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Added pyeo. Some changes needed to be made for include files and the like

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in some files (and some bugs were fixed as well [Marc: eoOneToOneBreeder was a mess])

eoFunctor.h now contains static functor_category members, this shouldn't hurt anyone.
This commit is contained in:
maartenkeijzer 2003-01-05 16:31:50 +00:00
commit 131e0e033d
40 changed files with 2300 additions and 18 deletions
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3
eo/src/EO.h
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@ -120,9 +120,6 @@ public:
_is.seekg(pos); // rewind
_is >> repFitness;
}
}
/**

4
eo/src/Makefile.am
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@ -4,12 +4,12 @@
##
###############################################################################
SUBDIRS = es ga gp utils other
SUBDIRS = es ga gp utils other do
CPPFLAGS = -O2
lib_LIBRARIES = libeo.a
libeo_a_SOURCES = eoFunctorStore.cpp eoPersistent.cpp eoPrintable.cpp eoCtrlCContinue.cpp eoParetoFitness.cpp
libeoincdir = $(includedir)/eo
libeoinc_HEADERS = *.h eo
libeoinc_HEADERS = *.h eo do/*.h

2
eo/src/eoDetTournamentSelect.h
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@ -60,7 +60,7 @@ template <class EOT> class eoDetTournamentSelect: public eoSelectOne<EOT>
*/
virtual const EOT& operator()(const eoPop<EOT>& _pop)
{
return deterministic_tournament(_pop, tSize);
return deterministic_tournament(_pop, tSize);
}
private:

17
eo/src/eoFunctor.h
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@ -20,7 +20,7 @@
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
mak@dhi.dk
CVS Info: $Date: 2001-03-21 12:10:13 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoFunctor.h,v 1.5 2001-03-21 12:10:13 jmerelo Exp $ $Author: jmerelo $
CVS Info: $Date: 2003-01-05 16:31:47 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/eoFunctor.h,v 1.6 2003-01-05 16:31:47 maartenkeijzer Exp $ $Author: maartenkeijzer $
*/
//-----------------------------------------------------------------------------
@ -75,6 +75,11 @@ public :
/// The pure virtual function that needs to be implemented by the subclass
virtual R operator()() = 0;
static eoFunctorBase::procedure_tag functor_category()
{
return eoFunctorBase::procedure_tag();
}
};
/**
@ -106,6 +111,11 @@ public :
/// The pure virtual function that needs to be implemented by the subclass
virtual R operator()(A1) = 0;
static eoFunctorBase::unary_function_tag functor_category()
{
return eoFunctorBase::unary_function_tag();
}
};
/**
@ -140,6 +150,11 @@ public :
/// The pure virtual function that needs to be implemented by the subclass
virtual R operator()(A1, A2) = 0;
static eoFunctorBase::binary_function_tag functor_category()
{
return eoFunctorBase::binary_function_tag();
}
};
/**

8
eo/src/eoGenOp.h
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@ -67,7 +67,7 @@ class eoGenOp : public eoOp<EOT>, public eoUF<eoPopulator<EOT> &, void>
virtual string className() const = 0;
void operator()(eoPopulator<EOT>& _pop)
{
_pop.reserve(max_production());
_pop.reserve(max_production());
apply(_pop);
}
@ -163,13 +163,15 @@ class eoQuadGenOp : public eoGenOp<EOT>
void apply(eoPopulator<EOT>& _pop)
{
EOT& a = *_pop;
EOT& b = *++_pop;
EOT& b = *++_pop;
if(op(a, b))
{
a.invalidate();
b.invalidate();
}
}
virtual string className() const {return op.className();}

7
eo/src/eoOneToOneBreeder.h
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@ -32,7 +32,10 @@
#include <eoGenOp.h>
#include <eoPopulator.h>
#include <eoSelectOne.h>
#include <eoSequentialSelect.h>
#include <eoBreed.h>
#include <eoEvalFunc.h>
#include <eoPopulator.h>
#include <utils/eoHowMany.h>
/*****************************************************************************
@ -79,7 +82,7 @@ class eoOneToOneBreeder: public eoBreed<EOT>
_offspring.clear();
eoSelectivePopulator<EOT> popit(_parents, _offspring, select);
for (unsigned iParent=0; iParent<_parents.size(); iParent++)
for (unsigned iParent=0; iParent<target; iParent++)
{
unsigned pos = popit.tellp(); // remember current position
EOT theParent = *popit; // remember the parent itself
@ -100,8 +103,6 @@ class eoOneToOneBreeder: public eoBreed<EOT>
if (theParent > leOffspring) // old parent better than offspring
if (rng.uniform() < pReplace) // if probability
leOffspring = theParent; // replace
cout << "============ Final =========================\n";
cout << _offspring << endl;
// finally, go to next guy to handle
++popit;
}

2
eo/src/eoOpContainer.h
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@ -93,7 +93,7 @@ class eoSequentialOp : public eoOpContainer<EOT>
void apply(eoPopulator<EOT>& _pop)
{
position_type pos = _pop.tellp();
position_type pos = _pop.tellp();
for (size_t i = 0; i < rates.size(); ++i)
{

2
eo/src/eoTruncSelect.h
View file

@ -44,7 +44,7 @@ class eoTruncSelect : public eoSelect<EOT>
{
public:
/** Ctor: from an eoSelect (and an eoMany to tell how many are kept for selectino */
eoSelectMany(eoSelectOne<EOT>& _select, eoHowMany _howMany)
eoTruncSelect(eoSelectOne<EOT>& _select, eoHowMany _howMany)
: select(_select), howMany(_howMany) {}
/**

3
eo/src/pyeo/AUTHORS Normal file
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@ -0,0 +1,3 @@
Maarten Keijzer (mkeijzer@cs.vu.nl)

340
eo/src/pyeo/COPYING Normal file
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@ -0,0 +1,340 @@
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48
eo/src/pyeo/Makefile Normal file
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@ -0,0 +1,48 @@
# Note for however is foolish enough to attempt to build this thing
#
# You need:
# Python 2.2
# Stlport
# Boost.Python v2
#
#
# On my debian (unstable), I used libstlport_gcc.so.4.5
# and libboost_python.so.1.29.0
#
# Obviously together with python2.2 (as Boost.Python.v2 needs that)
#
# I'm pretty sure any stlport will do, but less convinced about boost.python
# That lib seems to be pretty much under development (as I found out, the hard way)
# but this version 1.29 seems to work for me.
#
# My version of boost was found in /usr/include, modify INC to your system
CXX = g++ #-3.2
CXXFLAGS = -g #-DNDEBUG
CPPFLAGS = -Wall #-O2
LDFLAGS =
COMPILE = $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c
LINK = $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS)
INC=-I/usr/include/python2.2/ -I/usr/include/stlport -I.. -ftemplate-depth-50
OBJECTS=eoFunctorStore.o pyeo.o abstract1.o algos.o \
random_numbers.o geneticOps.o selectOne.o continuators.o\
reduce.o replacement.o selectors.o breeders.o\
mergers.o valueParam.o perf2worth.o
all: pyeo.so
clean:
rm *.so *.o test/*.pyc
pyeo.so: $(OBJECTS)
$(LINK) -o pyeo.so $(OBJECTS) -lboost_python -lpython2.2 -shared -lstlport
eoFunctorStore.o: ../eoFunctorStore.h ../eoFunctorStore.cpp
$(COMPILE) -o eoFunctorStore.o ../eoFunctorStore.cpp $(INC)
%.o:%.cpp pyeo.h def_abstract_functor.h
$(COMPILE) $< $(INC)

0
eo/src/pyeo/NEWS Normal file
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3
eo/src/pyeo/README Normal file
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@ -0,0 +1,3 @@

43
eo/src/pyeo/abstract1.cpp Normal file
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@ -0,0 +1,43 @@
/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoEvalFunc.h>
#include <eoInit.h>
#include <eoTransform.h>
#include <eoSGATransform.h>
#include <eoPopEvalFunc.h>
#include "pyeo.h"
#include "def_abstract_functor.h"
void abstract1()
{
/* Abstract Classes: overrideble from python */
def_abstract_functor<eoEvalFunc<PyEO> >("eoEvalFunc");
def_abstract_functor<eoInit< PyEO > >("eoInit");
def_abstract_functor<eoTransform<PyEO> >("eoTransform");
class_<eoSGATransform<PyEO>, bases<eoTransform<PyEO> > >("eoSGATransform",
init< eoQuadOp<PyEO>&, double,
eoMonOp<PyEO>&, double>());
def_abstract_functor<eoPopEvalFunc<PyEO> >("eoPopEvalFunc");
}

93
eo/src/pyeo/algos.cpp Normal file
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@ -0,0 +1,93 @@
/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoSGA.h>
#include <eoEasyEA.h>
#include <eoDetSelect.h>
#include <eoCellularEasyEA.h>
#include "pyeo.h"
#include "def_abstract_functor.h"
void algos()
{
def_abstract_functor<eoAlgo<PyEO> >("eoAlgo");
/* Algorithms */
class_<eoSGA<PyEO>, bases<eoAlgo<PyEO> >, boost::noncopyable>("eoSGA",
init<eoSelectOne<PyEO>&,
eoQuadOp<PyEO>&, float,
eoMonOp<PyEO>&, float,
eoEvalFunc<PyEO>&,
eoContinue<PyEO>&>())
.def("__call__", &eoSGA<PyEO>::operator())
;
class_<eoEasyEA<PyEO>, bases<eoAlgo<PyEO> > >("eoEasyEA",
init<
eoContinue<PyEO>&,
eoEvalFunc<PyEO>&,
eoBreed<PyEO>&,
eoReplacement<PyEO>& >() )
.def( init<
eoContinue<PyEO>&,
eoPopEvalFunc<PyEO>&,
eoBreed<PyEO>&,
eoReplacement<PyEO>&>() )
.def( init<
eoContinue<PyEO>&,
eoEvalFunc<PyEO>&,
eoBreed<PyEO>&,
eoMerge<PyEO>&,
eoReduce<PyEO>& >() )
.def( init<
eoContinue<PyEO>&,
eoEvalFunc<PyEO>&,
eoSelect<PyEO>&,
eoTransform<PyEO>&,
eoReplacement<PyEO>&>())
.def( init<
eoContinue<PyEO>&,
eoEvalFunc<PyEO>&,
eoSelect<PyEO>&,
eoTransform<PyEO>&,
eoMerge<PyEO>&,
eoReduce<PyEO>&>())
.def("__call__", &eoEasyEA<PyEO>::operator())
;
/*
class_<eoCellularEasyEA<PyEO>, bases< eoAlgo<PyEO> > >("eoCellularEasyEA",
init< eoContinue<PyEO>&,
eoEvalFunc<PyEO>&,
eoSelectOne<PyEO>&,
eoBinOp<PyEO>&,
eoMonOp<PyEO>&,
eoSelectOne<PyEO>&>())
.def(
init< eoContinue<PyEO>&,
eoEvalFunc<PyEO>&,
eoSelectOne<PyEO>&,
eoQuadOp<PyEO>&,
eoMonOp<PyEO>&,
eoSelectOne<PyEO>&>())
;
*/
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoBreed.h>
#include <eoGeneralBreeder.h>
#include <eoOneToOneBreeder.h>
#include "pyeo.h"
#include "def_abstract_functor.h"
#define DEF(x) class_<x<PyEO>, bases<eoBreed<PyEO > > >(#x).def("__call__", &eoBreed<PyEO>::operator())
#define DEF2(x, i1) class_<x<PyEO>, bases<eoBreed<PyEO > > >(#x, init<i1>() ).def("__call__", &eoBreed<PyEO>::operator())
#define DEF3(x, i1, i2) class_<x<PyEO>, bases<eoBreed<PyEO > > >(#x, init<i1, i2 >() ).def("__call__", &eoBreed<PyEO>::operator())
void breeders()
{
def_abstract_functor<eoBreed<PyEO> >("eoBreed");
DEF3(eoSelectTransform, eoSelect<PyEO>&, eoTransform<PyEO>&);
DEF3(eoGeneralBreeder, eoSelectOne<PyEO>&, eoGenOp<PyEO>&)
.def( init<eoSelectOne<PyEO>&, eoGenOp<PyEO>&, double>() )
.def( init<eoSelectOne<PyEO>&, eoGenOp<PyEO>&, double, bool>() )
.def( init<eoSelectOne<PyEO>&, eoGenOp<PyEO>&, eoHowMany>() );
DEF3(eoOneToOneBreeder, eoGenOp<PyEO>&, eoEvalFunc<PyEO>&)
.def( init<eoGenOp<PyEO>&, eoEvalFunc<PyEO>&, double>() )
.def( init<eoGenOp<PyEO>&, eoEvalFunc<PyEO>&, double, eoHowMany>() );
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoGenContinue.h>
#include <eoCombinedContinue.h>
#include <eoEvalContinue.h>
#include <eoFitContinue.h>
#include <eoSteadyFitContinue.h>
#include "pyeo.h"
#include "def_abstract_functor.h"
#define DEF(x) class_<x<PyEO>, bases<eoContinue<PyEO > > >(#x).def("__call__", &eoContinue<PyEO>::operator())
#define DEF2(x, i1) class_<x<PyEO>, bases<eoContinue<PyEO > > >(#x, init<i1>() ).def("__call__", &eoContinue<PyEO>::operator())
#define DEF3(x, i1, i2) class_<x<PyEO>, bases<eoContinue<PyEO > > >(#x, init<i1, i2 >() ).def("__call__", &eoContinue<PyEO>::operator())
void continuators()
{
/* Counters, wrappers etc */
class_<eoEvalFuncCounter<PyEO>, bases<eoEvalFunc<PyEO> > >("eoEvalFuncCounter",
init< eoEvalFunc<PyEO>&, std::string>())
.def("__call__", &eoEvalFuncCounter<PyEO>::operator())
;
/* Continuators */
def_abstract_functor<eoContinue<PyEO> >("eoContinue");
class_<eoGenContinue<PyEO>, bases<eoContinue<PyEO> >, boost::noncopyable >("eoGenContinue", init<unsigned long>() )
.def("__call__", &eoGenContinue<PyEO>::operator())
;
class_<eoCombinedContinue<PyEO>, bases<eoContinue<PyEO> > >("eoCombinedContinue", init<eoContinue<PyEO>&>())
.def( init<eoContinue<PyEO>&, eoContinue<PyEO>& >() )
.def("add", &eoCombinedContinue<PyEO>::add)
.def("__call__", &eoCombinedContinue<PyEO>::operator())
;
class_<eoEvalContinue<PyEO>, bases<eoContinue<PyEO> > >("eoEvalContinue",
init<eoEvalFuncCounter<PyEO>&, unsigned long>())
.def("__call__", &eoEvalContinue<PyEO>::operator())
;
DEF2(eoFitContinue, object); // object is the fitness type
DEF3(eoSteadyFitContinue, unsigned long, unsigned long);
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#ifndef MAKE_ABSTRACT_FUNCTOR_H
#define MAKE_ABSTRACT_FUNCTOR_H
#include <eoFunctor.h>
namespace eoutils {
using namespace boost::python;
template <class Proc>
class ProcWrapper : public Proc
{
public:
PyObject* self;
ProcWrapper(PyObject* s) : self(s) {}
typename Proc::result_type operator()(void)
{
return boost::python::call_method<typename Proc::result_type>(self, "__call__");
}
};
template <class Proc>
void make_abstract_functor(std::string name, typename eoFunctorBase::procedure_tag)
{
typedef ProcWrapper<Proc> Wrapper;
boost::python::class_<Proc, Wrapper,boost::noncopyable>(name.c_str(), boost::python::init<>() )
.def("__call__", &Wrapper::operator());
}
template <class Proc>
void make_abstract_functor_ref(std::string name, typename eoFunctorBase::procedure_tag)
{
typedef ProcWrapper<Proc> Wrapper;
boost::python::class_<Proc, Wrapper,boost::noncopyable>(name.c_str(), boost::python::init<>() )
.def("__call__", &Wrapper::operator(), boost::python::return_internal_reference<>());
}
template <class Unary>
class UnaryWrapper : public Unary
{
public:
PyObject* self;
UnaryWrapper(PyObject* s) : self(s) {}
typename Unary::result_type operator()(typename Unary::argument_type a)
{
return boost::python::call_method<typename Unary::result_type>(self, "__call__", boost::ref(a) );
}
};
template <class Unary>
void make_abstract_functor(std::string name, typename eoFunctorBase::unary_function_tag)
{
typedef UnaryWrapper<Unary> Wrapper;
boost::python::class_<Unary, Wrapper, boost::noncopyable>(name.c_str(), boost::python::init<>() )
.def("__call__", &Wrapper::operator())
;
}
template <class Unary>
void make_abstract_functor_ref(std::string name, typename eoFunctorBase::unary_function_tag)
{
typedef UnaryWrapper<Unary> Wrapper;
boost::python::class_<Unary, Wrapper, boost::noncopyable>(name.c_str(), boost::python::init<>() )
.def("__call__", &Wrapper::operator(), boost::python::return_internal_reference<>() )
;
}
template <class Binary>
class BinaryWrapper : public Binary
{
public:
PyObject* self;
BinaryWrapper(PyObject* s) : self(s) {}
typename Binary::result_type operator()(typename Binary::first_argument_type a1, typename Binary::second_argument_type a2)
{
return boost::python::call_method<
typename Binary::result_type>(self, "__call__", boost::ref(a1), boost::ref(a2) );
}
};
template <class Binary>
void make_abstract_functor(std::string name, typename eoFunctorBase::binary_function_tag)
{
typedef BinaryWrapper<Binary> Wrapper;
boost::python::class_<Binary, Wrapper, boost::noncopyable>(name.c_str(), boost::python::init<>() )
.def("__call__", &Wrapper::operator());
}
template <class Binary>
void make_abstract_functor_ref(std::string name, typename eoFunctorBase::binary_function_tag)
{
typedef BinaryWrapper<Binary> Wrapper;
boost::python::class_<Binary, Wrapper, boost::noncopyable>(name.c_str(), boost::python::init<>() )
.def("__call__", &Wrapper::operator(), boost::python::return_internal_reference<>() );
}
}// namespace eoutils
template <class Functor>
void def_abstract_functor(std::string name)
{
eoutils::make_abstract_functor<Functor>(name, Functor::functor_category());
}
template <class Functor>
void def_abstract_functor_ref(std::string name)
{
eoutils::make_abstract_functor_ref<Functor>(name, Functor::functor_category());
}
#endif

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoGenOp.h>
#include <eoOp.h>
#include <eoCloneOps.h>
#include <eoPopulator.h>
#include <eoOpContainer.h>
#include "pyeo.h"
class GenOpWrapper : public eoGenOp<PyEO>
{
public:
PyObject* self;
GenOpWrapper(PyObject* p) : self(p) {}
unsigned max_production(void)
{
return call_method<unsigned>(self,"max_production");
}
std::string className() const
{
return "GenOpDerivative"; // never saw the use of className anyway
}
void apply(eoPopulator<PyEO>& populator )
{
boost::python::call_method<void>(self,"apply", boost::ref( populator ) );
}
};
class PopulatorWrapper : public eoPopulator<PyEO>
{
public:
PyObject* self;
PopulatorWrapper(PyObject* p, const eoPop<PyEO>& src, eoPop<PyEO>& dest)
: eoPopulator<PyEO>(src, dest), self(p)
{
//throw std::runtime_error("abstract base class");
}
const PyEO& select()
{
return call_method<const PyEO&>(self,"select");
}
};
class MonOpWrapper : public eoMonOp<PyEO>
{
public:
PyObject* self;
MonOpWrapper(PyObject* p) : self(p) {}
bool operator()(PyEO& _eo)
{ return boost::python::call_method<bool>(self, "__call__", boost::ref( _eo )); }
};
class BinOpWrapper : public eoBinOp<PyEO>
{
public:
PyObject* self;
BinOpWrapper(PyObject* p) : self(p) {}
bool operator()(PyEO& _eo, const PyEO& _eo2)
{ return boost::python::call_method<bool>(self, "__call__", boost::ref( _eo ), boost::ref(_eo2)); }
};
class QuadOpWrapper : public eoQuadOp<PyEO>
{
public:
PyObject* self;
QuadOpWrapper(PyObject* p) : self(p) {}
bool operator()(PyEO& _eo, PyEO& _eo2)
{ return boost::python::call_method<bool>(self, "__call__", boost::ref( _eo ), boost::ref(_eo2)); }
};
void geneticOps()
{
class_<eoPopulator<PyEO>, PopulatorWrapper, boost::noncopyable>
("eoPopulator", init<const eoPop<PyEO>&, eoPop<PyEO>&>() )
.def("select", &PopulatorWrapper::select, return_internal_reference<>() )
.def("get", &eoPopulator<PyEO>::operator*, return_internal_reference<>() )
.def("next", &eoPopulator<PyEO>::operator++, return_internal_reference<>() )
.def("insert", &eoPopulator<PyEO>::insert)
.def("reserve", &eoPopulator<PyEO>::reserve)
.def("source", &eoPopulator<PyEO>::source, return_internal_reference<>() )
.def("offspring", &eoPopulator<PyEO>::offspring, return_internal_reference<>() )
.def("tellp", &eoPopulator<PyEO>::tellp)
.def("seekp", &eoPopulator<PyEO>::seekp)
.def("exhausted", &eoPopulator<PyEO>::exhausted)
;
class_<eoSeqPopulator<PyEO>, bases<eoPopulator<PyEO> > >
("eoSeqPopulator", init<const eoPop<PyEO>&, eoPop<PyEO>&>() )
.def("select", &eoSeqPopulator<PyEO>::select, return_internal_reference<>() )
;
class_<eoSelectivePopulator<PyEO>, bases<eoPopulator<PyEO> > >
("eoSelectivePopulator", init<const eoPop<PyEO>&, eoPop<PyEO>&, eoSelectOne<PyEO>& >() )
.def("select", &eoSeqPopulator<PyEO>::select, return_internal_reference<>() )
;
enum_<eoOp<PyEO>::OpType>("OpType")
.value("unary", eoOp<PyEO>::unary)
.value("binary", eoOp<PyEO>::binary)
.value("quadratic", eoOp<PyEO>::quadratic)
.value("general", eoOp<PyEO>::general)
;
class_<eoOp<PyEO> >("eoOp", init<eoOp<PyEO>::OpType>())
.def("getType", &eoOp<PyEO>::getType);
class_<eoMonOp<PyEO>, MonOpWrapper, bases<eoOp<PyEO> >, boost::noncopyable>("eoMonOp", init<>())
.def("__call__", &MonOpWrapper::operator(), "an example docstring");
class_<eoBinOp<PyEO>, BinOpWrapper, bases<eoOp<PyEO> >, boost::noncopyable>("eoBinOp", init<>())
.def("__call__", &BinOpWrapper::operator());
class_<eoQuadOp<PyEO>, QuadOpWrapper, bases<eoOp<PyEO> >, boost::noncopyable>("eoQuadOp", init<>())
.def("__call__", &QuadOpWrapper::operator());
class_<eoGenOp<PyEO>, GenOpWrapper, bases<eoOp<PyEO> >, boost::noncopyable>("eoGenOp", init<>())
.def("max_production", &GenOpWrapper::max_production)
.def("className", &GenOpWrapper::className)
.def("apply", &GenOpWrapper::apply)
.def("__call__", &eoGenOp<PyEO>::operator())
;
class_<eoSequentialOp<PyEO>, bases<eoGenOp<PyEO> >, boost::noncopyable>("eoSequentialOp", init<>())
.def("add", &eoSequentialOp<PyEO>::add)
.def("apply", &eoSequentialOp<PyEO>::apply)
;
class_<eoProportionalOp<PyEO>, bases<eoGenOp<PyEO> >, boost::noncopyable>("eoProportionalOp", init<>())
.def("add", &eoProportionalOp<PyEO>::add)
.def("apply", &eoProportionalOp<PyEO>::apply)
;
/* Cloning */
class_<eoMonCloneOp<PyEO>, bases<eoMonOp<PyEO> > >("eoMonCloneOp").def("__call__", &eoMonCloneOp<PyEO>::operator());
class_<eoBinCloneOp<PyEO>, bases<eoBinOp<PyEO> > >("eoBinCloneOp").def("__call__", &eoBinCloneOp<PyEO>::operator());
class_<eoQuadCloneOp<PyEO>, bases<eoQuadOp<PyEO> > >("eoQuadCloneOp").def("__call__", &eoQuadCloneOp<PyEO>::operator());
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoMerge.h>
#include "pyeo.h"
#include "def_abstract_functor.h"
#define DEF(x) class_<x<PyEO>, bases<eoMerge<PyEO > > >(#x).def("__call__", &eoMerge<PyEO>::operator())
#define DEF2(x, i1) class_<x<PyEO>, bases<eoMerge<PyEO > > >(#x, init<i1>() ).def("__call__", &eoMerge<PyEO>::operator())
#define DEF3(x, i1, i2) class_<x<PyEO>, bases<eoMerge<PyEO > > >(#x, init<i1, i2 >() ).def("__call__", &eoMerge<PyEO>::operator())
void mergers()
{
def_abstract_functor<eoMerge<PyEO> >("eoMerge");
DEF2(eoElitism, double)
.def( init<double, bool>() );
DEF(eoNoElitism);
DEF(eoPlus);
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <utils/eoMonitor.h>
#include "pyeo.h"
void monitors()
{
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
//#include <eoPerf2Worth.h>
//#include <eoNDSorting.h>
//#include "pyeo.h"
void perf2worth() // will have to rethink this
{
// class_<eoNDSorting_II<PyEO> >("eoNDSorting_II");
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#ifndef PICKLE_H
#define PICKLE_h
#include <boost/python.hpp>
#include <strstream>
/** Implements pickle support for eoPersistent derivatives */
template <class T>
struct T_pickle_suite : boost::python::pickle_suite
{
static
std::string print_to_string(const T& t)
{
std::ostrstream os;
t.printOn(os);
os << ends;
return os.str();
}
static
boost::python::tuple getstate(const T& t)
{
std::string s = print_to_string(t);
return boost::python::make_tuple( boost::python::str(s));
}
static
void setstate(T& t, boost::python::tuple pickled)
{
std::string s = extract<std::string>(pickled[0]);
std::istrstream is(s.c_str(), s.size());
t.readFrom(is);
}
};
/** Defines persistency through pickle support by using strings
* so while we're at it, we will .def("__str__") as well
*/
template <class Persistent, class X1, class X2, class X3>
boost::python::class_<Persistent, X1, X2, X3>& pickle(boost::python::class_<Persistent, X1, X2, X3>& c)
{
return c.def_pickle(T_pickle_suite<Persistent>())
.def("__str__", T_pickle_suite<Persistent>::print_to_string);
}
#endif

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoPop.h>
#include "pyeo.h"
ostream& operator<<(ostream& os, const PyEO& _eo)
{
os << _eo.to_string();
return os;
}
struct pyPop_pickle_suite : boost::python::pickle_suite
{
static boost::python::tuple getstate(const eoPop<PyEO>& _pop)
{
boost::python::list entries;
for (unsigned i = 0; i != _pop.size(); ++i)
entries.append( PyEO_pickle_suite::getstate(_pop[i]) );
return make_tuple(object(_pop.size()), entries);
}
static void setstate( eoPop<PyEO>& _pop, boost::python::tuple pickled)
{
int sz = extract<int>(pickled[0]);
boost::python::list entries = pickled[1];
_pop.resize(sz);
for (unsigned i = 0; i != _pop.size(); ++i)
PyEO_pickle_suite::setstate(_pop[i], tuple(entries[i]) );
}
};
template <class T>
boost::python::str to_string(T& _p)
{
std::ostrstream os;
_p.printOn(os);
os << ends;
std::string s(os.str());
return str(s.c_str());
}
void pop_sort(eoPop<PyEO>& pop) { pop.sort(); }
void pop_shuffle(eoPop<PyEO>& pop) { pop.shuffle(); }
struct index_error { index_error(std::string w) : what(w) {}; std::string what; };
void translate_index_error(index_error const& e)
{
PyErr_SetString(PyExc_IndexError, e.what.c_str());
}
PyEO& pop_getitem(eoPop<PyEO>& pop, object key)
{
extract<int> x(key);
if (!x.check())
throw index_error("Slicing not allowed");
int i = x();
if (static_cast<unsigned>(i) >= pop.size())
{
throw index_error("Index out of bounds");
}
return pop[i];
}
void pop_setitem(eoPop<PyEO>& pop, object key, PyEO& value)
{
extract<int> x(key);
if (!x.check())
throw index_error("Slicing not allowed");
int i = x();
if (static_cast<unsigned>(i) >= pop.size())
{
throw index_error("Index out of bounds");
}
pop[i] = value;
}
void pop_push_back(eoPop<PyEO>& pop, PyEO& p) { pop.push_back(p); }
void pop_resize( eoPop<PyEO>& pop, unsigned i) { pop.resize(i); }
extern void abstract1();
extern void algos();
extern void random_numbers();
extern void geneticOps();
extern void selectOne();
extern void continuators();
extern void reduce();
extern void replacement();
extern void selectors();
extern void breeders();
extern void mergers();
extern void valueParam();
extern void perf2worth();
BOOST_PYTHON_MODULE(pyeo)
{
register_exception_translator<index_error>(&translate_index_error);
class_<PyEO>("EO")
.add_property("fitness", &PyEO::getFitness, &PyEO::setFitness)
.add_property("genome", &PyEO::getGenome, &PyEO::setGenome)
.def_pickle(PyEO_pickle_suite())
.def("invalidate", &PyEO::invalidate)
.def("invalid", &PyEO::invalid)
.def("__str__", &PyEO::to_string)
;
class_<eoPop<PyEO> >("Pop", init<>() )
.def( init< unsigned, eoInit<PyEO>& >() )
.def("append", &eoPop<PyEO>::append)
.def("__str__", to_string<eoPop<PyEO> >)
.def("__len__", &eoPop<PyEO>::size)
.def("sort", pop_sort )
.def("shuffle", pop_shuffle)
.def("__getitem__", pop_getitem, return_internal_reference<>() )
.def("__setitem__", pop_setitem)
.def("best", &eoPop<PyEO>::best_element, return_internal_reference<>() )
.def("push_back", pop_push_back)
.def("resize", pop_resize)
.def_pickle(pyPop_pickle_suite())
;
// Other definitions in different compilation units,
// this to avoid having g++ to choke on the load
random_numbers();
valueParam();
abstract1();
geneticOps();
selectOne();
selectors();
perf2worth();
continuators();
reduce();
replacement();
breeders();
mergers();
algos();
}
// to avoid having to build with libeo.a
ostream & operator << ( ostream& _os, const eoPrintable& _o ) {
_o.printOn(_os);
return _os;
};

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#ifndef PYEO_H
#define PYEO_H
#include <EO.h>
#include <boost/python.hpp>
using namespace boost::python;
/*
class PyFitness : public boost::python::object
{
public :
PyFitness() : object() {}
template <class T>
PyFitness(const T& o) : object(o) {}
static unsigned nObjectives() { return 1; }
static double tol() { return 1e-6; }
static bool maximizing(int which) { return true; }
static bool dominates(const PyFitness& one, const PyFitness& oth) { return true; } // for the moment
operator unsigned() const { return 1; } // for the moment
operator double() const { return 1; } // for the moment
PyFitness operator[](int i) { return PyFitness(object::operator[](i)); }
friend ostream& operator<<(ostream& os, const PyFitness& p) { const object& o = p; os << o; return os; }
friend istream& operator>>(istream& is, PyFitness& p) { object o; is >> o; p = o; return is; }
typedef PyFitness AtomType;
};
object fabs(object obj)
{
object zero(0.0);
if (obj < zero )
return zero-obj;
return obj;
}
object max(object a, object b)
{
if (a < b)
return b;
return a;
}
*/
struct PyEO : public EO< object >
{
typedef object Fitness;
Fitness getFitness() const { return invalid()? Fitness(): fitness(); }
void setFitness(Fitness f) { if (f == Fitness()) invalidate(); else fitness(f); }
object getGenome() const { return genome; }
void setGenome(object g) { genome = g; }
object genome;
std::string to_string() const
{
std::string result;
result += extract<const char*>(str(getFitness()));
result += ' ';
result += extract<const char*>(str(genome));
return result;
}
bool operator<(const PyEO& other) const { return EO<Fitness>::operator<(other); }
bool operator>(const PyEO& other) const { return EO<Fitness>::operator>(other); }
};
ostream& operator<<(ostream& os, const PyEO& _eo);
struct PyEO_pickle_suite : boost::python::pickle_suite
{
typedef PyEO::Fitness Fitness;
static
boost::python::tuple getstate(const PyEO& _eo)
{
return make_tuple(_eo.getFitness(), _eo.genome);
}
static
void setstate(PyEO& _eo, boost::python::tuple pickled)
{
_eo.setFitness( Fitness(pickled[0]) );
_eo.genome = pickled[1];
}
};
#endif

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <utils/eoRNG.h>
#include <boost/python.hpp>
#include <strstream>
using namespace boost::python;
namespace eo
{
eoRng rng(time(0));
}
eoRng& get_rng() { return rng; }
double normal(eoRng& rng) { return rng.normal(); }
std::string rng_to_string(const eoRng& _rng)
{
std::ostrstream os;
_rng.printOn(os);
os << std::ends;
return os.str();
}
void rng_from_string(eoRng& _rng, std::string s)
{
std::istrstream is(s.c_str(), s.size());
_rng.readFrom(is);
}
void random_numbers()
{
class_<eoRng, boost::noncopyable>("eoRng", init<uint32>())
.def("flip", &eoRng::flip)
.def("random", &eoRng::random)
.def("rand", &eoRng::rand)
.def("rand_max", &eoRng::rand_max)
.def("reseed", &eoRng::reseed)
.def("uniform", &eoRng::uniform)
.def("normal", normal)
.def("negexp", &eoRng::negexp)
.def("to_string", rng_to_string)
.def("from_string", rng_from_string)
;
def("rng", get_rng, return_value_policy<reference_existing_object>());
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoReduce.h>
#include "pyeo.h"
// unfortunately have to define it specially
class eoReduceWrapper : public eoReduce<PyEO>
{
public:
PyObject* self;
eoReduceWrapper(PyObject* s) : self(s) {}
void operator()(eoPop<PyEO>& pop, unsigned i)
{
boost::python::call_method<void>(self, "__call__", pop, i );
}
};
void reduce()
{
// ref trick in def_abstract_functor does not work for unsigned int :-(
class_<eoReduce<PyEO>, eoReduceWrapper, boost::noncopyable>("eoReduce", init<>())
.def("__call__", &eoReduceWrapper::operator());
class_<eoTruncate<PyEO>, bases<eoReduce<PyEO> > >("eoTruncate", init<>() )
.def("__call__", &eoReduce<PyEO>::operator())
;
class_<eoRandomReduce<PyEO>, bases<eoReduce<PyEO> > >("eoRandomReduce")
.def("__call__", &eoReduce<PyEO>::operator())
;
class_<eoEPReduce<PyEO>, bases<eoReduce<PyEO> > >("eoEPReduce", init<unsigned>())
.def("__call__", &eoReduce<PyEO>::operator())
;
class_<eoLinearTruncate<PyEO>, bases<eoReduce<PyEO> > >("eoLinearTruncate")
.def("__call__", &eoReduce<PyEO>::operator())
;
class_<eoDetTournamentTruncate<PyEO>, bases<eoReduce<PyEO> > >("eoDetTournamentTruncate", init<unsigned>())
.def("__call__", &eoReduce<PyEO>::operator())
;
class_<eoStochTournamentTruncate<PyEO>, bases<eoReduce<PyEO> > >("eoStochTournamentTruncate", init<double>())
.def("__call__", &eoReduce<PyEO>::operator())
;
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoReplacement.h>
#include <eoMergeReduce.h>
#include <eoReduceMerge.h>
#include <eoReduceMergeReduce.h>
#include <eoMGGReplacement.h>
#include "pyeo.h"
#include "def_abstract_functor.h"
#define DEF(x) class_<x<PyEO>, bases<eoReplacement<PyEO > > >(#x).def("__call__", &eoReplacement<PyEO>::operator())
#define DEF2(x, i1) class_<x<PyEO>, bases<eoReplacement<PyEO > > >(#x, init<i1>() ).def("__call__", &eoReplacement<PyEO>::operator())
#define DEF3(x, i1, i2) class_<x<PyEO>, bases<eoReplacement<PyEO > > >(#x, init<i1, i2 >() ).def("__call__", &eoReplacement<PyEO>::operator())
void replacement()
{
def_abstract_functor<eoReplacement<PyEO> >("eoReplacement");
// eoReplacement.h
DEF(eoGenerationalReplacement);
DEF2(eoWeakElitistReplacement, eoReplacement<PyEO>& );
// eoMergeReduce.h
DEF3(eoMergeReduce, eoMerge<PyEO>&, eoReduce<PyEO>& );
DEF(eoPlusReplacement);
DEF(eoCommaReplacement);
DEF2(eoEPReplacement, unsigned);
// eoReduceMerge.h
DEF3(eoReduceMerge, eoReduce<PyEO>&, eoMerge<PyEO>& );
DEF(eoSSGAWorseReplacement);
DEF2(eoSSGADetTournamentReplacement, unsigned);
DEF2(eoSSGAStochTournamentReplacement, double);
// eoReduceMergeReduce.h
class_<eoReduceMergeReduce<PyEO>, bases<eoReplacement<PyEO> > >("eoReplacement",
init<eoHowMany, bool, eoHowMany, eoReduce<PyEO>&,
eoHowMany, eoReduce<PyEO>&, eoReduce<PyEO>&>())
.def("__call__", &eoReplacement<PyEO>::operator());
//eoMGGReplacement
DEF(eoMGGReplacement)
.def( init<eoHowMany>() )
.def( init<eoHowMany, unsigned>() );
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoSelectOne.h>
#include <eoDetTournamentSelect.h>
#include <eoRandomSelect.h>
#include <eoStochTournamentSelect.h>
#include <eoTruncatedSelectOne.h>
#include <eoSequentialSelect.h>
#include "pyeo.h"
#include "pickle.h"
class eoSelectOneWrapper : public eoSelectOne<PyEO>
{
public:
PyObject* self;
eoSelectOneWrapper(PyObject* p) : self(p) {}
const PyEO& operator()(const eoPop<PyEO>& pop)
{
return boost::python::call_method< const PyEO& >(self, "__call__", boost::ref(pop));
}
};
template <class Select>
void add_select(std::string name)
{
class_<Select, bases<eoSelectOne<PyEO> > >(name.c_str(), init<>() )
.def("__call__", &Select::operator(), return_internal_reference<>() )
;
}
template <class Select, class Init>
void add_select(std::string name, Init init)
{
class_<Select, bases<eoSelectOne<PyEO> > >(name.c_str(), init)
.def("__call__", &Select::operator(), return_internal_reference<>() )
;
}
template <class Select, class Init1, class Init2>
void add_select(std::string name, Init1 init1, Init2 init2)
{
class_<Select, bases<eoSelectOne<PyEO> > >(name.c_str(), init1)
.def( init2 )
.def("__call__", &Select::operator(), return_internal_reference<>() )
.def("setup", &Select::setup);
}
void selectOne()
{
/* Concrete classes */
pickle(class_<eoHowMany>("eoHowMany", init<>())
.def( init<double>() )
.def( init<double, bool>() )
.def( init<int>() )
.def("__call__", &eoHowMany::operator())
.def("__neg__", &eoHowMany::operator-)
);
class_<eoSelectOne<PyEO>, eoSelectOneWrapper, boost::noncopyable>("eoSelectOne", init<>())
.def("__call__", &eoSelectOneWrapper::operator(), return_internal_reference<>() )
.def("setup", &eoSelectOne<PyEO>::setup);
/* SelectOne derived classes */
add_select<eoDetTournamentSelect<PyEO> >("eoDetTournamentSelect", init<>(), init<unsigned>() );
add_select<eoStochTournamentSelect<PyEO> >("eoStochTournamentSelect", init<>(), init<double>() );
add_select<eoTruncatedSelectOne<PyEO> >("eoTruncatedSelectOne",
init<eoSelectOne<PyEO>&, double>(), init<eoSelectOne<PyEO>&, eoHowMany >() );
// eoProportionalSelect is not feasible to implement at this point as fitness is not recognizable as a float
// use eoDetTournament instead: with a t-size of 2 it is equivalent to eoProportional with linear scaling
//add_select<eoProportionalSelect<PyEO> >("eoProportionalSelect", init<eoPop<PyEO>&>() );
add_select<eoRandomSelect<PyEO> >("eoRandomSelect");
add_select<eoBestSelect<PyEO> >("eoBestSelect");
add_select<eoNoSelect<PyEO> >("eoNoSelect");
add_select<eoSequentialSelect<PyEO> >("eoSequentialSelect", init<>(), init<bool>());
add_select<eoEliteSequentialSelect<PyEO> >("eoEliteSequentialSelect");
/*
* eoSelectFromWorth.h:class eoSelectFromWorth : public eoSelectOne<EOT>
*/
}

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/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <eoSelect.h>
#include <eoDetSelect.h>
#include <eoSelectMany.h>
#include <eoSelectNumber.h>
#include <eoSelectPerc.h>
#include <eoTruncSelect.h>
#include <eoTruncatedSelectMany.h>
#include "pyeo.h"
#include "def_abstract_functor.h"
#define DEF(x) class_<x<PyEO>, bases<eoSelect<PyEO > > >(#x).def("__call__", &eoSelect<PyEO>::operator())
#define DEF2(x, i1) class_<x<PyEO>, bases<eoSelect<PyEO > > >(#x, init<i1>() ).def("__call__", &eoSelect<PyEO>::operator())
#define DEF3(x, i1, i2) class_<x<PyEO>, bases<eoSelect<PyEO > > >(#x, init<i1, i2 >() ).def("__call__", &eoSelect<PyEO>::operator())
void selectors()
{
def_abstract_functor<eoSelect<PyEO> >("eoSelect");
DEF(eoDetSelect).def( init<double>() ).def( init<double, bool>() );
DEF3(eoSelectMany, eoSelectOne<PyEO>&, double)
.def( init< eoSelectOne<PyEO>&, double, bool>() )
.def( init< eoSelectOne<PyEO>&, eoHowMany>() );
DEF2(eoSelectNumber, eoSelectOne<PyEO>&)
.def( init< eoSelectOne<PyEO>&, unsigned>());
DEF2(eoSelectPerc, eoSelectOne<PyEO>&)
.def( init<eoSelectOne<PyEO>&, float>() );
DEF3(eoTruncSelect, eoSelectOne<PyEO>&, eoHowMany);
class_<eoTruncatedSelectMany<PyEO>, bases<eoSelect<PyEO> > >("eoTruncatedSelectMany",
init<eoSelectOne<PyEO>&, double, double> ())
.def(init<eoSelectOne<PyEO>&, double, double, bool> ())
.def(init<eoSelectOne<PyEO>&, double, double, bool, bool> ())
.def(init<eoSelectOne<PyEO>&, eoHowMany, eoHowMany> ());
}

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import sys
sys.path.append('..')
print 'importing pyeo'
from pyeo import *
print 'done'
from copy import copy
class EvalFunc(eoEvalFunc):
def __call__(self, eo):
eo.fitness = reduce(lambda x,y: x+y, eo.genome, 0)
class Init(eoInit):
def __init__(self, genome_length = 10):
eoInit.__init__(self)
self.length = genome_length
def __call__(self, eo):
eo.genome = [rng().flip(0.5) for x in range(self.length)]
class Mutate(eoMonOp):
def __call__(self, eo):
eo.genome = copy(eo.genome)
prob = 1. / len(eo.genome)
for i in range(len(eo.genome)):
if rng().flip(0.5):
eo.genome[i] = 1-eo.genome[i];
return 1
class Crossover(eoQuadOp):
def __call__(self, eo1, eo2):
eo1.genome = copy(eo1.genome);
eo2.genome = copy(eo2.genome);
point = rng().random( len(eo1.genome) );
eo1.genome[:point] = eo2.genome[:point];
eo2.genome[point:] = eo1.genome[point:];
return 1
evaluate = EvalFunc()
init = Init(3)
mutate = Mutate()
xover = Crossover()
if __name__ == '__main__':
eo = EO()
eo1 = EO()
init(eo1)
init(eo)
evaluate(eo)
print eo
for i in range(10):
xover(eo, eo1)
mutate(eo)
evaluate(eo)
print eo, eo1
print
print
print
pop = Pop(1, init)
pop[0] = eo;
mutate(pop[0])
pop[0].invalidate()
evaluate(pop[0])
print pop[0], eo

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#!/bin/sh
for i in *.py
do
python $i
done

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from maxone import *
import unittest
evaluate = EvalFunc()
init = Init(20)
mutate = Mutate()
xover = Crossover()
class TestSGA(unittest.TestCase):
def runtest(self, breed):
pop = Pop(50, init)
for indy in pop: evaluate(indy)
newpop = Pop();
breed(pop,newpop)
print pop.best()
for indy in newpop: evaluate(indy)
print newpop.best()
def testGeneralBreeder(self):
seq = eoSequentialOp();
seq.add(xover, 0.7)
seq.add(mutate, 0.9)
sel = eoDetTournamentSelect(3)
breed = eoGeneralBreeder(sel, seq)
self.runtest(breed)
if __name__=='__main__':
unittest.main()

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from maxone import *
import unittest
import cPickle
import tempfile
import os
class TestPickling(unittest.TestCase):
def do_pickle(self, object):
filename = tempfile.mktemp()
file = open(filename, 'wb')
pickler = cPickle.Pickler(file)
pickler.dump(object);
del pickler
file.close()
file = open(filename)
unpickler = cPickle.Unpickler(file)
object2 = unpickler.load()
del unpickler
file.close()
os.remove(filename)
return object2
def testInvalidEO(self):
eo = EO();
eo.genome = [1,2,3];
eo2 = self.do_pickle(eo)
self.failUnlessEqual( str(eo), str(eo2) )
def testValidEO(self):
eo = EO();
eo.genome = [1,2,3];
eo.fitness = 10
eo2 = self.do_pickle(eo)
self.failUnlessEqual( str(eo), str(eo2) )
def testPop(self):
pop = Pop(40, init)
for indy in pop:
evaluate(indy)
pop2 = self.do_pickle(pop)
self.failUnlessEqual( str(pop), str(pop2) )
def testHowMany(self):
howmany = eoHowMany(0.8);
howmany2 = self.do_pickle(howmany)
self.failUnlessEqual(howmany(10), howmany2(10))
self.failUnlessEqual( str(howmany), str(howmany) )
def testRNG(self):
for i in range(10):
rng().rand()
filename = tempfile.mktemp()
file = open(filename, 'wb')
pickler = cPickle.Pickler(file)
s = rng().to_string()
pickler.dump(s);
del pickler
file.close()
file = open(filename)
unpickler = cPickle.Unpickler(file)
s = unpickler.load()
rng2 = eoRng(1)
rng2.from_string(s)
del unpickler
file.close()
os.remove(filename)
for i in range(100):
a = rng().rand()
b = rng2.rand()
self.failUnlessEqual(a,b)
if __name__=='__main__':
unittest.main()

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print 'importing maxone'
from maxone import *
print 'done'
import unittest
class Mut(Mutate):
def __init__(self):
Mutate.__init__(self)
self.cnt = 0;
def __call__(self, eo):
self.cnt += 1;
return Mutate.__call__(self, eo)
class Xover(Crossover):
def __init__(self):
Crossover.__init__(self)
self.cnt = 0;
def __call__(self, eo1, eo2):
self.cnt += 1;
return Crossover.__call__(self, eo1, eo2)
class TestPopulator(unittest.TestCase):
def make_pop(self):
pop = Pop(20, init)
for indy in pop: evaluate(indy)
return pop
def test_sequential(self):
pop = self.make_pop()
populator = eoSeqPopulator(pop, pop)
print populator.get()
print populator.get()
def test_selective(self):
sel = eoDetTournamentSelect(2)
pop = self.make_pop()
populator = eoSelectivePopulator(pop, pop, sel)
print populator.get()
print populator.get()
def runOpContainer(self, opcontainer):
mutate = Mut()
xover = Xover()
print 'making seq'
seq = opcontainer()
print "xovertype", xover.getType()
print "mutationtype", mutate.getType()
seq.add(mutate, 0.4)
seq.add(xover, 0.8)
pop = self.make_pop();
offspring = Pop()
sel = eoDetTournamentSelect(2)
print "making populator"
populator = eoSelectivePopulator(pop, offspring, sel)
print 'made'
for i in xrange(1000):
seq(populator)
print mutate.cnt
print xover.cnt
def test_sequentialOp(self):
print '*'*20, "SequentialOp", '*'*20
self.runOpContainer(eoSequentialOp)
def test_proportionalOp(self):
print '*'*20, "ProportionalOp", '*'*20
self.runOpContainer(eoProportionalOp)
if __name__=='__main__':
unittest.main()

34
eo/src/pyeo/test/test_reduce.py Normal file
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@ -0,0 +1,34 @@
from maxone import *
import unittest
class TestReduce(unittest.TestCase):
def run_test(self, ReduceClass, Arg = None):
pop = Pop(10, init)
for indy in pop: evaluate(indy)
if Arg:
red = ReduceClass(Arg)
else:
red = ReduceClass()
red(pop, 5);
self.failUnlessEqual( len(pop), 5)
def test_eoTruncate(self):
self.run_test(eoTruncate)
def test_eoRandomeReduce(self):
self.run_test(eoRandomReduce)
def test_eoEPRReduce(self):
self.run_test(eoEPReduce, 2)
def test_eoLinearTruncate(self):
self.run_test(eoLinearTruncate)
def test_eoDetTournamentTruncate(self):
self.run_test(eoDetTournamentTruncate, 2)
def test_eoStochTournamentTruncate(self):
self.run_test(eoStochTournamentTruncate, 0.9)
if __name__=='__main__':
unittest.main()

66
eo/src/pyeo/test/test_selectone.py Normal file
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@ -0,0 +1,66 @@
from maxone import *
import unittest
class Init(eoInit):
def __call__(self, eo):
pass
class TestSGA(unittest.TestCase):
def __init__(self, a):
unittest.TestCase.__init__(self, a)
self.pop = Pop(4, Init())
for i in range(len(self.pop)):
self.pop[i].fitness = i;
def do_test(self, selectOne):
print '*'*20, "Testing", str(selectOne.__class__), '*'*20
selection = [0. for i in range(len(self.pop))]
nTries = 500
for i in range(nTries):
selection[ selectOne(self.pop).fitness ] += 1
for i in range(len(self.pop)):
print i, selection[i], selection[i] / nTries
return selection, nTries
def test_eoDetTournamenSelect(self):
selectOne = eoDetTournamentSelect(2)
self.do_test(selectOne)
def test_eoRandomSelect(self):
selectOne = eoRandomSelect()
self.do_test(selectOne)
def test_eoBestSelect(self):
selectOne = eoBestSelect()
(sel, nTries) = self.do_test(selectOne)
self.failUnlessEqual(sel[0], 0);
self.failUnlessEqual(sel[-1], nTries);
def test_eoNoSelect(self):
selectOne = eoNoSelect()
self.do_test(selectOne)
def test_eoStochTournament(self):
selectOne = eoStochTournamentSelect(0.75)
self.do_test(selectOne)
def test_eoSequentialSelect(self):
selectOne = eoSequentialSelect();
self.do_test(selectOne)
def test_eoEliteSequentialSelect(self):
selectOne = eoEliteSequentialSelect();
self.do_test(selectOne)
if __name__=='__main__':
unittest.main()

25
eo/src/pyeo/test/test_sga.py Normal file
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@ -0,0 +1,25 @@
from maxone import *
import unittest
class TestSGA(unittest.TestCase):
def test(self):
evaluate = EvalFunc()
init = Init(20)
mutate = Mutate()
xover = Crossover()
pop = Pop(50, init)
for indy in pop: evaluate(indy)
select = eoDetTournamentSelect(3);
cont = eoGenContinue(20);
sga = eoSGA(select, xover, 0.6, mutate, 0.4, evaluate, cont);
sga(pop)
print pop.best()
if __name__=='__main__':
unittest.main()

85
eo/src/pyeo/valueParam.cpp Normal file
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@ -0,0 +1,85 @@
/*
pyeo
Copyright (C) 2003 Maarten Keijzer
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <utils/eoParam.h>
#include <boost/python.hpp>
using namespace boost::python;
class ParamWrapper : public eoParam
{
public:
PyObject* self;
ParamWrapper(PyObject* p) : self(p) {}
ParamWrapper(PyObject* p,
std::string a,
std::string b,
std::string c,
char d,
bool e) : eoParam(a,b,c,d,e), self(p) {}
std::string getValue() const
{
return call_method<std::string>(self, "getValue");
}
void setValue(std::string s)
{
call_method<void>(self, "setValue", s);
}
};
template <class T> T getv(const eoValueParam<T>& v) { return v.value(); }
template <class T> void setv(eoValueParam<T>& v, T val) { v.value() = val; }
template <class T>
void define_valueParam(std::string prefix)
{
class_<eoValueParam<T>, bases<eoParam> >( (prefix + "ValueParam").c_str(), init<>())
.def(init<T, std::string, std::string, char, bool>())
.def(init<T, std::string, std::string, char>())
.def(init<T, std::string, std::string>())
.def(init<T, std::string>())
.def("getValue", &eoValueParam<T>::getValue)
.def("__str__", &eoValueParam<T>::getValue)
.def("setValue", &eoValueParam<T>::setValue)
//.add_property("value", getv<T>, setv<T>)
;
}
void valueParam()
{
class_<eoParam, ParamWrapper, boost::noncopyable>("eoParam", init<>())
.def(init< std::string, std::string, std::string, char, bool>())
.def("getValue", &ParamWrapper::getValue)
.def("setValue", &ParamWrapper::setValue)
.def("longName", &eoParam::longName, return_value_policy<copy_const_reference>())
//.def("defValue", &eoParam::defValue, return_value_policy<copy_const_reference>())
.def("description", &eoParam::description, return_value_policy<copy_const_reference>())
.def("shortName", &eoParam::shortName)
.def("required", &eoParam::required)
;
define_valueParam<int>("int");
define_valueParam<std::vector<double> >("vec");
}

6
eo/src/utils/selectors.h
View file

@ -56,8 +56,8 @@ bool minimizing_fitness()
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);
eo1.fitness( typename EOT::Fitness(0.0) ); // tried to cast it to an EOT::Fitness, but for some reason GNU barfs on this
eo2.fitness( typename EOT::Fitness(1.0) );
return eo2 < eo1; // check whether we have a minimizing fitness
};
@ -194,7 +194,7 @@ It deterministic_tournament(It _begin, It _end, unsigned _t_size, eoRng& _gen =
It competitor = _begin + _gen.random(_end - _begin);
if (*best < *competitor)
{
{
best = competitor;
}
}