Ok, updated the Makefile.am again to use the
make check Command I picked up in the automake documentation (RTFM, you know) Tagged a lot of header functions in the GnuPlot files with 'inline', so they can be used from more than one sourcefile. Ok, now the interesting news. Started a new library libga (not to be confused with Matthew's GaLib). Here I suggest we put a fairly complete and configurable genetic algorithm. Just to see how far we can stretch ourselves and also to have a GA-componenent that can be used in other applications without having to rebuild the entire thing. test/t-eoGA.cpp tests this library
This commit is contained in:
maartenkeijzer
parent
9f5069b23a
commit
dea8a51f7e
12 changed files with 260 additions and 81 deletions
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@ -4,7 +4,7 @@
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##
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###############################################################################
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SUBDIRS = src win tutorial app
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SUBDIRS = src test win tutorial app
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#Directory for documents
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DOCDIR = ~/public_html/eodocs
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#Directory for indices -- not useful for the user
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@ -17,8 +17,9 @@ EXTRA_DIST=LICENSE
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lib:
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pushd src; $(MAKE) all; popd
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test: test/run_tests
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pushd test; $(MAKE) all; ./run_tests; touch run_tests; popd
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# The test directory should be run explicitely, to check if nothing is broken
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test: test/run_tests test/Makefile
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pushd test; touch run_tests; $(MAKE) all; ./run_tests; popd
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# so that make doc always compiles the doc ...
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doc: doc/eo.cfg
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@ -4,5 +4,11 @@
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##
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###############################################################################
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INCLUDES = -I$(top_builddir)/src
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lib_LIBRARIES = libga.a
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libga_a_SOURCES = ga.cpp
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CPPFLAGS = -O2 -Wall
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libeoincdir = $(includedir)/eo/ga
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libeoinc_HEADERS = eoBit.h eoBitOp.h eoBitOpFactory.h
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libeoinc_HEADERS = eoBit.h eoBitOp.h eoBitOpFactory.h ga.h
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91
eo/src/ga/ga.cpp
Normal file
91
eo/src/ga/ga.cpp
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@ -0,0 +1,91 @@
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#include <eo>
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#include <ga/ga.h>
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eoValueParam<float> xoverRate(0.6f, "xoverrate", "The crossover rate", 'x');
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eoValueParam<float> mutRate(1.0f, "mutationrate", "The mutation rate", 'm');
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eoValueParam<unsigned> chromSize(unsigned(10), "chromosomeSize", "The length of the bitstrings", 'n');
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eoValueParam<unsigned> popSize(unsigned(20), "PopSize", "Population Size", 'P');
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template <class FitT>
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eoAlgo<eoBit<FitT> >& do_make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<FitT> >& _eval, eoCheckPoint<eoBit<FitT> >& _checkpoint, eoState& _state)
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{
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typedef eoBit<FitT> EOT;
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_parser.processParam(xoverRate, "genetics");
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_parser.processParam(mutRate, "genetics");
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_parser.processParam(chromSize, "initialization");
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eoBitMutation<EOT>* mutOp = new eoBitMutation<EOT>(1. / float(chromSize.value()));
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_state.storeFunctor(mutOp);
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eo1PtBitXover<EOT>* crossOp = new eo1PtBitXover<EOT>;
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_state.storeFunctor(crossOp);
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eoSelectOne<EOT>* select = new eoDetTournamentSelect<EOT>(2);
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_state.storeFunctor(select);
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eoSGA<eoBit<FitT> >* sga = new eoSGA<EOT>(*select, *crossOp, xoverRate.value(), *mutOp, mutRate.value(), _eval, _checkpoint);
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_state.storeFunctor(sga);
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return *sga;
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}
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template <class FitT>
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eoPop<eoBit<FitT> >& do_init_ga(eoParameterLoader& _parser, eoState& _state, FitT)
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{
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typedef eoBit<FitT> EOT;
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_parser.processParam(chromSize, "initialization");
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_parser.processParam(popSize, "initialization");
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eoInitFixedLength<EOT, boolean_generator> init(chromSize.value(), boolean_generator());
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// Let the state handle the memory
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eoPop<EOT>& pop = _state.takeOwnership(eoPop<EOT>());
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_state.registerObject(pop);
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// initialize the population
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pop.append(popSize.value(), init);
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return pop;
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}
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template <class FitT>
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void do_run_ga(eoAlgo<eoBit<FitT> >& _ga, eoPop<eoBit<FitT> >& _pop)
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{
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_ga(_pop);
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}
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/// The following function merely call the templatized do_* functions above
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eoAlgo<eoBit<double> >& make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<double> >& _eval, eoCheckPoint<eoBit<double> >& _checkpoint, eoState& _state)
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{
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return do_make_ga(_parser, _eval, _checkpoint, _state);
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}
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eoAlgo<eoBit<eoMinimizingFitness> >& make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<eoMinimizingFitness> >& _eval, eoCheckPoint<eoBit<eoMinimizingFitness> >& _checkpoint, eoState& _state)
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{
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return do_make_ga(_parser, _eval, _checkpoint, _state);
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}
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eoPop<eoBit<double> >& init_ga(eoParameterLoader& _parser, eoState& _state, double _d)
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{
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return do_init_ga(_parser, _state, _d);
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}
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eoPop<eoBit<eoMinimizingFitness> >& init_ga(eoParameterLoader& _parser, eoState& _state, eoMinimizingFitness _d)
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{
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return do_init_ga(_parser, _state, _d);
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}
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void run_ga(eoAlgo<eoBit<double> >& _ga, eoPop<eoBit<double> >& _pop)
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{
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do_run_ga(_ga, _pop);
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}
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void run_ga(eoAlgo<eoBit<eoMinimizingFitness> >& _ga, eoPop<eoBit<eoMinimizingFitness> >& _pop)
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{
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do_run_ga(_ga, _pop);
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}
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24
eo/src/ga/ga.h
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24
eo/src/ga/ga.h
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@ -0,0 +1,24 @@
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#ifndef ga_h
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#define ga_h
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#include <eoAlgo.h>
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#include <eoScalarFitness.h>
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#include <utils/eoParser.h>
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#include <eoEvalFunc.h>
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#include <utils/eoCheckPoint.h>
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#include <eoPop.h>
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#include <ga/eoBit.h>
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#include <ga/eoBitOp.h>
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eoAlgo<eoBit<double> >& make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<double> >& _eval, eoCheckPoint<eoBit<double> >& _checkpoint, eoState& state);
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eoAlgo<eoBit<eoMinimizingFitness> >& make_ga(eoParameterLoader& _parser, eoEvalFunc<eoBit<eoMinimizingFitness> >& _eval, eoCheckPoint<eoBit<eoMinimizingFitness> >& _checkpoint, eoState& state);
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eoPop<eoBit<double> >& init_ga(eoParameterLoader& _parser, eoState& _state, double);
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eoPop<eoBit<eoMinimizingFitness> >& init_ga(eoParameterLoader& _parser, eoState& _state, eoMinimizingFitness);
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void run_ga(eoAlgo<eoBit<double> >& _ga, eoPop<eoBit<double> >& _pop);
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void run_ga(eoAlgo<eoBit<eoMinimizingFitness> >& _ga, eoPop<eoBit<eoMinimizingFitness> >& _pop);
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#endif
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@ -5,7 +5,7 @@
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###############################################################################
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INCLUDES = -I$(top_builddir)/src
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CPPFLAGS = -O2
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CPPFLAGS = -O2 -Wall
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lib_LIBRARIES = libeoutils.a
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libeoutils_a_SOURCES = eoParser.cpp eoRNG.cpp eoState.cpp eoUpdater.cpp eoFileMonitor.cpp eoStdoutMonitor.cpp
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@ -91,7 +91,7 @@ private:
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static unsigned numWindow=0;
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////////////////////////////////////////////////////////////
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void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
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inline void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
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/////////////////////////////////////////////////////////
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{
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char snum[255];
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@ -129,7 +129,7 @@ void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
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* Created......: Mon Mar 13 13:50:11 1995
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* Description..: Communication par pipe bidirectionnel avec un autre process
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*
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* Ident........: $Id: eoGnuplot.h,v 1.2 2001-02-01 05:17:16 evomarc Exp $
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* Ident........: $Id: eoGnuplot.h,v 1.3 2001-02-12 13:58:51 maartenkeijzer Exp $
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* ----------------------------------------------------------------------
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*/
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@ -142,7 +142,7 @@ void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
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// #include "pipecom.h"
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int Check( PCom *com )
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inline int Check( PCom *com )
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{
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if( ! com ) {
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fprintf( stderr, "PipeCom: Null pointer.\n" );
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@ -158,7 +158,7 @@ int Check( PCom *com )
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}
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PCom * PipeComOpen( char *prog )
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inline PCom * PipeComOpen( char *prog )
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{
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char *args[2];
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args[0] = prog;
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@ -167,7 +167,7 @@ PCom * PipeComOpen( char *prog )
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}
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PCom * PipeComOpenArgv( char *prog, char *argv[] )
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inline PCom * PipeComOpenArgv( char *prog, char *argv[] )
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{
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int toFils[2];
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int toPere[2];
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}
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int PipeComSend( PCom *to, const char *line )
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inline int PipeComSend( PCom *to, const char *line )
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{
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int nb = 0;
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if( ! Check(to ) )
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@ -231,7 +231,7 @@ int PipeComSend( PCom *to, const char *line )
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}
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int PipeComSendn( PCom *to, const char *data, int n )
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inline int PipeComSendn( PCom *to, const char *data, int n )
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{
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int nb = 0;
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if( ! Check(to) )
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@ -243,7 +243,7 @@ int PipeComSendn( PCom *to, const char *data, int n )
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}
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int PipeComReceive( PCom *from, char *data, int max )
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inline int PipeComReceive( PCom *from, char *data, int max )
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{
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if( ! Check(from) )
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return 0;
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@ -259,7 +259,7 @@ int PipeComReceive( PCom *from, char *data, int max )
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int PipeComClose( PCom *to )
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inline int PipeComClose( PCom *to )
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{
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if( ! Check(to) )
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return 0;
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@ -271,7 +271,7 @@ int PipeComClose( PCom *to )
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int PipeComWaitFor( PCom *from, char *what )
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inline int PipeComWaitFor( PCom *from, char *what )
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{
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char buffer[256];
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do {
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@ -73,9 +73,9 @@ private:
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};
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// the following should be placed in a separate eoGnuplot1DMonitor.cpp
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// then the inline specifier should dissappear
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////////////////////////////////////////////////////////////
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eoMonitor& eoGnuplot1DMonitor::operator() (void)
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inline eoMonitor& eoGnuplot1DMonitor::operator() (void)
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/////////////////////////////////////////////////////////
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{
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// update file using the eoFileMonitor
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@ -98,7 +98,7 @@ eoMonitor& eoGnuplot1DMonitor::operator() (void)
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}
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////////////////////////////////////////////////////////////
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void eoGnuplot1DMonitor::FirstPlot()
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inline void eoGnuplot1DMonitor::FirstPlot()
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////////////////////////////////////////////////////////
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{
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if (vec.size() < 2)
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@ -81,7 +81,7 @@ private:
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// the following should be placed in a separate eoGnuplot1DMonitor.cpp
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////////////////////////////////////////////////////////////
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eoMonitor& eoGnuplot1DSnapshot::operator() (void)
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inline eoMonitor& eoGnuplot1DSnapshot::operator() (void)
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/////////////////////////////////////////////////////////
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{
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// update file using the eoFileMonitor
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@ -32,6 +32,8 @@
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#include <map>
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#include <vector>
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#include <eoFunctorStore.h>
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class eoObject;
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class eoPersistent;
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@ -66,6 +68,12 @@ public :
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return static_cast<T&>(*ownedObjects.back());
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}
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void storeFunctor(eoFunctorBase* _functor)
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{
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// add it to the functorStore, fo
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functorStore.add(_functor);
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}
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/**
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* Loading error thrown when nothing seems to work.
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*/
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@ -113,9 +121,11 @@ private :
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ObjectMap objectMap;
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std::vector<ObjectMap::iterator> creationOrder;
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std::vector<eoPersistent*> ownedObjects;
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// And a functor store to boot
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eoFunctorStore functorStore;
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// private copy and assignment as eoState is supposed to be unique
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eoState(const eoState&);
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eoState& operator=(const eoState&);
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@ -13,16 +13,17 @@ LDADDS = $(top_builddir)/src/libeo.a $(top_builddir)/src/utils/libeoutils.a
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CXXFLAGS = -g
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###############################################################################
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noinst_PROGRAMS = t-eofitness t-eobin t-eoStateAndParser t-eoCheckpointing t-eoExternalEO t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp
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check_PROGRAMS = t-eofitness t-eobin t-eoStateAndParser t-eoCheckpointing t-eoExternalEO t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp t-eoGA
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TESTS=run_tests
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# removing temporarily t-eoESFull
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# noinst_PROGRAMS = t-eofitness t-eobin t-eoStateAndParser t-eoCheckpointing t-eoExternalEO t-eoESFull t-eoSymreg t-eo t-eoReplacement t-eoSelect
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#noinst_PROGRAMS = t-eofitness t-eobin t-eoStateAndParser t-eoCheckpointing t-eoExternalEO t-eoESFull t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp t-eoGA
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###############################################################################
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# t_eoESFull_SOURCES = t-eoESFull.cpp real_value.h
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# t_eoESFull_DEPENDENCIES = $(DEPS)
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# t_eoESFull_LDFLAGS = -lm
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# t_eoESFull_LDADD = $(LDADDS)
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#t_eoESFull_SOURCES = t-eoESFull.cpp real_value.h
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#t_eoESFull_DEPENDENCIES = $(DEPS)
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#t_eoESFull_LDFLAGS = -lm
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#t_eoESFull_LDADD = $(LDADDS)
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###############################################################################
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@ -93,3 +94,10 @@ t_eoGenOp_LDFLAGS = -lm
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t_eoGenOp_LDADD = $(LDADDS)
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###############################################################################
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t_eoGA_SOURCES = t-eoGA.cpp binary_value.h
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t_eoGA_DEPENDENCIES = $(DEPS) $(top_builddir)/src/ga/libga.a
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t_eoGA_LDFLAGS = -lm
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t_eoGA_LDADD = $(top_builddir)/src/ga/libga.a $(LDADDS)
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###############################################################################
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@ -33,6 +33,9 @@ echo "Testing t-eobin"
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echo "Testing t-eofitness"
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./t-eofitness > fitness.log
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echo "Testing t-eoGA"
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./t-eoGA > t-eoGA.log
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echo "Finished"
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#TODO test if an error occured
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36
eo/test/t-eoGA.cpp
Normal file
36
eo/test/t-eoGA.cpp
Normal file
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@ -0,0 +1,36 @@
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#include <iostream>
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#include <ga/ga.h>
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#include "binary_value.h"
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#include <apply.h>
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using namespace std;
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int main(int argc, char* argv[])
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{
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try
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{
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typedef eoBit<double> EoType;
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eoParser parser(argc, argv);
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eoState state; // keeps all things allocated, including eoEasyEA and eoPop!
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eoEvalFuncPtr<EoType, float> eval( binary_value<EoType> );
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eoGenContinue<EoType> term(20);
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eoCheckPoint<EoType> checkpoint(term);
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eoAlgo<EoType>& ga = make_ga(parser, eval, checkpoint, state);
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eoPop<EoType>& pop = init_ga(parser, state, double());
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apply(eval, pop);
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run_ga(ga, pop); // run the ga
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}
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catch(exception& e)
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{
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cout << e.what() << endl;
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}
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}
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Reference in a new issue