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A full working version of ES is now available in tutorial/Lesson4,

Browse source 
that makes full use of libes.a.
The user guide is in Lesson4 of the tutorial - programmer's guide
will come later.
Plus many small changes here and there
This commit is contained in:
evomarc 2001-05-04 16:51:29 +00:00
commit 5508869d00
19 changed files with 653 additions and 189 deletions
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32
eo/src/do/make_checkpoint.h
View file

@ -33,6 +33,9 @@
#include <eoEvalFuncCounter.h>
#include <utils/checkpointing>
// at the moment, in utils/make_help.cpp
// this should become some eoUtils.cpp with corresponding eoUtils.h
bool testDirRes(std::string _dirName, bool _erase);
/////////////////// The checkpoint and other I/O //////////////
@ -58,6 +61,12 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParameterLoader& _parser, eoState& _stat
// and store it in the state
_state.storeFunctor(increment);
// dir for DISK output
eoValueParam<string>& dirNameParam = _parser.createParam(string("Res"), "resDir", "Directory to store DISK outputs", '\0', "Output - Disk");
// shoudl we empty it if exists
eoValueParam<bool>& eraseParam = _parser.createParam(false, "eraseDir", "erase files in dirName if any", '\0', "Output - Disk");
bool dirOK = false; // not tested yet
/////////////////////////////////////////
// now some statistics on the population:
/////////////////////////////////////////
@ -78,12 +87,8 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParameterLoader& _parser, eoState& _stat
//---------------------------
eoValueParam<bool>& printBestParam = _parser.createParam(true, "printBestStat", "Print Best/avg/stdev every gen.", '\0', "Output");
eoValueParam<bool>& plotBestParam = _parser.createParam(false, "plotBestStat", "Plot Best/avg Stat", '\0', "Output - Graphical");
// dir for DISK output
eoValueParam<string>& dirNameParam = _parser.createParam(string("Res"), "resDir", "Directory to store DISK outputs", '\0', "Output - Disk");
eoValueParam<bool>& fileBestParam = _parser.createParam(false, "fileBestStat", "Output bes/avg/std to file", '\0', "Output - Disk");
eoBestFitnessStat<EOT> *bestStat = NULL;
if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() )
// we need the bestStat for at least one of the 3 above
@ -152,6 +157,9 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParameterLoader& _parser, eoState& _stat
checkpoint->add(*fdcStat);
}
// do we wnat some histogram of fitnesses snpashots?
eoValueParam<bool> plotHistogramParam = _parser.createParam(false, "plotHisto", "Plot histogram of fitnesses", '\0', "Output - Graphical");
///////////////
// The monitors
///////////////
@ -183,6 +191,12 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParameterLoader& _parser, eoState& _stat
monitor->add(*popStat);
}
// first handle the dir test - if we need at least one file
if ( ( fileBestParam.value() || plotBestParam.value() ||
plotFDCParam.value() || plotHistogramParam.value() )
&& !dirOK ) // just in case we add something before
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
if (fileBestParam.value()) // A file monitor for best & secondMoment
{
string stmp = dirNameParam.value() + "/best.xg";
@ -227,7 +241,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParameterLoader& _parser, eoState& _stat
checkpoint->add(*fdcGnuplot);
}
eoValueParam<bool> plotHistogramParam = _parser.createParam(false, "plotHisto", "Plot histogram of fitnesses", '\0', "Output - Graphical");
// historgram?
if (plotHistogramParam.value()) // want to see how the fitness is spread?
{
eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
@ -252,6 +266,10 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParameterLoader& _parser, eoState& _stat
if (_parser.isItThere(saveFrequencyParam))
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
unsigned freq = (saveFrequencyParam.value()>0 ? saveFrequencyParam.value() : UINT_MAX );
string stmp = dirNameParam.value() + "/generations";
eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
@ -263,6 +281,10 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParameterLoader& _parser, eoState& _stat
eoValueParam<unsigned>& saveTimeIntervalParam = _parser.createParam(unsigned(0), "saveTimeInterval", "Save every T seconds (0 or absent = never)", '\0',"Persistence" );
if (_parser.isItThere(saveTimeIntervalParam) && saveTimeIntervalParam.value()>0)
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
string stmp = dirNameParam.value() + "/time";
eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
_state.storeFunctor(stateSaver2);

3
eo/src/do/make_pop.h
View file

@ -27,6 +27,7 @@
#ifndef _make_pop_h
#define _make_pop_h
#include <sys/time.h> // for time(0) for random seeding
#include <eoPop.h>
#include <eoInit.h>
#include <utils/eoRNG.h>
@ -50,7 +51,7 @@ eoPop<EOT>& do_make_pop(eoParser & _parser, eoState& _state, eoInit<EOT> & _ini
// random seed
eoValueParam<uint32>& seedParam = _parser.createParam(uint32(0), "seed", "Random number seed", 'S');
if (seedParam.value() == 0)
seedParam.value() = random_seed();
seedParam.value() = time(0);
eoValueParam<unsigned>& popSize = _parser.createParam(unsigned(20), "popSize", "Population Size", 'P', "Evolution Engine");
// Either load or initialize

4
eo/src/es/eoEsMutationInit.h
View file

@ -90,10 +90,10 @@ class eoEsMutationInit
virtual std::string section(void)
{ return repSection; }
virtual std::string TauLclName(void) const { return "TauLcL"; }
virtual std::string TauLclName(void) const { return "TauLoc"; }
virtual char TauLclShort(void) const { return 'l'; }
virtual std::string TauGlbName(void) const { return "TauGlb"; }
virtual std::string TauGlbName(void) const { return "TauGlob"; }
virtual char TauGlbShort(void) const { return 'g'; }
virtual std::string TauBetaName(void) const { return "Beta"; }

18
eo/src/es/eoRealOp.h
View file

@ -329,13 +329,13 @@ protected:
double range; // == 1+2*alpha
};
/** eoArithmeticCrossover --> uniform choice in hypercube
/** eoHypercubeCrossover --> uniform choice in hypercube
== arithmetical with different values for each coordinate
\class eoArithmeticCrossover eoRealOp.h Tutorial/eoRealOp.h
\ingroup parameteric
*/
template<class EOT> class eoArithmeticCrossover: public eoQuadOp<EOT>
template<class EOT> class eoHypercubeCrossover: public eoQuadOp<EOT>
{
public:
/**
@ -347,7 +347,7 @@ template<class EOT> class eoArithmeticCrossover: public eoQuadOp<EOT>
* 0 == contractive application
* Must be positive
*/
eoArithmeticCrossover(const double& _alpha = 0.0):
eoHypercubeCrossover(const double& _alpha = 0.0):
bounds(eoDummyVectorNoBounds), alpha(_alpha), range(1+2*_alpha)
{
if (_alpha < 0)
@ -362,7 +362,7 @@ template<class EOT> class eoArithmeticCrossover: public eoQuadOp<EOT>
* 0 == contractive application
* Must be positive
*/
eoArithmeticCrossover(eoRealVectorBounds & _bounds,
eoHypercubeCrossover(eoRealVectorBounds & _bounds,
const double& _alpha = 0.0):
bounds(_bounds), alpha(_alpha), range(1+2*_alpha)
{
@ -371,10 +371,10 @@ template<class EOT> class eoArithmeticCrossover: public eoQuadOp<EOT>
}
/// The class name.
virtual string className() const { return "eoArithmeticCrossover"; }
virtual string className() const { return "eoHypercubeCrossover"; }
/**
* arithmetical crossover - modifies both parents
* hypercube crossover - modifies both parents
* @param _eo1 The first parent
* @param _eo2 The first parent
*/
@ -434,21 +434,21 @@ protected:
\ingroup parameteric
*/
template<class EOT> class eoRealUxOver: public eoQuadOp<EOT>
template<class EOT> class eoRealUXover: public eoQuadOp<EOT>
{
public:
/**
* (Default) Constructor.
* @param _preference bias in the choice (usually, no bias == 0.5)
*/
eoRealUxOver(const float& _preference = 0.5): preference(_preference)
eoRealUXover(const float& _preference = 0.5): preference(_preference)
{
if ( (_preference <= 0.0) || (_preference >= 1.0) )
runtime_error("UxOver --> invalid preference");
}
/// The class name.
virtual string className() const { return "eoRealUxOver"; }
virtual string className() const { return "eoRealUXover"; }
/**
* Uniform crossover for real vectors

18
eo/src/es/make_op_es.h
View file

@ -130,10 +130,10 @@ eoGenOp<EOT> & do_make_op(eoParameterLoader& _parser, eoState& _state, eoRealIni
// crossover
/////////////
// ES crossover
eoValueParam<string>& crossTypeParam = _parser.createParam(string("Global"), "crossType", "Type of ES recombination (gloabl or local)", 'C', "Variation Operators");
eoValueParam<string>& crossTypeParam = _parser.createParam(string("global"), "crossType", "Type of ES recombination (global or standard)", 'C', "Variation Operators");
eoValueParam<string>& crossObjParam = _parser.createParam(string("Discrete"), "crossObj", "Recombination of object variables (Discrete or Intermediate)", 'O', "Variation Operators");
eoValueParam<string>& crossStdevParam = _parser.createParam(string("Intermediate"), "crossStdev", "Recombination of mutation strategy parameters (Intermediate or Discrete)", 'S', "Variation Operators");
eoValueParam<string>& crossObjParam = _parser.createParam(string("discrete"), "crossObj", "Recombination of object variables (discrete or intermediate)", 'O', "Variation Operators");
eoValueParam<string>& crossStdevParam = _parser.createParam(string("intermediate"), "crossStdev", "Recombination of mutation strategy parameters (intermediate or discrete)", 'S', "Variation Operators");
// The pointers: first the atom Xover
eoBinOp<double> *ptObjAtomCross = NULL;
@ -142,22 +142,22 @@ eoGenOp<EOT> & do_make_op(eoParameterLoader& _parser, eoState& _state, eoRealIni
eoGenOp<EOT> *ptCross;
// check for the atom Xovers
if (crossObjParam.value() == string("Discrete"))
if (crossObjParam.value() == string("discrete"))
ptObjAtomCross = new eoRealAtomExchange;
else if (crossObjParam.value() == string("Intermediate"))
else if (crossObjParam.value() == string("intermediate"))
ptObjAtomCross = new eoRealAtomExchange;
else throw runtime_error("Invalid Object variable crossover type");
if (crossStdevParam.value() == string("Discrete"))
if (crossStdevParam.value() == string("discrete"))
ptStdevAtomCross = new eoRealAtomExchange;
else if (crossStdevParam.value() == string("Intermediate"))
else if (crossStdevParam.value() == string("intermediate"))
ptStdevAtomCross = new eoRealAtomExchange;
else throw runtime_error("Invalid mutation strategy parameter crossover type");
// and build the indi Xover
if (crossTypeParam.value() == string("Global"))
if (crossTypeParam.value() == string("global"))
ptCross = new eoEsGlobalXover<EOT>(*ptObjAtomCross, *ptStdevAtomCross);
else if (crossTypeParam.value() == string("Local"))
else if (crossTypeParam.value() == string("standard"))
ptCross = new eoEsLocalXover<EOT>(*ptObjAtomCross, *ptStdevAtomCross);
else throw runtime_error("Invalide Object variable crossover type");

32
eo/src/es/make_op_real.h
View file

@ -131,19 +131,30 @@ eoGenOp<EOT> & do_make_op(eoParameterLoader& _parser, eoState& _state, eoRealIni
// the crossovers
/////////////////
// the parameters
eoValueParam<double>& alphaParam = _parser.createParam(double(0.0), "alpha", "Bound for factor of linear recombinations", 'a', "Variation Operators" );
// minimum check
if ( (alphaParam.value() < 0) )
throw runtime_error("Invalid BLX coefficient alpha");
eoValueParam<double>& segmentRateParam = _parser.createParam(double(1.0), "segmentRate", "Relative rate for segment crossover", 's', "Variation Operators" );
// minimum check
if ( (segmentRateParam.value() < 0) )
throw runtime_error("Invalid segmentRate");
eoValueParam<double>& arithmeticRateParam = _parser.createParam(double(2.0), "arithmeticRate", "Relative rate for arithmetic crossover", 'A', "Variation Operators" );
eoValueParam<double>& hypercubeRateParam = _parser.createParam(double(1.0), "hypercubeRate", "Relative rate for hypercube crossover", 'A', "Variation Operators" );
// minimum check
if ( (arithmeticRateParam.value() < 0) )
throw runtime_error("Invalid arithmeticRate");
if ( (hypercubeRateParam.value() < 0) )
throw runtime_error("Invalid hypercubeRate");
eoValueParam<double>& uxoverRateParam = _parser.createParam(double(1.0), "uxoverRate", "Relative rate for uniform crossover", 'A', "Variation Operators" );
// minimum check
if ( (uxoverRateParam.value() < 0) )
throw runtime_error("Invalid uxoverRate");
// minimum check
bool bCross = true;
if (segmentRateParam.value()+arithmeticRateParam.value()==0)
if (segmentRateParam.value()+hypercubeRateParam.value()+uxoverRateParam.value()==0)
{
cerr << "Warning: no crossover" << endl;
bCross = false;
@ -156,14 +167,19 @@ eoGenOp<EOT> & do_make_op(eoParameterLoader& _parser, eoState& _state, eoRealIni
if (bCross)
{
// segment crossover for bitstring - pass it the bounds
ptQuad = new eoSegmentCrossover<EOT>(*ptBounds);
ptQuad = new eoSegmentCrossover<EOT>(*ptBounds, alphaParam.value());
_state.storeFunctor(ptQuad);
ptCombinedQuadOp = new eoPropCombinedQuadOp<EOT>(*ptQuad, segmentRateParam.value());
// arithmetic crossover
ptQuad = new eoArithmeticCrossover<EOT>(*ptBounds);
// hypercube crossover
ptQuad = new eoHypercubeCrossover<EOT>(*ptBounds, alphaParam.value());
_state.storeFunctor(ptQuad);
ptCombinedQuadOp->add(*ptQuad, arithmeticRateParam.value());
ptCombinedQuadOp->add(*ptQuad, hypercubeRateParam.value());
// uniform crossover
ptQuad = new eoRealUXover<EOT>();
_state.storeFunctor(ptQuad);
ptCombinedQuadOp->add(*ptQuad, uxoverRateParam.value());
// don't forget to store the CombinedQuadOp
_state.storeFunctor(ptCombinedQuadOp);

15
eo/src/utils/eoRNG.cpp
View file

@ -1,22 +1,9 @@
#include <ctime>
#include "eoRNG.h"
#include <sys/time.h>
/** this function retunrs a "truly random" seed for RNG
* Replaces the call to time(0) that seems to be non-portable???
*/
uint32 random_seed()
{
struct timeval tval;
struct timezone tzp;
gettimeofday (&tval, &tzp); // milliseconds since midnight January 1, 1970.
return uint32(tval.tv_usec);
}
namespace eo
{
/// The Global random number generator.
eoRng rng(random_seed());
eoRng rng(time(0));
}

3
eo/src/utils/eoRNG.h
View file

@ -288,9 +288,6 @@ extern eoRng rng;
using eo::rng;
/** the random_seed utility in eoRNG.cpp */
extern uint32 random_seed();
// Implementation of some eoRng members.... Don't mind the mess, it does work.

38
eo/src/utils/make_help.cpp
View file

@ -25,6 +25,7 @@
//-----------------------------------------------------------------------------
#include <utils/eoParser.h>
#include <fstream.h>
#include <stdexcept>
/** Generation of the status file, and output of the help message if needed
*
@ -60,3 +61,40 @@ void make_help(eoParser & _parser)
exit(1);
}
}
/** test a dir.
* Creates it if does not exist
* If exists, throws an exception or erase everything there,
* depending on last parameter
*
* Always return true (for code easy writing on the other side :-)
*/
bool testDirRes(std::string _dirName, bool _erase)
{
string s = "test -d " + _dirName;
int res = system(s.c_str());
// test for (unlikely) errors
if ( (res==-1) || (res==127) )
{
s = "Problem executing test of dir " + _dirName;
throw runtime_error(s);
}
// now make sure there is a dir without any file in it - or quit
if (res) // no dir present
{
s = string("mkdir ")+ _dirName;
system(s.c_str());
return true;
}
// else
if (_erase) // OK to erase
{
s = string("/bin/rm ")+ _dirName + "/*";
system(s.c_str());
return true;
}
//else
s = "Dir " + _dirName + " is not empty";
throw runtime_error(s);
return true;
}