~eoDrawable() {};
/**Draws the object. It must be redefined in any subclass, it´s impossible
to have a general drawing method
@param _x, _y coorinates */
virtual void draw( unsigned _x, unsigned _y) = 0;
};
#endif EODRAWABLE_H

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eo/src/eoESChrom.h
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoESChrom.h
// (c) GeNeura Team, 1998
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef _eoESCHROM_H
#define _eoESCHROM_H
// STL libraries
#include <vector> // For vector<>
#include <stdexcept>
#include <strstream>
#include <iostream> // for ostream
// EO includes
#include <eoVector.h>
/**@name Chromosomes for evolution strategies
Each chromosome in an evolution strategies is composed of a vector of floating point
values plus a vector of sigmas, that are added to them during mutation
*/
//@{
/** Each gene in an Evolution Strategies is composed of a value plus an standard
deviation, sigma, used for mutation*/
struct eoESGene {
double val, sigma;
eoESGene( double _val = 0, double _sigma = 0 ): val( _val ), sigma( _sigma ) {};
};
/// Tricky operator to avoid errors in some VC++ systems, namely VC 5.0 SP3
bool operator < ( eoESGene _e1, eoESGene _e2 ) {
return _e1.val < _e2.val;
}
/// Tricky operator to avoid errors in some VC++ systems
bool operator == ( eoESGene _e1, eoESGene _e2 ) {
return ( _e1.val == _e2.val ) && ( _e1.sigma == _e2.sigma ) ;
}
///
ostream & operator << ( ostream& _s, const eoESGene& _e ) {
_s << _e.val << ", " << _e.sigma << " | ";
return _s;
}
/// Dummy >>
istream & operator >> ( istream& _s, const eoESGene& _e ) {
_s >> _e.val;
_s >> _e.sigma;
return _s;
}
/** Basic chromosome for evolution strategies (ES), as defined by Rechenberg and
Schwefel. Each chromosomes is composed of "genes"; each one of then is an eoESGene
@see eoESGene
*/
template <typename fitT = float >
class eoESChrom: public eoVector<eoESGene, fitT> {
public:
/// Basic ctor
eoESChrom( ):eoVector<eoESGene, fitT>() {};
/** Ctor using a couple of random number generators
@param _size Lineal length of the object
@param _rnd a random number generator, which returns a random value each time it´s called.
@param _rndS another one, for the sigma
*/
eoESChrom( unsigned _size, eoRnd<double>& _rnd, eoRnd<double>& _rndS )
: eoVector<eoESGene, fitT>( _size ){
for ( iterator i = begin(); i != end(); i ++ ) {
i->val = _rnd();
i->sigma = _rndS();
}
};
/// Copy ctor
eoESChrom( const eoESChrom& _eoes): eoVector<eoESGene, fitT>( _eoes ) {};
/// Assignment operator
const eoESChrom& operator =( const eoESChrom & _eoes ) {
if ( this != &_eoes ){
eoVector<eoESGene, fitT>::operator=( _eoes );
}
return *this;
}
///
~eoESChrom() {};
/** @name Methods from eoObject
readFrom and printOn are directly inherited from eo1d
*/
//@{
/** Inherited from eoObject
@see eoObject
*/
string className() const {return "eoESChrom";};
//@}
};
//@}
#endif

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eo/src/eoESFullChrom.h
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoESInd.h
// (c) GeNeura Team, 1998 - EEAAX 1999
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
*/
//-----------------------------------------------------------------------------
#ifndef _EOESFULLCHROM_H
#define _EOESFULLCHROM_H
// STL libraries
#include <vector> // For vector<>
#include <stdexcept>
#include <strstream>
#include <iostream> // for ostream
// EO includes
#include <eoVector.h>
#include <eoRNG.h>
/**@name Chromosomes for evolution strategies
Each chromosome in an evolution strategies is composed of a vector of floating point
values plus a vector of sigmas, that are added to them during mutation and a vector of correlations
*/
//@{
/**@name individuals for evolution strategies -MS- 22/10/99
Each individual in an evolution strategy is composed of
a vector of floating point values
a vector of std deviations
a vector of rotation angles (for correlated mutations)
THese individuals CANNOT BE IMPLEMENTED as vectors of anything
at least in the case of correlated mutations
*/
//@{
template <typename fitT = float >
class eoESFullChrom : public eoVector<double, fitT> {
public:
/// constructor
eoESFullChrom( unsigned _num_genes = 1,
unsigned _num_sigma = 1, unsigned _num_correl = 0,
bool _verbose = false,
double _ObjMin = 0, double _ObjMax = 1,
double _StdDevInit = 0.3 ):
eoVector<double, fitT>(_num_genes),
// ObjVar( _num_genes ), now an eoVector<double>
StdDev( _num_sigma ),
CorCff( _num_correl ),
verbose( _verbose ),
ObjMin( _ObjMin ),
ObjMax(_ObjMax ),
StdDevInit( _StdDevInit ) {}
/// copy constructor
eoESFullChrom( const eoESFullChrom& _eo ):
eoVector<double, fitT> ( _eo ), // ObjVar ( _eo.ObjVar ),
StdDev ( _eo.StdDev ), CorCff( _eo.CorCff ), verbose( _eo.verbose ),
ObjMin( _eo.ObjMin ), ObjMax(_eo.ObjMax ), StdDevInit( _eo.StdDevInit ) {}
/* another constructor, for compatibility reasons */
eoESFullChrom(istream& _s) { cout << "Not Yet implemented\n";exit(1);};
/* And now the useful constructor: from a parser (should be in the
factory, if such a thing exists one day for eoESFullChrom
*/
eoESFullChrom(Parser & parser) : StdDev(0), CorCff(0) {
parser.AddTitle("Description of ES individuals");
int num_genes, num_sigma;
bool correlated_mutations;
try {
num_genes = parser.getInt("-Io", "--NbObjVar", "2",
"Number of Object Variables" );
num_sigma = parser.getInt("-Is", "--NbSigma", "1",
"Number of Standard Deviations" );
correlated_mutations = parser.getBool("-Ic", "--Correlated",
"Correlated mutation?" );
ObjMin = parser.getFloat("-Im", "--min", "0",
"Minimum value for object variables" );
ObjMax = parser.getFloat("-IM", "--max", "1",
"Maximum value for object variables" );
StdDevInit = parser.getFloat("-II", "--SigmaInit", "0.3",
"Initial value for std. dev. (scaled by range)" );
verbose = parser.getBool("-Iv", "--verbose",
"Verbose listing of ES individuals (mutation parameters");
}
catch (exception & e)
{
cout << e.what() << endl;
parser.printHelp();
exit(1);
}
// consistency tests
if (! num_sigma) { // no std dev??? EXCEPTION
throw invalid_argument( "No standard deviation: choose another representation please" );
}
if (num_sigma > num_genes) {
cout << "WARNING, Number of Standard Deviations > Number of Object Variables\nAdjusted!\n";
num_sigma = num_genes;
// modify the Param value - so .status is OK
ostrstream sloc;
sloc << num_genes;
parser.setParamValue("--NbSigma", sloc.str());
}
// adjust the sizes!!!
resize(num_genes);
if (num_sigma)
StdDev.resize(num_sigma);
if (correlated_mutations) {
if (num_sigma < num_genes) {
cout << "WARNING less Std Dev. than number of variables + Correlated mutations\n";
cout << "Though possible, this is a strange setting" << endl;
}
// nb of rotation angles: N*(N-1)/2 (in general!)
CorCff.resize ( (2*num_genes - num_sigma)*(num_sigma - 1) / 2 );
}
};
/// Operator =
const eoESFullChrom& operator = ( const eoESFullChrom& _eo ) {
if ( this != &_eo ) {
// Change EO part
eoVector<double, fitT>::operator = (_eo);
// Change this part
// ObjVar = _eo.ObjVar;
StdDev = _eo.StdDev;
CorCff = _eo.CorCff;
verbose = _eo.verbose;
ObjMin = _eo.ObjMin;
ObjMax = _eo.ObjMax;
StdDevInit = _eo.StdDevInit;
}
return *this;
}
/// destructor
virtual ~eoESFullChrom() {}
///
double getStdDev( unsigned _i ) const {
if ( _i >= length() )
throw out_of_range( "out_of_range when reading StdDev");
return StdDev[ _i ];
}
///
void setStdDev( unsigned _i, double _val ) {
if ( _i < length() ) {
StdDev[_i] = _val;
} else
throw out_of_range( "out_of_range when writing StdDev");
}
///
double getCorCff( unsigned _i ) const {
if ( _i >= length() )
throw out_of_range( "out_of_range when reading CorCff");
return CorCff[ _i ];
}
///
void setCorCff( unsigned _i, double _val ) {
if ( _i < length() ) {
CorCff[_i] = _val;
} else
throw out_of_range( "out_of_range when writing CorCff");
}
///
void insertGene( unsigned _i, double _val ) {
throw FixedLengthChromosome();
};
///
void deleteGene( unsigned _i ) {
throw FixedLengthChromosome();
};
///
unsigned length() const { return size();}/* formerly ObjVar.size() */
unsigned StdDevLength() const { return StdDev.size();}
unsigned CorCffLength() const { return CorCff.size();}
/** Print itself: inherited from eoObject implementation.
Instance from base classes are processed in
base classes, so you don´t have to worry about, for instance, fitness.
@param _s the ostream in which things are written*/
virtual void printOn( ostream& _s ) const{
copy( begin(), end(), ostream_iterator<double>( _s, " ") );
// The formatting instructinos shoudl be left to the caller
// _s << "\n";
if (verbose) {
_s << "\n\tStd Dev. " ;
copy( StdDev.begin(), StdDev.end(), ostream_iterator<double>( _s, " ") );
if (CorCff.size()) {
_s << "\n\t";
copy( CorCff.begin(), CorCff.end(), ostream_iterator<double>( _s, " ") );
}
}
};
/** This exception should be thrown when trying to insert or delete a gene
in a fixed length chromosome
*/
class FixedLengthChromosome : public exception {
public:
/**
* Constructor
*/
FixedLengthChromosome()
: exception() { };
~FixedLengthChromosome() {};
};
// accessors
double getObjMin() const {return ObjMin;}
double getObjMax() const {return ObjMax;}
double getStdDevInit () const {return StdDevInit;}
/** Inherited from eoObject
@see eoObject
*/
virtual string className() const {return "eoESFullChrom";};
private:
// vector<double> ObjVar; /* object variable vector */
// or shoudl the class be subclass of EOVector<double> ???
vector<double> StdDev; /* standard deviation vector */
vector<double> CorCff; /* correlation coefficient vector */
bool verbose; /* Print std deviations or not */
/** the range is used for mutation AND random initialization,
* while the StdDevInit is used only for random initialization
* this in a little inconsistent!
*/
double ObjMin, ObjMax; /* Range for Object variables */
double StdDevInit; /* Initial value of Standard Deviations */
};
#endif

253
eo/src/eoESFullMut.h
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@ -1,253 +0,0 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoESMute.h : ES mutation
// (c) GeNeura Team, 1998 for the EO part
// Th. Baeck 1994 and EEAAX 1999 for the ES part
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
marc.schoenauer@polytechnique.fr
http://eeaax.cmap.polytchnique.fr/
*/
//-----------------------------------------------------------------------------
#ifndef _EOESMUT_H
#define _EOESMUT_H
#include <eoParser.h>
#include <eoRNG.h>
#include <cmath> // for exp
#include <eoESFullChrom.h>
#include <eoOp.h>
#ifndef M_PI
#define M_PI 3.1415926535897932384626433832795
#endif
const double ES_SIGEPS = 1.0e-40; /* ES lower bound for sigma values */
// should not be a parameter ...
/** ES-style mutation in the large: Obviously, valid only for eoESInd
*/
template <class fitT>
class eoESMutate: public eoMonOp< eoESFullChrom<fitT> > {
public:
eoESMutate(double n)
{
TauLcl = 1/sqrt(2*sqrt(n));
TauGlb= 1 / sqrt(2 * n);
TauBeta = 0.0873;
}///
eoESMutate( double _TauLcl, double _TauGlb, double _TauBeta )
: eoMonOp< eoESFullChrom<fitT> >( ), TauLcl(_TauLcl), TauGlb(_TauGlb),
TauBeta(_TauBeta) {};
/* The parser constructor
*/
eoESMutate(Parser & parser, unsigned _stdDevLength, unsigned _size, bool _correlated ):
eoMonOp< eoESFullChrom<fitT> >( ) {
parser.AddTitle("Parameters of ES mutation (before renormalization)");
try { // we know that there is at least 1 std dev.
if (_stdDevLength == 1) {
TauLcl = parser.getInt("-Ml", "--TauLcl", "1",
"TauLcl, Mutation rate for the only Std Dev." );
// different normalization in that case -- Thomas Baeck
TauLcl /= sqrt((double) _size);
}
else { /* more than 1 std dev */
TauLcl = parser.getFloat("-Ml", "--TauLcl", "1",
"Local mutation rate for Std Dev." );
TauGlb = parser.getFloat("-Mg", "--TauGlb", "1",
"Global mutation rate for Std Dev." );
// renormalization
TauLcl /= sqrt( 2.0 * sqrt( (double)_size ) );
TauGlb /= sqrt( 2.0 * ( (double) _size ) );
if ( _correlated ) { // Correlated Mutations
TauBeta = parser.getFloat("-Mb", "--TauBeta", "0.0873",
"Mutation rate for corr. coeff." );
// rotation angles: no normalization
}
}
}
catch (exception & e)
{
cout << e.what() << endl;
parser.printHelp();
exit(1);
}
};
/// needed virtual dtor
virtual ~eoESMutate() {};
// virtual separation depending wether correlated mutations are present
virtual void operator() ( eoESFullChrom<fitT> & _eo ) const {
if (_eo.CorCffLength())
CorrelatedMutation(_eo);
else
StandardMutation(_eo);
}
/** @name Methods from eoObject
readFrom and printOn are directly inherited from eoObject
*/
//@{
/** Inherited from eoObject
@see eoObject
*/
virtual string className() const {return "eoESMutate";};
private:
/// mutations - standard et correlated
// =========
/*
* Standard mutation of object variables and standard
* deviations in ESs.
* If there are fewer different standard deviations available
* than the dimension of the objective function requires, the
* last standard deviation is responsible for ALL remaining
* object variables.
* Schwefel 1977: Numerische Optimierung von Computer-Modellen
* mittels der Evolutionsstrategie, pp. 165 ff.
*/
virtual void StandardMutation( eoESFullChrom<fitT> & _eo ) const {
unsigned i,k;
double Glb, StdLoc;
if (_eo.StdDevLength() == 1) { /* single StdDev -> No global factor */
StdLoc = _eo.getStdDev(0);
StdLoc *= exp(TauLcl*rng.normal());
if (StdLoc < ES_SIGEPS)
StdLoc = ES_SIGEPS;
_eo.setStdDev(0, StdLoc);
_eo.setGene( 0, _eo.getGene(0) + StdLoc*rng.normal());
i = 1;
}
else { /* more than one std dev. */
Glb = exp(TauGlb*rng.normal());
for (i = 0; i < _eo.length() && i < _eo.StdDevLength(); i++) {
StdLoc = _eo.getStdDev(i);
StdLoc *= Glb * exp(TauLcl*rng.normal());
if (StdLoc < ES_SIGEPS)
StdLoc = ES_SIGEPS;
_eo.setStdDev(i, StdLoc);
_eo.setGene( i, _eo.getGene(i) + StdLoc*rng.normal());
}
}
// last object variables: same STdDev than the preceding one
for (k = i; k < _eo.length(); k++) {
_eo.setGene( k, _eo.getGene(k) + StdLoc*rng.normal() );
}
}
/*
* Correlated mutations in ESs, according to the following
* sources:
* H.-P. Schwefel: Internal Report of KFA Juelich, KFA-STE-IB-3/80
* p. 43, 1980
* G. Rudolph: Globale Optimierung mit parallelen Evolutions-
* strategien, Diploma Thesis, University of Dortmund, 1990
*/
// Code from Thomas Baeck
virtual void CorrelatedMutation( eoESFullChrom<fitT> & _eo ) const {
int i, k, n1, n2, nq;
double d1, d2, S, C, Glb;
double tmp;
/*
* First: mutate standard deviations (as above).
*/
Glb = exp(TauGlb*rng.normal());
for (i = 0; i < _eo.StdDevLength(); i++) {
tmp = _eo.getStdDev(i);
_eo.setStdDev( i, tmp*Glb*exp(TauLcl*rng.normal()) );
}
/*
* Mutate rotation angles.
*/
for (i = 0; i < _eo.CorCffLength(); i++) {
tmp = _eo.getCorCff(i);
tmp += TauBeta*rng.normal();
// danger of VERY long loops --MS--
// while (CorCff[i] > M_PI)
// CorCff[i] -= 2.0 * M_PI;
// while (CorCff[i] < - M_PI)
// CorCff[i] += 2.0 * M_PI;
if ( fabs(tmp) > M_PI ) {
tmp -= M_PI * (int) (tmp/M_PI) ;
}
_eo.setCorCff(i, tmp);
}
/*
* Perform correlated mutations.
*/
vector<double> VarStp(_eo.size());
for (i = 0; i < _eo.size() && i < _eo.StdDevLength(); i++)
VarStp[i] = _eo.getStdDev(i)*rng.normal();
for (k = i; k < _eo.size(); k++)
VarStp[k] = _eo.getStdDev(i-1)*rng.normal();
nq = _eo.CorCffLength() - 1;
for (k = _eo.size()-_eo.StdDevLength(); k < _eo.size()-1; k++) {
n1 = _eo.size() - k - 1;
n2 = _eo.size() - 1;
for (i = 0; i < k; i++) {
d1 = VarStp[n1];
d2 = VarStp[n2];
S = sin( _eo.getCorCff(nq) );
C = cos( _eo.getCorCff(nq) );
VarStp[n2] = d1 * S + d2 * C;
VarStp[n1] = d1 * C - d2 * S;
n2--;
nq--;
}
}
for (i = 0; i < _eo.size(); i++)
_eo[i] += VarStp[i];
}
// the data
//=========
double TauLcl; /* Local factor for mutation of std deviations */
double TauGlb; /* Global factor for mutation of std deviations */
double TauBeta; /* Factor for mutation of correlation parameters */
};
/*
* Correlated mutations in ESs, according to the following
* sources:
* H.-P. Schwefel: Internal Report of KFA Juelich, KFA-STE-IB-3/80
* p. 43, 1980
* G. Rudolph: Globale Optimierung mit parallelen Evolutions-
* strategien, Diploma Thesis, University of Dortmund, 1990
*/
// Not yet implemented!
#endif

72
eo/src/eoException.h
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/** -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
-----------------------------------------------------------------------------
eoException.h
Exceptions that are possibly thrown at initialization and such should be
defined here.
(c) GeNeura Team, 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef eoException_h
#define eoException_h
#include <exception>
#include "eoObject.h"
struct eoException
{
eoException() {}
eoException(const eoObject& caller) : who_caught_it(caller.className()) {}
virtual ~eoException(){} // otherwise compiler complains
std::string who(void) const { return who_caught_it; }
virtual std::string what(void) const{ return "";}
private :
std::string who_caught_it;
};
struct eoFitnessException : public eoException
{
eoFitnessException() : eoException() {}
eoFitnessException(const eoObject& caller) : eoException(caller) {}
virtual ~eoFitnessException(){} // otherwise compiler complains
};
struct eoNegativeFitnessException : public eoFitnessException
{
eoNegativeFitnessException() : eoFitnessException() {}
eoNegativeFitnessException(const eoObject& caller) : eoFitnessException(caller) {}
virtual ~eoNegativeFitnessException(){} // otherwise compiler complains
std::string what(void) const { return "negative fitness encountered"; }
};
struct eoMinimizingFitnessException : public eoFitnessException
{
eoMinimizingFitnessException() : eoFitnessException() {}
eoMinimizingFitnessException(const eoObject& caller) : eoFitnessException(caller) {}
virtual ~eoMinimizingFitnessException(){} // otherwise compiler complains
std::string what(void) const { return "smaller fitness is better fitness, which is quite inappropriate here"; }
};
#endif

838
eo/src/eoParser.h
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@ -1,838 +0,0 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
/* eoParser.h
some classes to parser either the command line or a parameter file
(c) Marc Schoenauer and Geneura team, 1999
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef _PARSER_H
#define _PARSER_H
#include <string.h> // for strcasecmp ... maybe there's a c++ way of doing it?
// Yep there is, but needs either a simple functor for the equal function
// or a hand-rolled string template class (this isn't that horrible as
// it sounds, it just means a new string_traits class with two changed
// function definitions. (Maarten)
#ifdef _MSC_VER
#define strcasecmp(a,b) _strnicmp(a,b,strlen(a))
#endif
// STL includes
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <strstream>
#include <ctime>
// include for exceptions
#include <stdexcept> // logic_error
//-----------------------------------------------------------------------------
// Class Param
//-----------------------------------------------------------------------------
/**
* A param repesents an argument that can be passed to a program in the command line
*/
class Param {
public:
/**
* Type of params
*/
enum valueType { INT, UL, FLOAT, STRING, BOOL, ARRAY, TITLE };
/**
* Construct an Param.
* @param _shortName Short name of the argument
* @param _longName Long name of the argument
* @param _default The default value
* @param _valueType Type of the parameter ("integer","unsigned long", "float","char", "bool" and so on)
* @param _description Description of the parameter. What is useful for.
* @param _required If it is a necessary parameter or not
*/
Param (string _shortName="-h", string _longName="--help",
string _default = "", valueType _valType= STRING,
string _description="Shows this help",
bool _required=false )
: repShortName(_shortName), repLongName(_longName),
repDescription(_description ), repEnv(""), repDefault(_default),
repValue(_default), repValType( _valType),
repRequired( _required), repChanged(false) {
const char *c = repLongName.c_str();
for(unsigned i=0; i<repLongName.length() ; i++,c++) {
if( *c != '-' ) break;
}
//initialize "repEnv" depending on the long name of the parameter.
//previously the "-" (if exist) are skiped.
repEnv = c ;
};
/**
* Copy constructor
* @param _param The source param.
*/
Param (const Param& _param) :
repShortName(_param.repShortName), repLongName(_param.repLongName),
repDescription(_param.repDescription ), repEnv(_param.repEnv),
repDefault(_param.repDefault),
repValue(_param.repValue), repValType(_param.repValType),
repRequired(_param.repRequired), repChanged(_param.repChanged) {};
/**
* Virtual destructor is needed.
*/
virtual ~Param () {};
/**
* Returns the short name.
*/
const string& shortName ( void ) const { return repShortName; };
/**
* Returns the long name.
*/
const string& longName ( void ) const { return repLongName; };
/**
* Returns the description of the argument
*/
const string& description ( void ) const { return repDescription; };
/**
* Returns the environment variable of the argument
*/
const string& environment ( void ) const { return repEnv; };
/**
* Returns the default value of the argument
*/
const string& defValue ( void ) const { return repDefault; };
/**
* Sets a value for the param.
* @param _value The new value.
*/
void value ( const string& _value ) { repValue = _value; repChanged = true; };
/**
* Returns the value of the param.
*/
const string& value ( void ) const { return repValue; };
/**
* Returns if required or not.
*/
bool required ( void ) const { return repRequired; };
/**
* Returns the type of the param's value.
*/
Param::valueType valType( void ) const { return repValType; };
/**
* Returns true if the default value of the param has changed.
*/
bool changed( void ) const { return repChanged; };
private:
string repShortName;
string repLongName;
string repDescription;
string repEnv;
string repDefault;
string repValue;
Param::valueType repValType;
bool repRequired;
bool repChanged;
};
/// This operator is defined to avoid errors in some systems
inline bool operator < ( const Param& _p1, const Param& _p2 ) {
return ( _p1.shortName() < _p2.shortName() );
}
/// This operator is defined to avoid errors in some systems
inline bool operator == ( const Param& _p1, const Param& _p2 ) {
return ( _p1.shortName() == _p2.shortName() );
}
//-----------------------------------------------------------------------------
// Class Parser
//-----------------------------------------------------------------------------
/**
* Parses the command line / input parameter file / environment variables.
*/
class Parser {
public:
/**
* Constructor
* @param _argc, _ argv command line arguments
* @param _programDescription Description of the work the program does
*/
Parser ( int _argc, char **_argv , string _programDescription,
string _sFileParamName = "-P",
string _lFileParamName = "--Param") :
params(),
programName( _argv[0]), programDescription( _programDescription),
parse_argc(_argc), parse_argv(_argv), InputFileName("") {
// the input file name has to be read immediately - from command-line or environement (not input0file :-)
string _default = _argv[0];
_default += ".param";
Param param (_sFileParamName, _lFileParamName, _default, Param::STRING, "Name of the input file", 0);
// FIRST: look for the corresponding environment variable
if( getenv( param.environment().c_str() ) )
param.value(getenv(param.environment().c_str()) );
// LAST (highest priority) parse the command line arguments
for (int i=1 ; i<parse_argc ; i++)
if( ( ! strcasecmp(param.longName().c_str(), parse_argv[i]) ) ||
( ! strcmp(param.shortName().c_str(), parse_argv[i]) )
) { // found the parameter name
param.value(parse_argv[i+1]);
break;
}
// Now try to open the file
ifstream is(param.value().c_str());
if (is) // file exists ???
InputFileName = param.value().c_str();
params.push_back( param );
};
/**
* Copy constructor
* @param _parser The source parser
*/
Parser ( const Parser& _parser ) :
params(_parser.params),
programName( _parser.programName),
programDescription(_parser.programDescription),
parse_argc(_parser.parse_argc),
parse_argv(_parser.parse_argv),
InputFileName(_parser.InputFileName)
{};
/**
* Virtual destructor is needed.
*/
virtual ~Parser () {};
/**
* Adds a fake parameter == title in the output file
* @param the title
*/
void AddTitle (const string& _title)
{
Param param ( "", "", "", Param::TITLE, _title, false );
params.push_back( param );
}
/**
* Description of all parameter readings:
* @param _shortName Short name of the param.
* @param _longName Long name of the param.
* @param _default Default value.
* @param _valType Type of the parameter
* @param _description Parameter utility
* @param _required If the parameter is necessary or not
*/
/**
* Gets the string value of a param from the full parameter description
* @param see above
*/
string getString (const string& _shortName, const string& _longName,
const string& _default = "",
const string& _description="", bool _required=false) {
Param param ( _shortName, _longName, _default, Param::STRING, _description, _required );
parse( param );
params.push_back( param );
return param.value();
};
/**
* Gets the bool value of a param-flag from the full parameter description
* @param see above
*/
bool getBool (const string& _shortName, const string& _longName,
const string& _description="") {
Param param ( _shortName, _longName, "false", Param::BOOL, _description, false );
parse( param );
params.push_back( param );
if (param.value() == "true") {
return true;
}
else {
return false;
}
};
/**
* Gets the "array" (vector of strings) value of a param from the full parameter description
* @param see above
*/
vector<string> getArray (const string& _shortName, const string& _longName,
const string& _default = "",
const string& _description="", bool _required=false) {
Param param ( _shortName, _longName, _default, Param::ARRAY, _description, _required );
parse( param );
params.push_back( param );
istrstream is(param.value().c_str());
vector<string> retValue;
string tmpStr;
is >> tmpStr;
while(is){
retValue.push_back(tmpStr);
is >> tmpStr;
}
return retValue;
};
/**
* Gets the int value of a param given the full description of the parameter
* @param see above
* @exception BadType if the param's value isn't a correct int
*/
int getInt (const string& _shortName, const string& _longName,
const string& _default = "",
const string& _description="", bool _required=false) {
Param param ( _shortName, _longName, _default, Param::INT, _description, _required );
parse( param );
params.push_back( param );
// now gets the value
istrstream is( param.value().c_str());
int retValue;
is >> retValue;
if (!is) {
throw Parser::BadType(param.longName().c_str(), param.value().c_str(), "float");
return 0;
} else {
return retValue;
}
};
/**
* Gets the unsigned lon value of a param given ...
* @param see above
* @exception BadType if the param's value isn't a correct unsigned long
*/
int getUnsignedLong (const string& _shortName, const string& _longName,
const string& _default = "",
const string& _description="", bool _required=false) {
Param param ( _shortName, _longName, _default, Param::UL, _description, _required );
parse( param );
params.push_back( param );
// now gets the value
istrstream is( param.value().c_str());
unsigned long retValue;
is >> retValue;
if (!is) {
throw Parser::BadType(param.longName().c_str(), param.value().c_str(), "float");
return 0;
} else {
return retValue;
}
};
/**
* Gets the float value of a param given the description of the parameter
* @param see above
* @exception BadType if the param's value isn't a correct int
*/
float getFloat (const string& _shortName, const string& _longName,
const string& _default = "",
const string& _description="", bool _required=false) {
Param param ( _shortName, _longName, _default, Param::FLOAT, _description, _required );
parse( param );
params.push_back( param );
// now gets the value
istrstream is( param.value().c_str());
float retValue;
is >> retValue;
if (!is) {
throw Parser::BadType(param.longName().c_str(), param.value().c_str(), "float");
return 0;
} else {
return retValue;
}
};
string parse_string (istream & _is) {
string paramValue;
_is >> paramValue;
//if the first character of the string or array is not a " => just one word or array-element.
if( paramValue[0] != '\"' )
return paramValue;
if( paramValue[1] == '\"' ) // the empty string
return "" ;
//else => read until the next " (the end of the string).
const char *c = paramValue.c_str();
string tmpStr = c+1;// skip the "
if (tmpStr[tmpStr.length()-1] == '\"') { // one word only
//tmpStr[tmpStr.length()-1] = '\0';
tmpStr.erase( &tmpStr[tmpStr.length()-1] );
return tmpStr;
}
bool stop = false;
while (_is && !stop) {
_is >> paramValue;
// test last character of paramValue for "
if (paramValue[paramValue.length()-1] == '\"') {
paramValue.erase( &paramValue[paramValue.length()-1] );
//paramValue[paramValue.length()-1] = '\0';
stop = true;
}
tmpStr = tmpStr + " " + paramValue ;
}
return tmpStr;
};
void parse (Param & param) {
int i;
string tmpStr, ReadStr, FirstWord;
// FIRST: look if the associated environment variables have any value, to use them.
if( getenv( param.environment().c_str() ) ) {
//cout <<"\t\t ENV param: ,"<<p->shortName()<<", ,"<<getenv(p->environment().c_str())<<endl;
param.value(getenv(param.environment().c_str()) );
}
// SECOND: search the file parameter, if present
if ( InputFileName != "" ) {
ifstream is(InputFileName.c_str());
while (is) {
is >> tmpStr;
if ( ( !strcmp(tmpStr.c_str(), param.shortName().c_str()) ) ||
( !strcasecmp(tmpStr.c_str(), param.longName().c_str()) )
) { // found the keyword
Param::valueType tmp = param.valType();
switch ( tmp ) {
case Param::TITLE:
cerr << "Error, we should not be there" << endl;
exit(1);
break;
case Param::BOOL :
param.value("true" );
break;
case Param::INT:
case Param::UL:
case Param::FLOAT:
is >> tmpStr;
param.value(tmpStr);
break;
case Param::STRING:
tmpStr = parse_string(is);
param.value(tmpStr);
break;
case Param::ARRAY:
ReadStr = parse_string(is);
if ( ReadStr != "<" ) { // no "<" ">" --> a single string in the array
param.value(ReadStr);
break;
}
// read next word - and keep it in case of <> mismatch
FirstWord = parse_string(is);
// test for empty array
if (FirstWord == ">") {
param.value("");
break;
}
// else, read all words until ">"
tmpStr = FirstWord;
ReadStr = parse_string(is);
while ( is && (ReadStr != ">") ) {
tmpStr = tmpStr + " " + ReadStr;
ReadStr = parse_string(is);
}
if (!is) { // there was a "<" without the corresponding ">"
throw Parser::BadArrayParam( param.longName(), FirstWord );
param.value(FirstWord); // assume unique string
}
else
param.value(tmpStr);
break;
}
}
}
}
// LAST (highest priority) parse the command line arguments
for (i=1 ; i<parse_argc ; i++)
if( ( ! strcasecmp(param.longName().c_str(), parse_argv[i]) ) ||
( ! strcmp(param.shortName().c_str(), parse_argv[i]) )
) { // found the parameter name
if (param.valType() == Param::BOOL) {
//cout <<"BOOL: "<<parse_argv[i]<<" <-- true"<<endl;
param.value("true");
}else{
if (param.valType() != Param::ARRAY) { //only if it is not an array
//cout <<"TYPE: "<<parse_argv[i]<<" <-- "<<parse_argv[i+1]<<endl;
param.value(parse_argv[i+1]);
}else{ //if it is an ARRAY
i++;
ReadStr = parse_argv[i++];
//cout <<"ARRAY: <-- ";
if ( ReadStr != "<" ) { // no "<" ">" --> a single string in the array
param.value(ReadStr);
}else{
// read next word - and keep it in case of <> mismatch
FirstWord = parse_argv[i++];
// test for empty array
if (FirstWord == ">") {
param.value("");
}else{
// else, read all words until ">"
tmpStr = FirstWord;
ReadStr = parse_argv[i++];
while ( (i<parse_argc) && (ReadStr != ">") ) {
tmpStr = tmpStr + " " + ReadStr;
ReadStr = parse_argv[i++];
}
//cout <<"tmpStr ;"<<tmpStr<<"; ("<<i<<","<<parse_argc<<") "<<endl;
if ( (i>=parse_argc) && (ReadStr != ">") ) { // there was a "<" without the corresponding ">"
throw Parser::BadArrayParam( param.longName(), FirstWord );
param.value(FirstWord); // assume unique string
}else{
param.value(tmpStr);
}
}
}
}
}
break;
}
//MS after trying all possibilities, and if the value has not changed
// though the parameter was required, protest!
if (param.required() && !param.changed())
throw Parser::MissingReqParam(param.shortName());
};
/**
* Sets a new value for a param given its short name or its long name.
* @param _name One of the names of the param.
* @param _value Value to be assigned.
* @exception UnknownArg if the param doesn't exist
* @exception MissingVal if the param hasn't got a value
*/
Param::valueType setParamValue (const string& _name, const char* _value){
vector<Param>::iterator pos;
for (pos=params.begin() ; pos!=params.end() ; pos++)
if (pos->shortName()==_name || pos->longName()==_name)
break;
// if found ...
if (pos!=params.end()) {
switch ( pos->valType() ) {
case Param::TITLE:
cerr << "Error, we should not be there" << endl;
exit(1);
break;
case Param::BOOL :
pos->value("true");
break;
case Param::ARRAY :
case Param::INT:
case Param::UL:
case Param::FLOAT:
case Param::STRING:
if (_value != NULL){
pos->value(_value);
}else{
throw Parser::MissingVal(_name);
return Param::BOOL;
}
break;
} // switch
return pos->valType();
}else{
throw Parser::UnknownArg(_name);
return Param::BOOL;
}
};
/// the output method - generate the .status file (unless other name is given)
friend ostream & operator<< ( ostream & os, Parser & _parser )
{
vector<Param>::iterator p;
//print every param with its value
for ( p=_parser.params.begin(); p!=_parser.params.end(); p++ ) {
switch ( p->valType() ) {
case Param::BOOL :
if( p->value() == (string) "true")
os << p->longName();
else
os << "#" << p->longName() ; // so the name of the bool is commented out
break;
case Param::INT:
case Param::UL:
case Param::FLOAT:
os << p->longName()<<" "<<p->value();
break;
case Param::ARRAY :
os << p->longName() << " < " << p->value().c_str() << " >" ;
break;
case Param::STRING:
os << p->longName()<<" \""<<p->value().c_str()<<"\" ";
break;
case Param::TITLE:
os << endl; // Title is in the description below
break;
} // switch
os << "\t #" << p->shortName() << " : " << p->description();
if (p->valType() != Param::TITLE)
os << " [" << p->defValue() << "]" ;
os << endl;
}
return os;
};
/**
* Prints out the list of parameters in the output file (if specified)
*/
void outputParam(string _OutputFile="")
{
if (_OutputFile == "") {
_OutputFile = parse_argv[0];
_OutputFile += ".status";
}
ofstream os(_OutputFile.c_str());
os << "Parameters used by \"" << programName << "\" ("
<< programDescription << ")" << endl << endl;
os << *this;
};
/**
* Prints an automatic help in the standard output using the information
* provided by parameters
*/
void printHelp() {
vector<Param>::iterator p;
// unsigned i;
// print program name and description
cout << this->programName <<": "<<programDescription<<endl<<endl;
// print the usage when calling the program from the command line
cout << "Usage: "<< programName<<" [Options]\n";
// only short usage!
cout << "Options of the form \"-ShortName value\" or \"--LongName value\"" << endl;
// for ( i=0,p=params.begin(); p!=params.end(); i++,p++ )
// if( p->valType() != Param::TITLE ) {
// if( p->valType() != Param::BOOL ){
// cout << ( (!p->required())?"[":"");
// cout <<p->shortName()<<" value"<<i;
// cout << ( (!p->required())?"]":"")<<" ";
// }else{
// cout << "["<<p->shortName()<<"] ";
// }
// } // for p
cout << "Where:"<<endl;
for ( p=params.begin(); p!=params.end(); p++ ) {
if( p->valType() != Param::TITLE ) {
// Victor: 04-Jan-2000
// Modified because the - and -- prefixes are not needed.
/*
cout << "-" << p->shortName()
<<", --"<<p->longName()<<":\t"
<<p->description()<<endl;
*/
cout << p->shortName()
<<", " << p->longName()<<":\t"
<<p->description()<<endl;
cout << "\t(";
switch ( p->valType() ) {
case Param::INT: cout <<"Integer"; break;
case Param::UL: cout <<"Unsigned Long Integer"; break;
case Param::FLOAT: cout <<"Float"; break;
case Param::STRING: cout <<"String"; break;
case Param::ARRAY: cout <<"An array of strings, enclosed within < >"; break;
case Param::BOOL: cout << "Flag"; break;
case Param::TITLE: break;
} // switch
if(p->valType() == Param::BOOL)
cout << ") True if present" << endl;
else
cout<<") "<<( (p->required())?"Required":"Optional" )<<". By default: "<<p->defValue()<<endl;
}
else {
cout << "\n\t # " << p->description() << endl;
}
} // for p
cout << endl;
};
/**
* This class managges unknown argument exceptions.
*/
class UnknownArg : public logic_error {
public:
/**
* Constructor
* @param _arg string to be shown when the exception occurs
*/
UnknownArg( const string& _arg): logic_error( "Invalid argument: "+_arg ) { };
};
/**
* This class managges bad param types.
*/
class BadType : public logic_error {
public:
/**
* Constructor
* @param _param The param
* @param _value The value of the param
*/
BadType(const string& _param, const string& _value, const string& _correctType)
: logic_error("The value '" + _value + "' assigned to the argument " + _param + " isn't a correct "+_correctType) { };
};
/**
* This class managges exceptions produced when there isn't a value for a parameter.
*/
class MissingVal : public logic_error {
public:
/**
* Constructor
* @param _param The param
*/
MissingVal(const string& _param) : logic_error("Missing value for parameter " + _param) {};
};
/**
* This class managges exceptions produced when the user forgot a required parameter.
*/
class MissingReqParam : public logic_error {
public:
/**
* Constructor
* @param _shortName The param's short name
*/
MissingReqParam(const string& _shortName) : logic_error("Missing required parameter " + _shortName) {};
};
/**
* This class managges exceptions du to < without a > in array value
*/
class BadArrayParam : public logic_error {
public:
/**
* Constructor
* @param _param The param
* @param _first_word The first word read after the "<"
*/
BadArrayParam(const string& _param, const string &_first_word) :
logic_error("Array parameter " + _param + ": No matching > (" + _first_word
+ "... )") {};
};
void createParamFile( ostream& _os ) {
vector<Param>::iterator p;
for ( p=params.begin(); p!=params.end(); p++ ) {
switch( p->valType() ) {
case Param::TITLE:
_os << endl << "# -- ";
break;
case Param::BOOL:
_os << ((p->value()=="true" )?"":"#")
<< p->longName();
break;
case Param::STRING:
_os << p->longName()<<"\t\""<<p->value()<<"\"";
break;
case Param::ARRAY:
_os << p->longName()<<"\t< "<<p->value()<<" >";
break;
default:
_os << p->longName()<<"\t"<<p->value();
break;
} // switch
_os << "\t #" << p->description() << endl;
}
}
private:
vector<Param> params;
string programName;
string programDescription;
int parse_argc;
char **parse_argv;
string InputFileName;
};
#endif

35
eo/src/eoParserUtils.cpp
View file

@ -1,35 +0,0 @@
// See eoParserUtils.h
#include <iostream.h>
#include <eoParserUtils.h>
/// Reproducible random seed
// For the Mersenne-Twister used in EO, the entire rng needs to be saved
//----------------------------------
void InitRandom( Parser & parser) {
//----------------------------------
unsigned long _seed;
try {
_seed = parser.getUnsignedLong("-S", "--seed", "0",
"Seed for Random number generator" );
}
catch (logic_error & e)
{
cout << e.what() << endl;
parser.printHelp();
exit(1);
}
if (_seed == 0) { // use clock to get a "random" seed
_seed = (unsigned long)( time( 0 ) );
ostrstream s;
s << _seed;
parser.setParamValue("--seed", s.str()); // so it will be printed out in the status file, and canbe later re-used to re-run EXACTLY the same run
}
#error This does not work: load and save the entire state of the rng object.
rng.reseed(_seed);
return;
}

24
eo/src/eoParserUtils.h
View file

@ -1,24 +0,0 @@
/*-------------------------------------------------------
File..........: eoParserUtils.h
Author........: Geneura Team, Marc Shoenauer
(this file: Victor Rivas, vrivas@ujaen.es)
Date..........: 17-Dec-1999
Description...: Some useful things that use eoParser.
Modifications.:
------------------- 1 -------------------
Author.......:
Date.........:
Description..:
*/
#ifndef EO_PARSER_UTILS
#define EO_PARSER_UTILS
#include <eoRNG.h>
#include <eoParser.h>
/// Reproducible random seed
//----------------------------------
void InitRandom( Parser & parser);
//----------------------------------
#endif

45
eo/src/eoProblem.h
View file

@ -1,45 +0,0 @@
//-----------------------------------------------------------------------------
// eoProblem.h
// (c) GeNeura Team 1998
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef EOPROBLEM_H
#define EOPROBLEM_H
//-----------------------------------------------------------------------------
template<class T> class Problem
{
public:
typedef T Chrom;
typedef typename T::Gene Gene;
typedef typename T::Fitness Fitness;
virtual Fitness operator()(const Chrom& chrom) = 0;
};
//-----------------------------------------------------------------------------
#endif EOPROBLEM_H

453
eo/src/eoRNG.h
View file

@ -1,453 +0,0 @@
/*
* Random number generator adapted from (see comments below)
*
* The random number generator is modified into a class
* by Maarten Keijzer (mak@dhi.dk). Also added the Box-Muller
* transformation to generate normal deviates.
*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
/* ************ DOCUMENTATION IN ORIGINAL FILE *********************/
// This is the ``Mersenne Twister'' random number generator MT19937, which
// generates pseudorandom integers uniformly distributed in 0..(2^32 - 1)
// starting from any odd seed in 0..(2^32 - 1). This version is a recode
// by Shawn Cokus (Cokus@math.washington.edu) on March 8, 1998 of a version by
// Takuji Nishimura (who had suggestions from Topher Cooper and Marc Rieffel in
// July-August 1997).
//
// Effectiveness of the recoding (on Goedel2.math.washington.edu, a DEC Alpha
// running OSF/1) using GCC -O3 as a compiler: before recoding: 51.6 sec. to
// generate 300 million random numbers; after recoding: 24.0 sec. for the same
// (i.e., 46.5% of original time), so speed is now about 12.5 million random
// number generations per second on this machine.
//
// According to the URL <http://www.math.keio.ac.jp/~matumoto/emt.html>
// (and paraphrasing a bit in places), the Mersenne Twister is ``designed
// with consideration of the flaws of various existing generators,'' has
// a period of 2^19937 - 1, gives a sequence that is 623-dimensionally
// equidistributed, and ``has passed many stringent tests, including the
// die-hard test of G. Marsaglia and the load test of P. Hellekalek and
// S. Wegenkittl.'' It is efficient in memory usage (typically using 2506
// to 5012 bytes of static data, depending on data type sizes, and the code
// is quite short as well). It generates random numbers in batches of 624
// at a time, so the caching and pipelining of modern systems is exploited.
// It is also divide- and mod-free.
//
// This library is free software; you can redistribute it and/or modify it
// under the terms of the GNU Library General Public License as published by
// the Free Software Foundation (either version 2 of the License or, at your
// option, any later version). This library is distributed in the hope that
// it will be useful, but WITHOUT ANY WARRANTY, without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See
// the GNU Library General Public License for more details. You should have
// received a copy of the GNU Library General Public License along with this
// library; if not, write to the Free Software Foundation, Inc., 59 Temple
// Place, Suite 330, Boston, MA 02111-1307, USA.
//
// The code as Shawn received it included the following notice:
//
// Copyright (C) 1997 Makoto Matsumoto and Takuji Nishimura. When
// you use this, send an e-mail to <matumoto@math.keio.ac.jp> with
// an appropriate reference to your work.
//
// It would be nice to CC: <Cokus@math.washington.edu> when you write.
//
//
// uint32 must be an unsigned integer type capable of holding at least 32
// bits; exactly 32 should be fastest, but 64 is better on an Alpha with
// GCC at -O3 optimization so try your options and see what's best for you
//
/* ************ END DOCUMENTATION IN ORIGINAL FILE *********************/
#ifndef EO_RANDOM_NUMBER_GENERATOR
#define EO_RANDOM_NUMBER_GENERATOR
#include <ctime>
#include <eoPersistent.h>
#include <eoObject.h>
// TODO: check for various compilers if this is exactly 32 bits
// Unfortunately MSVC's preprocessor does not comprehends sizeof()
// so neat preprocessing tricks will not work
typedef unsigned long uint32; // Compiler and platform dependent!
//-----------------------------------------------------------------------------
// eoRng
//-----------------------------------------------------------------------------
/**
eoRng is a persitent class that uses the ``Mersenne Twister'' random number generator MT19937
for generating random numbers. The various member functions implement useful functions
for evolutionary algorithms. Included are: rand(), random(), flip() and normal().
Note for people porting EO to other platforms: please make sure that the typedef
uint32 in the file eoRng.h is exactly 32 bits long. It may be longer, but not
shorter. If it is longer, file compatibility between EO on different platforms
may be broken.
*/
class eoRng : public eoObject, public eoPersistent
{
public :
/**
ctor takes a random seed; if you want another seed, use reseed
@see reseed
*/
eoRng(uint32 s = (uint32) time(0) ) : state(0), next(0), left(-1), cached(false), N(624), M(397), K(0x9908B0DFU) {
state = new uint32[N+1];
initialize(s);
}
~eoRng(void)
{
delete [] state;
}
/**
Re-initializes the Random Number Generator.
*/
void reseed(uint32 s)
{
initialize(s);
}
/**
uniform(m = 1.0) returns a random double in the range [0, m)
*/
double uniform(double m = 1.0)
{ // random number between [0, m]
return m * double(rand()) / double(rand_max());
}
/**
random() returns a random integer in the range [0, m)
*/
uint32 random(uint32 m)
{
return uint32(uniform() * double(m));
}
/**
flip() tosses a biased coin such that flip(x/100.0) will
returns true x% of the time
*/
bool flip(float bias)
{
return uniform() < bias;
}
/**
normal() zero mean gaussian deviate with standard deviation of 1
*/
double normal(void); // gaussian mutation, stdev 1
/**
normal(stdev) zero mean gaussian deviate with user defined standard deviation
*/
double normal(double stdev)
{
return stdev * normal();
}
/**
normal(mean, stdev) user defined mean gaussian deviate with user defined standard deviation
*/
double normal(double mean, double stdev)
{
return mean + normal(stdev);
}
/**
rand() returns a random number in the range [0, rand_max)
*/
uint32 rand();
/**
rand_max() the maximum returned by rand()
*/
uint32 rand_max(void) const { return (uint32) 0xffffffff; }
/**
roulette_wheel(vec, total = 0) does a roulette wheel selection
on the input vector vec. If the total is not supplied, it is
calculated. It returns an integer denoting the selected argument.
*/
template <class T>
int roulette_wheel(const std::vector<T>& vec, T total = 0)
{
if (total == 0)
{ // count
for (unsigned i = 0; i < vec.size(); ++i)
total += vec[i];
}
float change = uniform() * total;
int i = 0;
while (change > 0)
{
change -= vec[i++];
}
return --i;
}
///
void printOn(ostream& _os) const
{
for (int i = 0; i < N; ++i)
{
_os << state[i] << ' ';
}
_os << int(next - state) << ' ';
_os << left << ' ' << cached << ' ' << cacheValue;
}
///
void readFrom(istream& _is)
{
for (int i = 0; i < N; ++i)
{
_is >> state[i];
}
int n;
_is >> n;
next = state + n;
_is >> left;
_is >> cached;
_is >> cacheValue;
}
private :
uint32 restart(void);
void initialize(uint32 seed);
uint32* state; // the array for the state
uint32* next;
int left;
bool cached;
float cacheValue;
const int N;
const int M;
const uint32 K; // a magic constant
/**
Private copy ctor and assignment operator to make sure that
nobody accidentally copies the random number generator.
If you want similar RNG's, make two RNG's and initialize
them with the same seed.
*/
eoRng (const eoRng&); // no implementation
eoRng& operator=(const eoRng&); // dito
};
/**
The one and only global eoRng object
*/
extern eoRng rng;
/**
The class uniform_generator can be used in the STL generate function
to easily generate random floats and doubles between [0, _max). _max
defaults to 1.0
*/
template <class T = double> class uniform_generator
{
public :
uniform_generator(T _max = T(1.0), eoRng& _rng = rng) : maxim(_max), uniform(_rng) {}
virtual T operator()(void) { return (T) uniform.uniform(maxim); }
private :
T maxim;
eoRng& uniform;
};
/**
The class random_generator can be used in the STL generate function
to easily generate random ints between [0, _max).
*/
template <class T = uint32> class random_generator
{
public :
random_generator(int _max, eoRng& _rng = rng) : maxim(_max), random(_rng) {}
virtual T operator()(void) { return (T) random.random(max); }
private :
T maxim;
eoRng& random;
};
/**
The class normal_generator can be used in the STL generate function
to easily generate gaussian distributed floats and doubles. The user
can supply a standard deviation which defaults to 1.
*/
template <class T = double> class normal_generator
{
public :
normal_generator(T _stdev = T(1.0), eoRng& _rng = rng) : stdev(_stdev), normal(_rng) {}
virtual T operator()(void) { return (T) normal.normal(stdev); }
private :
T stdev;
eoRng& normal;
};
// Implementation of some eoRng members.... Don't mind the mess, it does work.
#define hiBit(u) ((u) & 0x80000000U) // mask all but highest bit of u
#define loBit(u) ((u) & 0x00000001U) // mask all but lowest bit of u
#define loBits(u) ((u) & 0x7FFFFFFFU) // mask the highest bit of u
#define mixBits(u, v) (hiBit(u)|loBits(v)) // move hi bit of u to hi bit of v
inline void eoRng::initialize(uint32 seed)
{
//
// We initialize state[0..(N-1)] via the generator
//
// x_new = (69069 * x_old) mod 2^32
//
// from Line 15 of Table 1, p. 106, Sec. 3.3.4 of Knuth's
// _The Art of Computer Programming_, Volume 2, 3rd ed.
//
// Notes (SJC): I do not know what the initial state requirements
// of the Mersenne Twister are, but it seems this seeding generator
// could be better. It achieves the maximum period for its modulus
// (2^30) iff x_initial is odd (p. 20-21, Sec. 3.2.1.2, Knuth); if
// x_initial can be even, you have sequences like 0, 0, 0, ...;
// 2^31, 2^31, 2^31, ...; 2^30, 2^30, 2^30, ...; 2^29, 2^29 + 2^31,
// 2^29, 2^29 + 2^31, ..., etc. so I force seed to be odd below.
//
// Even if x_initial is odd, if x_initial is 1 mod 4 then
//
// the lowest bit of x is always 1,
// the next-to-lowest bit of x is always 0,
// the 2nd-from-lowest bit of x alternates ... 0 1 0 1 0 1 0 1 ... ,
// the 3rd-from-lowest bit of x 4-cycles ... 0 1 1 0 0 1 1 0 ... ,
// the 4th-from-lowest bit of x has the 8-cycle ... 0 0 0 1 1 1 1 0 ... ,
// ...
//
// and if x_initial is 3 mod 4 then
//
// the lowest bit of x is always 1,
// the next-to-lowest bit of x is always 1,
// the 2nd-from-lowest bit of x alternates ... 0 1 0 1 0 1 0 1 ... ,
// the 3rd-from-lowest bit of x 4-cycles ... 0 0 1 1 0 0 1 1 ... ,
// the 4th-from-lowest bit of x has the 8-cycle ... 0 0 1 1 1 1 0 0 ... ,
// ...
//
// The generator's potency (min. s>=0 with (69069-1)^s = 0 mod 2^32) is
// 16, which seems to be alright by p. 25, Sec. 3.2.1.3 of Knuth. It
// also does well in the dimension 2..5 spectral tests, but it could be
// better in dimension 6 (Line 15, Table 1, p. 106, Sec. 3.3.4, Knuth).
//
// Note that the random number user does not see the values generated
// here directly since restart() will always munge them first, so maybe
// none of all of this matters. In fact, the seed values made here could
// even be extra-special desirable if the Mersenne Twister theory says
// so-- that's why the only change I made is to restrict to odd seeds.
//
left = -1;
register uint32 x = (seed | 1U) & 0xFFFFFFFFU, *s = state;
register int j;
for(left=0, *s++=x, j=N; --j;
*s++ = (x*=69069U) & 0xFFFFFFFFU);
}
inline uint32 eoRng::restart(void)
{
register uint32 *p0=state, *p2=state+2, *pM=state+M, s0, s1;
register int j;
left=N-1, next=state+1;
for(s0=state[0], s1=state[1], j=N-M+1; --j; s0=s1, s1=*p2++)
*p0++ = *pM++ ^ (mixBits(s0, s1) >> 1) ^ (loBit(s1) ? K : 0U);
for(pM=state, j=M; --j; s0=s1, s1=*p2++)
*p0++ = *pM++ ^ (mixBits(s0, s1) >> 1) ^ (loBit(s1) ? K : 0U);
s1=state[0], *p0 = *pM ^ (mixBits(s0, s1) >> 1) ^ (loBit(s1) ? K : 0U);
s1 ^= (s1 >> 11);
s1 ^= (s1 << 7) & 0x9D2C5680U;
s1 ^= (s1 << 15) & 0xEFC60000U;
return(s1 ^ (s1 >> 18));
}
inline uint32 eoRng::rand(void)
{
uint32 y;
if(--left < 0)
return(restart());
y = *next++;
y ^= (y >> 11);
y ^= (y << 7) & 0x9D2C5680U;
y ^= (y << 15) & 0xEFC60000U;
return(y ^ (y >> 18));
}
inline double eoRng::normal(void)
{
if (cached)
{
cached = false;
return cacheValue;
}
float rSquare, factor, var1, var2;
do
{
var1 = 2.0 * uniform() - 1.0;
var2 = 2.0 * uniform() - 1.0;
rSquare = var1 * var1 + var2 * var2;
}
while (rSquare >= 1.0 || rSquare == 0.0);
factor = sqrt(-2.0 * log(rSquare) / rSquare);
cacheValue = var1 * factor;
cached = true;
return (var2 * factor);
}
#endif

148
eo/src/eoString.h
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoString.h
// (c) GeNeura Team, 1998
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef _eoString_H
#define _eoString_H
// STL libraries
#include <string>
#include <stdexcept>
using namespace std;
// EO headers
#include <eo1d.h>
//-----------------------------------------------------------------------------
// eoString
//-----------------------------------------------------------------------------
/** Adaptor that turns an STL string into an EO */
template <class fitnessT >
class eoString: public eo1d<char, fitnessT>, public string {
public:
/// Canonical part of the objects: several ctors, copy ctor, dtor and assignment operator
//@{
/// ctor
eoString( const string& _str ="" )
: eo1d<char, fitnessT>(), string( _str ) {};
/** Ctor using a random number generator
@param _size Lineal length of the object
@param _rnd a random number generator, which returns a random value each time it´s called
*/
eoString( unsigned _size, eoRnd<char>& _rnd )
: eo1d<char, fitnessT>(), string(){
for ( unsigned i = 0; i < _size; i ++ ) {
*this += _rnd();
}
};
/** Ctor from a stream
@param _s input stream
*/
eoString( istream & _s )
: eo1d<char, fitnessT>(){
_s >> *this;
};
/// copy ctor
eoString( const eoString<fitnessT>& _eoStr )
:eo1d<char, fitnessT>( static_cast<const eo1d<char, fitnessT> & > ( _eoStr ) ),
string( _eoStr ){};
/// Assignment operator
const eoString& operator =( const eoString& _eoStr ) {
if ( this != & _eoStr ) {
eo1d<char, fitnessT>::operator = ( _eoStr );
string::operator = ( _eoStr );
}
return *this;
}
/// dtor
virtual ~eoString() {};
//@}
/** methods that implement the eo1d <em>protocol</em>
@exception out_of_range if _i is larger than EO´s size
*/
virtual char getGene( unsigned _i ) const {
if ( _i >= length() )
throw out_of_range( "out_of_range when reading gene");
return (*this)[_i];
};
/** methods that implement the eo1d <em>protocol</em>
@exception out_of_range if _i is larger than EO´s size
*/
virtual void setGene( unsigned _i, const char& _value ) {
if ( _i >= size() )
throw out_of_range( "out_of_range when writing a gene");
(*this)[_i] = _value;
};
/** Inserts a value after _i, displacing anything to the right
@exception out_of_range if _i is larger than EO´s size
*/
virtual void insertGene( unsigned _i, char _val ) {
if (_i <= this->size() ) {
string::iterator i = this->begin()+_i;
this->insert( i, _val );
} else
throw out_of_range( "out_of_range when inserting gene");
};
/** Eliminates the gene at position _i
@exception out_of_range if _i is larger than EO´s size
*/
virtual void deleteGene( unsigned _i ) {
if (_i < this->size() ) {
string::iterator i = this->begin()+_i;
this->erase( i );
} else
throw out_of_range( "out_of_range when deleting gene");
};
/// methods that implement the EO <em>protocol</em>
virtual unsigned length() const { return this->size(); };
/** @name Methods from eoObject
readFrom and printOn are directly inherited from eo1d
*/
//@{
/** Inherited from eoObject
@see eoObject
*/
virtual string className() const {return "eoString";};
//@}
};
#endif

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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoStringMutation.h
// (c) GeNeura Team, 1999
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef _EOSTRINGMUTATION_H
#define _EOSRTINGMUTATION_H
#include <math.h>
// EO includes
#include <eoOp.h>
#include <eoUniform.h>
#include <eoMutation.h>
/** Mutation of an eoString.
The eoString's genes are changed by adding or substracting 1 to
*/
template <class EOT>
class eoStringMutation: public eoMutation<EOT> {
public:
///
eoStringMutation(const double _rate=0.0) : eoMutation< EOT >(_rate) {};
///
virtual ~eoStringMutation() {};
/** @name Methods from eoObject
*/
//@{
/** Inherited from eoObject
@see eoObject
*/
string className() const {return "eoStringMutation";};
//@}
private:
#ifdef _MSC_VER
typedef EOT::Type Type;
#else
typedef typename EOT::Type Type;
#endif
/// applies operator to one gene in the EO. It increments or decrements the value of that gene by one.
virtual void applyAt( EOT& _eo, unsigned _i ) const {
eoUniform<double> uniform( 0, 1 );
if( rate < uniform() ) {
_eo.gene(_i) += ( uniform()>=0.5 )? (1) : (-1) ;
}
}
};
//-----------------------------------------------------------------------------
#endif

85
eo/src/rnd_generators.h
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/* -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
-----------------------------------------------------------------------------
rnd_generators.h
Some utility functors for generating random generators:
uniform_generator : generates uniform floats or doubles
random_generator : generates unsigneds, ints etc.
normal_generator : normally distributed floats or doubles
(c) Maarten Keijzer (mak@dhi.dk) and GeNeura Team, 1999, 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef eoRND_GENERATORS_H
#define eoRND_GENERATORS_H
#include "eoRNG.h"
/**
The class uniform_generator can be used in the STL generate function
to easily generate random floats and doubles between [0, _max). _max
defaults to 1.0
*/
template <class T = double> class uniform_generator
{
public :
uniform_generator(T _max = T(1.0), eoRng& _rng = rng) : maxim(_max), uniform(_rng) {}
virtual T operator()(void) { return (T) uniform.uniform(maxim); }
private :
T maxim;
eoRng& uniform;
};
/**
The class random_generator can be used in the STL generate function
to easily generate random ints between [0, _max).
*/
template <class T = uint32> class random_generator
{
public :
random_generator(int _max, eoRng& _rng = rng) : maxim(_max), random(_rng) {}
virtual T operator()(void) { return (T) random.random(max); }
private :
T maxim;
eoRng& random;
};
/**
The class normal_generator can be used in the STL generate function
to easily generate gaussian distributed floats and doubles. The user
can supply a standard deviation which defaults to 1.
*/
template <class T = double> class normal_generator
{
public :
normal_generator(T _stdev = T(1.0), eoRng& _rng = rng) : stdev(_stdev), normal(_rng) {}
virtual T operator()(void) { return (T) normal.normal(stdev); }
private :
T stdev;
eoRng& normal;
};
#endif

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eo/src/selectors.h
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/* -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
-----------------------------------------------------------------------------
selectors.h
A bunch of useful selector functions. They generally have three forms:
template <class It>
It select(It begin, It end, params, eoRng& gen = rng);
template <class EOT>
const EOT& select(const eoPop<EOT>& pop, params, eoRng& gen = rng);
template <class EOT>
EOT& select(eoPop<EOT>& pop, params, eoRng& gen = rng);
where select is one of: roulette_wheel, deterministic_tournament
and stochastic_tournament (at the moment).
(c) Maarten Keijzer (mak@dhi.dk) and GeNeura Team, 1999, 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
#ifndef SELECT__H
#define SELECT__H
#include "eoRNG.h"
#include "eoException.h"
template <class EOT>
bool minimizing_fitness()
{
EOT eo1; // Assuming people don't do anything fancy in the default constructor!
EOT eo2;
/* Dear user, when the two line below do not compile you are most
likely not working with scalar fitness values. In that case we're sorry
but you cannot use lottery or roulette_wheel selection...
*/
eo1.fitness(0.0); // tried to cast it to an EOT::Fitness, but for some reason GNU barfs on this
eo2.fitness(1.0);
return eo2 < eo1; // check whether we have a minimizing fitness
};
inline double scale_fitness(const std::pair<double, double>& _minmax, double _value)
{
if (_minmax.first == _minmax.second)
{
return 0.0; // no differences in fitness, population converged!
}
// else
return (_value - _minmax.first) / (_minmax.second - _minmax.first);
}
template <class It>
double sum_fitness(It begin, It end)
{
double sum = 0.0;
for (; begin != end; ++begin)
{
double v = static_cast<double>(begin->fitness());
if (v < 0.0)
throw eoNegativeFitnessException();
sum += v;
}
return sum;
}
template <class EOT>
double sum_fitness(const eoPop<EOT>& _pop)
{
return sum_fitness(_pop.begin(), _pop.end());
}
template <class EOT>
double sum_fitness(const eoPop<EOT>& _pop, std::pair<double, double>& _minmax)
{
eoPop<EOT>::const_iterator it = _pop.begin();
_minmax.first = it->fitness();
_minmax.second = it++->fitness();
for(; it != _pop.end(); ++it)
{
double v = static_cast<double>(it->fitness());
_minmax.first = std::min(_minmax.first, v);
_minmax.second = std::max(_minmax.second, v);
rawTotal += v;
}
if (minimizing_fitness<EOT>())
{
std::swap(_minmax.first, _minmax.second);
}
scaledTotal = 0.0;
// unfortunately a second loop is neccessary to scale the fitness
for (it = _pop.begin(); it != _pop.end(); ++it)
{
double v = scale_fitness(static_cast<double>(it->fitness()));
scaledTotal += v;
}
}
template <class It>
It roulette_wheel(It _begin, It _end, double total, eoRng& _gen = rng)
{
float roulette = _gen.uniform(total);
It i = _begin;
while (roulette > 0.0)
{
roulette -= static_cast<double>(*(i++));
}
return --i;
}
template <class EOT>
const EOT& roulette_wheel(const eoPop<EOT>& _pop, double total, eoRng& _gen = rng)
{
float roulette = _gen.uniform(total);
eoPop<EOT>::const_iterator i = _pop.begin();
while (roulette > 0.0)
{
roulette -= static_cast<double>((i++)->fitness());
}
return *--i;
}
template <class EOT>
EOT& roulette_wheel(eoPop<EOT>& _pop, double total, eoRng& _gen = rng)
{
float roulette = _gen.uniform(total);
eoPop<EOT>::iterator i = _pop.begin();
while (roulette > 0.0)
{
roulette -= static_cast<double>((i++)->fitness());
}
return *--i;
}
template <class It>
It deterministic_tournament(It _begin, It _end, unsigned _t_size, eoRng& _gen = rng)
{
It best = _begin + _gen.random(_end - _begin);
for (unsigned i = 0; i < _t_size - 1; ++i)
{
It competitor = _begin + _gen.random(_end - _begin);
if (*best < *competitor)
{
best = competitor;
}
}
return best;
}
template <class EOT>
const EOT& deterministic_tournament(const eoPop<EOT>& _pop, unsigned _t_size, eoRng& _gen = rng)
{
return *deterministic_tournament(_pop.begin(), _pop.end(), _t_size, _gen);
}
template <class EOT>
EOT& deterministic_tournament(eoPop<EOT>& _pop, unsigned _t_size, eoRng& _gen = rng)
{
return *deterministic_tournament(_pop.begin(), _pop.end(), _t_size, _gen);
}
template <class It>
It inverse_deterministic_tournament(It _begin, It _end, unsigned _t_size, eoRng& _gen = rng)
{
It worst = _begin + _gen.random(_end - _begin);
for (unsigned i = 0; i < _t_size - 1; ++i)
{
It competitor = _begin + _gen.random(_end - _begin);
if (competitor == worst)
{
--i;
continue; // try again
}
if (*competitor < *worst)
{
worst = competitor;
}
}
return worst;
}
template <class EOT>
const EOT& inverse_deterministic_tournament(const eoPop<EOT>& _pop, unsigned _t_size, eoRng& _gen = rng)
{
return *inverse_deterministic_tournament<EOT>(_pop.begin(), _pop.end(), _t_size, _gen);
}
template <class EOT>
EOT& inverse_deterministic_tournament(eoPop<EOT>& _pop, unsigned _t_size, eoRng& _gen = rng)
{
return *inverse_deterministic_tournament(_pop.begin(), _pop.end(), _t_size, _gen);
}
template <class It>
It stochastic_tournament(It _begin, It _end, double _t_rate, eoRng& _gen = rng)
{
It i1 = _begin + _gen.random(_end - _begin);
It i2 = _begin + _gen.random(_end - _begin);
bool return_better = _gen.flip(_t_rate);
if (*i1 < *i2)
{
if (return_better) return i2;
// else
return i1;
}
else
{
if (return_better) return i1;
// else
}
// else
return i2;
}
template <class EOT>
const EOT& stochastic_tournament(const eoPop<EOT>& _pop, double _t_rate, eoRng& _gen = rng)
{
return *stochastic_tournament(_pop.begin(), _pop.end(), _t_rate, _gen);
}
template <class EOT>
EOT& stochastic_tournament(eoPop<EOT>& _pop, double _t_rate, eoRng& _gen = rng)
{
return *stochastic_tournament(_pop.begin(), _pop.end(), _t_rate, _gen);
}
template <class It>
It inverse_stochastic_tournament(It _begin, It _end, double _t_rate, eoRng& _gen = rng)
{
It i1 = _begin + _gen.random(_end - _begin);
It i2 = _begin + _gen.random(_end - _begin);
bool return_worse = _gen.flip(_t_rate);
if (*i1 < *i2)
{
if (return_worse) return i1;
// else
return i2;
}
else
{
if (return_worse) return i2;
// else
}
// else
return i1;
}
template <class EOT>
const EOT& inverse_stochastic_tournament(const eoPop<EOT>& _pop, double _t_rate, eoRng& _gen = rng)
{
return *inverse_stochastic_tournament(_pop.begin(), _pop.end(), _t_rate, _gen);
}
template <class EOT>
EOT& inverse_stochastic_tournament(eoPop<EOT>& _pop, double _t_rate, eoRng& _gen = rng)
{
return *inverse_stochastic_tournament(_pop.begin(), _pop.end(), _t_rate, _gen);
}
#endif