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Merge branch 'master' of ssh://eodev.git.sourceforge.net/gitroot/eodev/eodev

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This commit is contained in:
nojhan 2012-07-06 18:25:15 +02:00
commit 07fede786f
36 changed files with 564 additions and 468 deletions
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1
eo/CMakeLists.txt
View file

@ -1,3 +1,4 @@
CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
######################################################################################
### 0) If you want to set your variables in eo-conf.cmake and avoid the cmd line

1
eo/eo-conf.cmake
View file

@ -5,3 +5,4 @@ SET(PROJECT_VERSION_MINOR 3)
SET(PROJECT_VERSION_PATCH 0)
SET(PROJECT_VERSION_MISC "-edge")
# ADD_DEFINITIONS(-DDEPRECATED_MESSAGES) # disable warning deprecated function messages

18
eo/install_symlink.py.cmake
View file

@ -9,8 +9,8 @@ PREFIX = "/usr"
DATA = {
'dirs': [ "%s/share/%s" % (PREFIX, NAME) ],
'links': [ ("%s/src" % SOURCE, "%s/include/%s" % (PREFIX, NAME)),
("%s/doc" % BINARY, "%s/share/%s/doc" % (PREFIX, NAME)),
("%s/%s.pc" % (BINARY, NAME), "%s/lib/pkgconfig/%s.pc" % (PREFIX, NAME)),
("%s/doc" % BINARY, "%s/share/%s/doc" % (PREFIX, NAME)),
("%s/%s.pc" % (BINARY, NAME), "%s/lib/pkgconfig/%s.pc" % (PREFIX, NAME)),
]
}
@ -21,19 +21,19 @@ import os, sys
def isroot():
if os.getuid() != 0:
print '[WARNING] you have to be root'
return False
print('[WARNING] you have to be root')
return False
return True
def uninstall():
for dummy, link in DATA['links']: os.remove(link)
for dirname in DATA['dirs']: os.rmdir(dirname)
print 'All symlinks have been removed.'
print('All symlinks have been removed.')
def install():
for dirname in DATA['dirs']: os.mkdir(dirname)
for src, dst in DATA['links']: os.symlink(src, dst)
print 'All symlinks have been installed.'
print('All symlinks have been installed.')
def data():
from pprint import pprint
@ -41,11 +41,11 @@ def data():
if __name__ == '__main__':
if not isroot():
sys.exit()
sys.exit()
if len(sys.argv) < 2:
print 'Usage: %s [install|uninstall|data]' % sys.argv[0]
sys.exit()
print(('Usage: %s [install|uninstall|data]' % sys.argv[0]))
sys.exit()
if sys.argv[1] == 'install': install()
elif sys.argv[1] == 'uninstall': uninstall()

607
eo/src/do/make_checkpoint.h
View file

@ -1,45 +1,32 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// make_checkpoint.h
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2000
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
mkeijzer@dhi.dk
*/
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
mkeijzer@dhi.dk
*/
//-----------------------------------------------------------------------------
#ifndef _make_checkpoint_h
#define _make_checkpoint_h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@ -52,521 +39,315 @@
#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 //////////////
/**
*
* CHANGE (March 2008): now receiving an eoValueParam instead of an eoEvalFuncCounter. This function is just interested
* in the value of the parameter calculated on the evaluation function, not in the actual function itself!!
*
* @ingroup Builders
*/
*/
template <class EOT>
eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValueParam<unsigned long>& _eval, eoContinue<EOT>& _continue)
{
// first, create a checkpoint from the eoContinue
eoCheckPoint<EOT> *checkpoint = new eoCheckPoint<EOT>(_continue);
// first, create a checkpoint from the eoContinue
eoCheckPoint<EOT> *checkpoint = new eoCheckPoint<EOT>(_continue);
_state.storeFunctor(checkpoint);
_state.storeFunctor(checkpoint);
////////////////////
// Signal monitoring
////////////////////
#ifndef _MSC_VER
// the CtrlC monitoring interception
eoSignal<EOT> *mon_ctrlCCont;
eoValueParam<bool>& mon_ctrlCParam = _parser.createParam(false, "monitor-with-CtrlC", "Monitor current generation upon Ctrl C",0, "Stopping criterion");
if (mon_ctrlCParam.value())
{
mon_ctrlCCont = new eoSignal<EOT>;
// store
_state.storeFunctor(mon_ctrlCCont);
// add to checkpoint
checkpoint->add(*mon_ctrlCCont);
}
#endif
///////////////////
// Counters
//////////////////
///////////////////
// is nb Eval to be used as counter?
eoValueParam<bool>& useEvalParam = _parser.createParam(true, "useEval", "Use nb of eval. as counter (vs nb of gen.)", '\0', "Output");
eoValueParam<bool>& useTimeParam = _parser.createParam(true, "useTime", "Display time (s) every generation", '\0', "Output");
// if we want the time, we need an eoTimeCounter
eoTimeCounter * tCounter = NULL;
// Counters
//////////////////
// is nb Eval to be used as counter?
eoValueParam<bool>& useEvalParam = _parser.createParam(true, "useEval", "Use nb of eval. as counter (vs nb of gen.)", '\0', "Output");
eoValueParam<bool>& useTimeParam = _parser.createParam(true, "useTime", "Display time (s) every generation", '\0', "Output");
// if we want the time, we need an eoTimeCounter
eoTimeCounter * tCounter = NULL;
// Create anyway a generation-counter
// Recent change (03/2002): it is now an eoIncrementorParam, both
// a parameter AND updater so you can store it into the eoState
eoIncrementorParam<unsigned> *generationCounter = new eoIncrementorParam<unsigned>("Gen.");
// store it in the state
_state.storeFunctor(generationCounter);
// And add it to the checkpoint,
checkpoint->add(*generationCounter);
// Create anyway a generation-counter
// Recent change (03/2002): it is now an eoIncrementorParam, both
// a parameter AND updater so you can store it into the eoState
eoIncrementorParam<unsigned> *generationCounter = new eoIncrementorParam<unsigned>("Gen.");
// store it in the state
_state.storeFunctor(generationCounter);
// And add it to the checkpoint,
checkpoint->add(*generationCounter);
// dir for DISK output
eoValueParam<std::string>& dirNameParam = _parser.createParam(std::string("Res"), "resDir", "Directory to store DISK outputs", '\0', "Output - Disk");
// shoudl we empty it if exists
eoValueParam<bool>& eraseParam = _parser.createParam(true, "eraseDir", "erase files in dirName if any", '\0', "Output - Disk");
bool dirOK = false; // not tested yet
/////////////////////////////////////////
// now some statistics on the population:
/////////////////////////////////////////
/**
* existing stats as of today, April 10. 2001
*
* eoBestFitnessStat : best value in pop - type EOT::Fitness
* eoAverageStat : average value in pop - type EOT::Fitness
* eoSecondMomentStat: average + stdev - type std::pair<double, double>
* eoSortedPopStat : whole population - type std::string (!!)
* eoScalarFitnessStat: the fitnesses - type std::vector<double>
*/
// Best fitness in population
//---------------------------
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");
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
{
bestStat = new eoBestFitnessStat<EOT>;
// store it
_state.storeFunctor(bestStat);
// add it to the checkpoint
checkpoint->add(*bestStat);
}
// we need the bestStat for at least one of the 3 above
{
bestStat = new eoBestFitnessStat<EOT>;
// store it
_state.storeFunctor(bestStat);
// add it to the checkpoint
checkpoint->add(*bestStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*bestStat);
}
// Average fitness alone
//----------------------
eoAverageStat<EOT> *averageStat = NULL; // do we need averageStat?
if ( plotBestParam.value() ) // we need it for gnuplot output
{
averageStat = new eoAverageStat<EOT>;
// store it
_state.storeFunctor(averageStat);
// add it to the checkpoint
checkpoint->add(*averageStat);
}
if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() ) // we need it for gnuplot output
{
averageStat = new eoAverageStat<EOT>;
// store it
_state.storeFunctor(averageStat);
// add it to the checkpoint
checkpoint->add(*averageStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*averageStat);
}
// Second moment stats: average and stdev
//---------------------------------------
eoSecondMomentStats<EOT> *secondStat = NULL;
if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output
{
secondStat = new eoSecondMomentStats<EOT>;
// store it
_state.storeFunctor(secondStat);
// add it to the checkpoint
checkpoint->add(*secondStat);
}
if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output
{
secondStat = new eoSecondMomentStats<EOT>;
// store it
_state.storeFunctor(secondStat);
// add it to the checkpoint
checkpoint->add(*secondStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*secondStat);
}
// Dump of the whole population
//-----------------------------
eoSortedPopStat<EOT> *popStat = NULL;
eoValueParam<bool>& printPopParam = _parser.createParam(false, "printPop", "Print sorted pop. every gen.", '\0', "Output");
if ( printPopParam.value() ) // we do want pop dump
{
popStat = new eoSortedPopStat<EOT>;
// store it
_state.storeFunctor(popStat);
// add it to the checkpoint
checkpoint->add(*popStat);
}
{
popStat = new eoSortedPopStat<EOT>;
// store it
_state.storeFunctor(popStat);
// add it to the checkpoint
checkpoint->add(*popStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*popStat);
}
// do we wnat some histogram of fitnesses snpashots?
eoValueParam<bool> plotHistogramParam = _parser.createParam(false, "plotHisto", "Plot histogram of fitnesses", '\0', "Output - Graphical");
///////////////
// The monitors
///////////////
// do we want an eoStdoutMonitor?
bool needStdoutMonitor = printBestParam.value()
|| printPopParam.value() ;
// The Stdout monitor will print parameters to the screen ...
if ( needStdoutMonitor )
{
eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
_state.storeFunctor(monitor);
{
// when called by the checkpoint (i.e. at every generation)
// check if monitoring with signal
if ( ! mon_ctrlCParam.value() )
checkpoint->add(*monitor);
else
mon_ctrlCCont->add(*monitor);
eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
// the monitor will output a series of parameters: add them
monitor->add(*generationCounter);
_state.storeFunctor(monitor);
// when called by the checkpoint (i.e. at every generation)
checkpoint->add(*monitor);
// the monitor will output a series of parameters: add them
monitor->add(*generationCounter);
if (useEvalParam.value()) // we want nb of evaluations
monitor->add(_eval);
if (useTimeParam.value()) // we want time
{
tCounter = new eoTimeCounter;
_state.storeFunctor(tCounter);
checkpoint->add(*tCounter);
monitor->add(*tCounter);
}
if (printBestParam.value())
{
monitor->add(*bestStat);
monitor->add(*secondStat);
}
if ( printPopParam.value())
monitor->add(*popStat);
}
if (useEvalParam.value()) // we want nb of evaluations
monitor->add(_eval);
if (useTimeParam.value()) // we want time
{
tCounter = new eoTimeCounter;
_state.storeFunctor(tCounter);
// check if monitoring with signal
if ( ! mon_ctrlCParam.value() )
checkpoint->add(*tCounter);
else
mon_ctrlCCont->add(*tCounter);
monitor->add(*tCounter);
}
if (printBestParam.value())
{
monitor->add(*bestStat);
monitor->add(*secondStat);
}
if ( printPopParam.value())
monitor->add(*popStat);
}
// first handle the dir test - if we need at least one file
if ( ( fileBestParam.value() || plotBestParam.value() ||
plotHistogramParam.value() )
&& !dirOK ) // just in case we add something before
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
if (fileBestParam.value()) // A file monitor for best & secondMoment
{
{
#ifdef _MSVC
std::string stmp = dirNameParam.value() + "\best.xg";
std::string stmp = dirNameParam.value() + "\best.xg";
#else
std::string stmp = dirNameParam.value() + "/best.xg";
std::string stmp = dirNameParam.value() + "/best.xg";
#endif
eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
// save and give to checkpoint
_state.storeFunctor(fileMonitor);
checkpoint->add(*fileMonitor);
// and feed with some statistics
fileMonitor->add(*generationCounter);
fileMonitor->add(_eval);
if (tCounter) // we want the time as well
{
// std::cout << "On met timecounter\n";
fileMonitor->add(*tCounter);
}
fileMonitor->add(*bestStat);
fileMonitor->add(*secondStat);
}
eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
// save and give to checkpoint
_state.storeFunctor(fileMonitor);
checkpoint->add(*fileMonitor);
// and feed with some statistics
fileMonitor->add(*generationCounter);
fileMonitor->add(_eval);
if (tCounter) // we want the time as well
{
// std::cout << "On met timecounter\n";
fileMonitor->add(*tCounter);
}
fileMonitor->add(*bestStat);
fileMonitor->add(*secondStat);
}
#if defined(HAVE_GNUPLOT)
if (plotBestParam.value()) // an eoGnuplot1DMonitor for best & average
{
std::string stmp = dirNameParam.value() + "/gnu_best.xg";
eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
// save and give to checkpoint
_state.storeFunctor(gnuMonitor);
checkpoint->add(*gnuMonitor);
// and feed with some statistics
if (useEvalParam.value()) // do we want eval as X coordinate
gnuMonitor->add(_eval);
else if (tCounter) // or time?
gnuMonitor->add(*tCounter);
else // default: generation
gnuMonitor->add(*generationCounter);
gnuMonitor->add(*bestStat);
gnuMonitor->add(*averageStat);
}
{
std::string stmp = dirNameParam.value() + "/gnu_best.xg";
eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
// save and give to checkpoint
_state.storeFunctor(gnuMonitor);
checkpoint->add(*gnuMonitor);
// and feed with some statistics
if (useEvalParam.value()) // do we want eval as X coordinate
gnuMonitor->add(_eval);
else if (tCounter) // or time?
gnuMonitor->add(*tCounter);
else // default: generation
gnuMonitor->add(*generationCounter);
gnuMonitor->add(*bestStat);
gnuMonitor->add(*averageStat);
}
// historgram?
if (plotHistogramParam.value()) // want to see how the fitness is spread?
{
eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
_state.storeFunctor(fitStat);
checkpoint->add(*fitStat);
// a gnuplot-based monitor for snapshots: needs a dir name
eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
_state.storeFunctor(fitSnapshot);
// add any stat that is a std::vector<double> to it
fitSnapshot->add(*fitStat);
// and of course add it to the checkpoint
checkpoint->add(*fitSnapshot);
}
{
eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
_state.storeFunctor(fitStat);
checkpoint->add(*fitStat);
// a gnuplot-based monitor for snapshots: needs a dir name
eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
_state.storeFunctor(fitSnapshot);
// add any stat that is a std::vector<double> to it
fitSnapshot->add(*fitStat);
// and of course add it to the checkpoint
checkpoint->add(*fitSnapshot);
}
#endif
//////////////////////////////////
// State savers
//////////////////////////////
// feed the state to state savers
// save state every N generation
eoValueParam<unsigned>& saveFrequencyParam = _parser.createParam(unsigned(0), "saveFrequency", "Save every F generation (0 = only final state, absent = never)", '\0', "Persistence" );
if (_parser.isItThere(saveFrequencyParam))
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
unsigned freq = (saveFrequencyParam.value()>0 ? saveFrequencyParam.value() : UINT_MAX );
unsigned freq = (saveFrequencyParam.value()>0 ? saveFrequencyParam.value() : UINT_MAX );
#ifdef _MSVC
std::string stmp = dirNameParam.value() + "\generations";
std::string stmp = dirNameParam.value() + "\generations";
#else
std::string stmp = dirNameParam.value() + "/generations";
std::string stmp = dirNameParam.value() + "/generations";
#endif
eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
_state.storeFunctor(stateSaver1);
checkpoint->add(*stateSaver1);
}
eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
_state.storeFunctor(stateSaver1);
checkpoint->add(*stateSaver1);
}
// save state every T seconds
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
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
#ifdef _MSVC
std::string stmp = dirNameParam.value() + "\time";
std::string stmp = dirNameParam.value() + "\time";
#else
std::string stmp = dirNameParam.value() + "/time";
std::string stmp = dirNameParam.value() + "/time";
#endif
eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
_state.storeFunctor(stateSaver2);
checkpoint->add(*stateSaver2);
}
eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
_state.storeFunctor(stateSaver2);
checkpoint->add(*stateSaver2);
}
// and that's it for the (control and) output
return *checkpoint;
}
#endif

5
eo/src/eoCombinedContinue.h
View file

@ -61,7 +61,9 @@ public:
eoCombinedContinue( eoContinue<EOT>& _cont1, eoContinue<EOT>& _cont2)
: eoContinue<EOT>(), std::vector<eoContinue<EOT>* >()
{
#ifndef DEPRECATED_MESSAGES
#pragma message "The double continuators constructor of eocombinedContinue is deprecated and will be removed in the next release."
#endif // !DEPRECATED_MESSAGES
this->push_back(&_cont1);
this->push_back(&_cont2);
@ -74,7 +76,10 @@ public:
void removeLast(void)
{
#ifndef DEPRECATED_MESSAGES
#pragma message "The removeLast method of eocombinedContinue is deprecated and will be removed in the next release, use pop_back instead."
#endif // !DEPRECATED_MESSAGES
this->pop_back();
}

2
eo/src/eoCtrlCContinue.h
View file

@ -30,7 +30,7 @@
#ifndef eoCtrlCContinue_h
#define eoCtrlCContinue_h
#include <signal.h>
#include <csignal>
#include <eoContinue.h>
/**

2
eo/src/eoFlight.h
View file

@ -46,7 +46,7 @@ public:
{
for (unsigned i = 0; i < _pop.size (); i++)
{
operator ()(_pop[i]);
this->operator ()(_pop[i]);
}
}

2
eo/src/eoInitializer.h
View file

@ -129,7 +129,7 @@ private :
class eoDummyEval : public eoPopEvalFunc<POT>
{
public:
void operator()(eoPop<POT> &,eoPop<POT> &_pop)
void operator()(eoPop<POT> &,eoPop<POT> &/*_pop*/)
{}
}
dummyEval;

2
eo/src/eoParticleBestInit.h
View file

@ -46,7 +46,7 @@ public:
{
for (unsigned i = 0; i < _pop.size (); i++)
{
operator ()(_pop[i]);
this->operator ()(_pop[i]);
}
}

2
eo/src/eoPeriodicContinue.h
View file

@ -39,7 +39,7 @@ public:
/** It returns 'true' only if the current number of generations modulo
the period doen't equal to zero. */
bool operator () (const eoPop <EOT> & pop)
bool operator () (const eoPop <EOT> & /*pop*/)
{
return ((++ counter) % period) != 0 ;
}

3
eo/src/eoProportionalCombinedOp.h
View file

@ -188,8 +188,11 @@ public:
virtual void add(eoQuadOp<EOT> & _op, const double _rate, bool _verbose)
{
#ifndef DEPRECATED_MESSAGES
#pragma message "The use of the verbose parameter in eoPropCombinedQuadOp::add is deprecated and will be removed in the next release."
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoPropCombinedQuadOp::add is deprecated and will be removed in the next release." << std::endl;
#endif // !DEPRECATED_MESSAGES
add(_op,_rate);
}

2
eo/src/eoProportionalSelect.h
View file

@ -46,7 +46,7 @@ template <class EOT> class eoProportionalSelect: public eoSelectOne<EOT>
{
public:
/// Sanity check
eoProportionalSelect(const eoPop<EOT>& pop = eoPop<EOT>())
eoProportionalSelect(const eoPop<EOT>& /*pop*/ = eoPop<EOT>())
{
if (minimizing_fitness<EOT>())
throw std::logic_error("eoProportionalSelect: minimizing fitness");

2
eo/src/eoReduceSplit.h
View file

@ -104,7 +104,7 @@ public:
unsigned eliminated = howMany(popSize);
if (!eliminated) // nothing to do
return ;
unsigned newsize = popSize - eliminated;
long newsize = static_cast<long>(popSize) - static_cast<long>(eliminated);
if (newsize < 0)
throw std::logic_error("eoLinearTruncateSplit: Cannot truncate to a larger size!\n");

2
eo/src/eoScalarFitnessAssembled.h
View file

@ -212,7 +212,7 @@ public:
//! Print term values and descriptions
void printAll(std::ostream& os) const {
for (size_type i=0; i < size(); ++i )
os << FitnessTraits::getDescription(i) << " = " << operator[](i) << " ";
os << FitnessTraits::getDescription(i) << " = " << this->operator[](i) << " ";
}
//! Comparison, using less by default

2
eo/src/eoSelectFromWorth.h
View file

@ -217,7 +217,7 @@ public:
#ifndef NDEBUG
// check whether the stuff is still in sync
check_sync(index, _pop[index]);
this->check_sync(index, _pop[index]);
#endif
return _pop[index];

2
eo/src/eoSyncEasyPSO.h
View file

@ -241,7 +241,7 @@ private:
{
public:
eoDummyFlight () {}
void operator () (POT & _po) {}
void operator () (POT & /*_po*/) {}
}dummyFlight;
// if the initializer does not need to be used, use the dummy one instead

4
eo/src/eoVelocity.h
View file

@ -49,7 +49,7 @@ public:
{
for (unsigned i = 0; i < _pop.size (); i++)
{
operator ()(_pop[i],i);
this->operator ()(_pop[i],i);
}
}
@ -57,7 +57,7 @@ public:
/**
* Update the neighborhood of the given particle.
*/
virtual void updateNeighborhood(POT & ,unsigned _indice){}
virtual void updateNeighborhood(POT & ,unsigned /*_indice*/){}
/**

58
eo/src/ga/eoBitOp.h
View file

@ -56,7 +56,7 @@ template<class Chrom> class eoOneBitFlip: public eoMonOp<Chrom>
bool operator()(Chrom& chrom)
{
unsigned i = eo::rng.random(chrom.size());
chrom[i] = (chrom[i]) ? false : true;
chrom[i] = !chrom[i];
return true;
}
};
@ -85,11 +85,11 @@ template<class Chrom> class eoDetBitFlip: public eoMonOp<Chrom>
*/
bool operator()(Chrom& chrom)
{
// does not check for duplicate: if someone volunteers ....
// for duplicate checking see eoDetSingleBitFlip
for (unsigned k=0; k<num_bit; k++)
{
unsigned i = eo::rng.random(chrom.size());
chrom[i] = (chrom[i]) ? false : true;
chrom[i] = !chrom[i];
}
return true;
}
@ -98,6 +98,58 @@ template<class Chrom> class eoDetBitFlip: public eoMonOp<Chrom>
};
/** eoDetSingleBitFlip --> changes exactly k bits with checking for duplicate
\class eoDetSingleBitFlip eoBitOp.h ga/eoBitOp.h
\ingroup bitstring
*/
template<class Chrom> class eoDetSingleBitFlip: public eoMonOp<Chrom>
{
public:
/**
* (Default) Constructor.
* @param _num_bit The number of bits to change
* default is one - equivalent to eoOneBitFlip then
*/
eoDetSingleBitFlip(const unsigned& _num_bit = 1): num_bit(_num_bit) {}
/// The class name.
virtual std::string className() const { return "eoDetSingleBitFlip"; }
/**
* Change num_bit bits.
* @param chrom The cromosome which one bit is going to be changed.
*/
bool operator()(Chrom& chrom)
{
std::vector< unsigned > selected;
// check for duplicate
for (unsigned k=0; k<num_bit; k++)
{
unsigned temp;
do
{
temp = eo::rng.random( chrom.size() );
}
while ( find( selected.begin(), selected.end(), temp ) != selected.end() );
selected.push_back(temp);
}
for ( size_t i = 0; i < selected.size(); ++i )
{
chrom[i] = !chrom[i];
}
return true;
}
private:
unsigned num_bit;
};
/** eoBitMutation --> classical mutation
\class eoBitMutation eoBitOp.h ga/eoBitOp.h
\ingroup bitstring

2
eo/src/ga/make_continue_ga.cpp
View file

@ -37,7 +37,7 @@
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in ga.h
* while the TEMPLATIZED code is define in make_contninue.h in the src/do dir
* while the TEMPLATIZED code is define in make_continue.h in the src/do dir
*
* Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations

4
eo/src/ga/make_ga.h
View file

@ -57,8 +57,8 @@
*/
// the genotypes
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo);
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo);
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo, float _bias=0.5);
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo, float _bias=0.5);
// the operators
eoGenOp<eoBit<double> >& make_op(eoParser& _parser, eoState& _state, eoInit<eoBit<double> >& _init);

8
eo/src/ga/make_genotype_ga.cpp
View file

@ -45,11 +45,11 @@
/// The following function merely call the templatized do_* functions above
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo)
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo, float _bias)
{
return do_make_genotype(_parser, _state, _eo);
return do_make_genotype(_parser, _state, _eo, _bias);
}
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo)
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo, float _bias)
{
return do_make_genotype(_parser, _state, _eo);
return do_make_genotype(_parser, _state, _eo, _bias);
}

4
eo/src/ga/make_genotype_ga.h
View file

@ -60,7 +60,7 @@
* @ingroup Builders
*/
template <class EOT>
eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT)
eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT, float _bias=0.5)
{
// for bitstring, only thing needed is the size
// but it might have been already read in the definition fo the performance
@ -68,7 +68,7 @@ eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT)
// Then we can built a bitstring random initializer
// based on boolean_generator class (see utils/rnd_generator.h)
eoBooleanGenerator * gen = new eoBooleanGenerator;
eoBooleanGenerator * gen = new eoBooleanGenerator(_bias);
_state.storeFunctor(gen);
eoInitFixedLength<EOT>* init = new eoInitFixedLength<EOT>(theSize, *gen);
// store in state

25
eo/src/ga/make_op.h
View file

@ -115,11 +115,11 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
throw std::runtime_error("Invalid uRate");
// minimum check
bool bCross = true;
// bool bCross = true; // not used ?
if (onePointRateParam.value()+twoPointsRateParam.value()+uRateParam.value()==0)
{
std::cerr << "Warning: no crossover" << std::endl;
bCross = false;
// bCross = false;
}
// Create the CombinedQuadOp
@ -156,17 +156,29 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
if ( (bitFlipRateParam.value() < 0) )
throw std::runtime_error("Invalid bitFlipRate");
// oneBitFlip
eoValueParam<double> & oneBitRateParam = _parser.createParam(0.01, "oneBitRate", "Relative rate for deterministic bit-flip mutation", 'd', "Variation Operators" );
// minimum check
if ( (oneBitRateParam.value() < 0) )
throw std::runtime_error("Invalid oneBitRate");
// kBitFlip
eoValueParam<unsigned> & kBitParam = _parser.createParam((unsigned)1, "kBit", "Number of bit for deterministic k bit-flip mutation", 0, "Variation Operators" );
// minimum check
bool bMut = true;
if ( ! kBitParam.value() )
throw std::runtime_error("Invalid kBit");
eoValueParam<double> & kBitRateParam = _parser.createParam(0.0, "kBitRate", "Relative rate for deterministic k bit-flip mutation", 0, "Variation Operators" );
// minimum check
if ( (kBitRateParam.value() < 0) )
throw std::runtime_error("Invalid kBitRate");
// minimum check
// bool bMut = true; // not used ?
if (bitFlipRateParam.value()+oneBitRateParam.value()==0)
{
std::cerr << "Warning: no mutation" << std::endl;
bMut = false;
// bMut = false;
}
// Create the CombinedMonOp
@ -184,6 +196,11 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
_state.storeFunctor(ptMon);
ptCombinedMonOp->add(*ptMon, oneBitRateParam.value());
// mutate exactly k bit per individual
ptMon = new eoDetBitFlip<EOT>(kBitParam.value());
_state.storeFunctor(ptMon);
ptCombinedMonOp->add(*ptMon, kBitRateParam.value());
_state.storeFunctor(ptCombinedMonOp);
// now build the eoGenOp:

4
eo/src/gp/eoParseTree.h
View file

@ -94,7 +94,7 @@ public:
while (size() > _size)
{
back() = operator[](size()-2);
back() = this->operator[](size()-2);
}
}
@ -150,7 +150,7 @@ public:
v[i] = node;
}
parse_tree<Node> tmp(v.begin(), v.end());
swap(tmp);
this->swap(tmp);
/*
* old code which caused problems for paradisEO

2
eo/src/pyeo/test/run_tests.sh
View file

@ -2,6 +2,6 @@
for i in *.py
do
python $i > /dev/null
python2 $i > /dev/null
done

1
eo/src/utils/CMakeLists.txt
View file

@ -29,6 +29,7 @@ SET(EOUTILS_SOURCES
pipecom.cpp
eoLogger.cpp
eoParallel.cpp
eoSignal.cpp
)
ADD_LIBRARY(eoutils STATIC ${EOUTILS_SOURCES})

33
eo/src/utils/checkpointing
View file

@ -1,3 +1,29 @@
/*
-----------------------------------------------------------------------------
checkpointing
(c) Maarten Keijzer (mak@dhi.dk) and GeNeura Team, 1999, 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
#ifndef _CHECKPOINTING_
#define _CHECKPOINTING_
#include <utils/eoParser.h>
#include <utils/eoState.h>
#include <utils/eoUpdater.h>
@ -10,6 +36,7 @@
#include <utils/eoGnuplot1DSnapshot.h>
#endif
#include <utils/eoCheckPoint.h>
#include <utils/eoSignal.h>
#include <utils/eoStat.h>
#include <utils/eoScalarFitnessStat.h>
#include <utils/eoAssembledFitnessStat.h>
@ -21,3 +48,9 @@
// and make_help - any better suggestion to include it?
void make_help(eoParser & _parser);
#endif // !_CHECKPOINTING_
// Local Variables:
// mode: C++
// End:

36
eo/src/utils/eoFuncPtrStat.h
View file

@ -4,6 +4,8 @@
#include <eoFunctorStore.h>
#include <utils/eoStat.h>
/** Wrapper to turn any stand-alone function and into an eoStat.
*
* The function should take an eoPop as argument.
@ -41,4 +43,38 @@ eoFuncPtrStat<EOT, T>& makeFuncPtrStat( T (*func)(const eoPop<EOT>&), eoFunctorS
);
}
/** Wrapper to turn any stand-alone function and into an eoStat.
*
* The function should take an eoPop as argument.
*
* @ingroup Stats
*/
template <class EOT, class T>
class eoFunctorStat : public eoStat<EOT, T>
{
public :
eoFunctorStat(eoUF< const eoPop<EOT>&, T >& f, std::string _description = "functor")
: eoStat<EOT, T>(T(), _description), func(f)
{}
using eoStat<EOT, T>::value;
void operator()(const eoPop<EOT>& pop) {
value() = func(pop);
}
private:
eoUF< const eoPop<EOT>&, T >& func;
};
/**
* @ingroup Stats
*/
template <class EOT, class T>
eoFunctorStat<EOT, T>& makeFunctorStat( eoUF< const eoPop<EOT>&, T >& func, eoFunctorStore& store, std::string description = "func") {
return store.storeFunctor(
new eoFunctorStat<EOT, T>( func, description)
);
}
#endif

3
eo/src/utils/eoLogger.cpp
View file

@ -194,8 +194,7 @@ int eoLogger::outbuf::overflow(int_type c)
{
if (_fd >= 0 && c != EOF)
{
size_t num;
num = ::write(_fd, &c, 1);
::write(_fd, &c, 1);
}
}
return c;

5
eo/src/utils/eoOStreamMonitor.h
View file

@ -44,12 +44,13 @@ Authors:
class eoOStreamMonitor : public eoMonitor
{
public :
eoOStreamMonitor( std::ostream & _out, bool _verbose=true, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
eoOStreamMonitor( std::ostream & _out, bool /*_verbose*/=true, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
out(_out), delim(_delim), width(_width), fill(_fill), firsttime(true)
{
(void)_verbose;
#ifndef DEPRECATED_MESSAGES
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoOStreamMonitor constructor is deprecated and will be removed in the next release" << std::endl;
#pragma message "WARNING: the use of the verbose parameter in eoOStreamMonitor constructor is deprecated and will be removed in the next release"
#endif // !DEPRECATED_MESSAGES
}
eoOStreamMonitor( std::ostream & _out, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :

36
eo/src/utils/eoSignal.cpp Normal file
View file

@ -0,0 +1,36 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/**
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net
Autors: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
mak@dhi.dk
Caner.Candan@univ-angers.fr
*/
#include <utils/eoSignal.h>
/**
* @addtogroup Continuators
* @{
*/
// --- Global variables - but don't know what else to do - MS ---
std::map< int, bool > signals_called;
/** @} */

106
eo/src/utils/eoSignal.h Normal file
View file

@ -0,0 +1,106 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/**
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net
Authors: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
mak@dhi.dk
Caner.Candan@univ-angers.fr
*/
#ifndef _eoSignal_h
#define _eoSignal_h
#include <csignal>
#include <utils/eoCheckPoint.h>
#include <utils/eoLogger.h>
#include <map>
#include <vector>
/**
* @addtogroup Continuators
* @{
*/
extern std::map< int, bool > signals_called;
/** eoSignal inherits from eoCheckPoint including signals handling (see signal(7))
*
* @ingroup Utilities
*/
template <class EOT>
class eoSignal : public eoCheckPoint<EOT>
{
public :
eoSignal( int sig = SIGINT ) : eoCheckPoint<EOT>( _dummyContinue ), _sig( sig )
{
::signals_called[_sig] = false;
#ifndef _WINDOWS
#ifdef SIGQUIT
::signal( _sig, handler );
#endif // !SIGQUIT
#endif // !_WINDOWS
}
eoSignal( eoContinue<EOT>& _cont, int sig = SIGINT ) : eoCheckPoint<EOT>( _cont ), _sig( sig )
{
::signals_called[_sig] = false;
#ifndef _WINDOWS
#ifdef SIGQUIT
::signal( _sig, handler );
#endif // !SIGQUIT
#endif // !_WINDOWS
}
bool operator()( const eoPop<EOT>& _pop )
{
bool& called = ::signals_called[_sig];
if ( called )
{
eo::log << eo::logging << "Signal granted…" << std::endl ;
called = false;
return this->eoCheckPoint<EOT>::operator()( _pop );
}
return true;
}
virtual std::string className(void) const { return "eoSignal"; }
static void handler( int sig )
{
::signals_called[sig] = true;
eo::log << eo::logging << "Signal wished…" << std::endl ;
}
private:
class DummyContinue : public eoContinue<EOT>
{
public:
bool operator() ( const eoPop<EOT>& ) { return true; }
} _dummyContinue;
int _sig;
};
/** @} */
#endif // !_eoSignal_h

4
eo/src/utils/eoStdoutMonitor.h
View file

@ -46,7 +46,9 @@ public :
eoStdoutMonitor(bool _verbose, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
eoOStreamMonitor( std::cout, _verbose, _delim, _width, _fill)
{
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoStdutMonitor constructor is deprecated and will be removed in the next release" << std::endl;
#ifndef DEPRECATED_MESSAGES
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoStdoutMonitor constructor is deprecated and will be removed in the next release" << std::endl;
#endif // !DEPRECATED_MESSAGES
}
eoStdoutMonitor(std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :

2
eo/test/CMakeLists.txt
View file

@ -66,7 +66,7 @@ SET (TEST_LIST
t-eoLogger
t-eoIQRStat
t-eoParallel
t-openmp
#t-openmp # does not work anymore since functions used in this test were removed from EO
#t-eoDualFitness
t-eoParser
)

2
eo/test/t-openmp.cpp
View file

@ -39,6 +39,8 @@ Caner Candan <caner.candan@thalesgroup.com>
#include <omp.h>
#include <unistd.h>
#include "real_value.h"
//-----------------------------------------------------------------------------