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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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22
edo/src/edoNormalMulti.h
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@ -1,4 +1,24 @@
// (c) Thales group, 2010 /*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
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 2.1 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., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/* /*
Authors: Authors:
Johann Dreo <johann.dreo@thalesgroup.com> Johann Dreo <johann.dreo@thalesgroup.com>

1
eo/CMakeLists.txt
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@ -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 ### 0) If you want to set your variables in eo-conf.cmake and avoid the cmd line

1
eo/eo-conf.cmake
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@ -5,3 +5,4 @@ SET(PROJECT_VERSION_MINOR 3)
SET(PROJECT_VERSION_PATCH 0) SET(PROJECT_VERSION_PATCH 0)
SET(PROJECT_VERSION_MISC "-edge") SET(PROJECT_VERSION_MISC "-edge")
# ADD_DEFINITIONS(-DDEPRECATED_MESSAGES) # disable warning deprecated function messages

8
eo/install_symlink.py.cmake
View file

@ -21,19 +21,19 @@ import os, sys
def isroot(): def isroot():
if os.getuid() != 0: if os.getuid() != 0:
print '[WARNING] you have to be root' print('[WARNING] you have to be root')
return False return False
return True return True
def uninstall(): def uninstall():
for dummy, link in DATA['links']: os.remove(link) for dummy, link in DATA['links']: os.remove(link)
for dirname in DATA['dirs']: os.rmdir(dirname) for dirname in DATA['dirs']: os.rmdir(dirname)
print 'All symlinks have been removed.' print('All symlinks have been removed.')
def install(): def install():
for dirname in DATA['dirs']: os.mkdir(dirname) for dirname in DATA['dirs']: os.mkdir(dirname)
for src, dst in DATA['links']: os.symlink(src, dst) for src, dst in DATA['links']: os.symlink(src, dst)
print 'All symlinks have been installed.' print('All symlinks have been installed.')
def data(): def data():
from pprint import pprint from pprint import pprint
@ -44,7 +44,7 @@ if __name__ == '__main__':
sys.exit() sys.exit()
if len(sys.argv) < 2: if len(sys.argv) < 2:
print 'Usage: %s [install|uninstall|data]' % sys.argv[0] print(('Usage: %s [install|uninstall|data]' % sys.argv[0]))
sys.exit() sys.exit()
if sys.argv[1] == 'install': install() if sys.argv[1] == 'install': install()

293
eo/src/do/make_checkpoint.h
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@ -1,13 +1,8 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*- // -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//----------------------------------------------------------------------------- //-----------------------------------------------------------------------------
// make_checkpoint.h // make_checkpoint.h
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2000 // (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2000
/* /*
This library is free software; you can redistribute it and/or This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public modify it under the terms of the GNU Lesser General Public
@ -24,22 +19,14 @@
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr Marc.Schoenauer@polytechnique.fr
mkeijzer@dhi.dk mkeijzer@dhi.dk
*/ */
//----------------------------------------------------------------------------- //-----------------------------------------------------------------------------
#ifndef _make_checkpoint_h #ifndef _make_checkpoint_h
#define _make_checkpoint_h #define _make_checkpoint_h
#ifdef HAVE_CONFIG_H #ifdef HAVE_CONFIG_H
#include <config.h> #include <config.h>
#endif #endif
@ -52,19 +39,11 @@
#include <eoEvalFuncCounter.h> #include <eoEvalFuncCounter.h>
#include <utils/checkpointing> #include <utils/checkpointing>
// at the moment, in utils/make_help.cpp // at the moment, in utils/make_help.cpp
// this should become some eoUtils.cpp with corresponding eoUtils.h // this should become some eoUtils.cpp with corresponding eoUtils.h
bool testDirRes(std::string _dirName, bool _erase); bool testDirRes(std::string _dirName, bool _erase);
/////////////////// The checkpoint and other I/O ////////////// /////////////////// The checkpoint and other I/O //////////////
/** /**
* *
* CHANGE (March 2008): now receiving an eoValueParam instead of an eoEvalFuncCounter. This function is just interested * CHANGE (March 2008): now receiving an eoValueParam instead of an eoEvalFuncCounter. This function is just interested
@ -75,498 +54,300 @@ bool testDirRes(std::string _dirName, bool _erase);
template <class EOT> template <class EOT>
eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValueParam<unsigned long>& _eval, eoContinue<EOT>& _continue) eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValueParam<unsigned long>& _eval, eoContinue<EOT>& _continue)
{ {
// first, create a checkpoint from the eoContinue // first, create a checkpoint from the eoContinue
eoCheckPoint<EOT> *checkpoint = new eoCheckPoint<EOT>(_continue); 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 // Counters
////////////////// //////////////////
// is nb Eval to be used as counter? // 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>& 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"); eoValueParam<bool>& useTimeParam = _parser.createParam(true, "useTime", "Display time (s) every generation", '\0', "Output");
// if we want the time, we need an eoTimeCounter // if we want the time, we need an eoTimeCounter
eoTimeCounter * tCounter = NULL; eoTimeCounter * tCounter = NULL;
// Create anyway a generation-counter // Create anyway a generation-counter
// Recent change (03/2002): it is now an eoIncrementorParam, both // Recent change (03/2002): it is now an eoIncrementorParam, both
// a parameter AND updater so you can store it into the eoState // a parameter AND updater so you can store it into the eoState
eoIncrementorParam<unsigned> *generationCounter = new eoIncrementorParam<unsigned>("Gen."); eoIncrementorParam<unsigned> *generationCounter = new eoIncrementorParam<unsigned>("Gen.");
// store it in the state // store it in the state
_state.storeFunctor(generationCounter); _state.storeFunctor(generationCounter);
// And add it to the checkpoint, // And add it to the checkpoint,
checkpoint->add(*generationCounter); checkpoint->add(*generationCounter);
// dir for DISK output // dir for DISK output
eoValueParam<std::string>& dirNameParam = _parser.createParam(std::string("Res"), "resDir", "Directory to store DISK outputs", '\0', "Output - Disk"); eoValueParam<std::string>& dirNameParam = _parser.createParam(std::string("Res"), "resDir", "Directory to store DISK outputs", '\0', "Output - Disk");
// shoudl we empty it if exists // shoudl we empty it if exists
eoValueParam<bool>& eraseParam = _parser.createParam(true, "eraseDir", "erase files in dirName if any", '\0', "Output - Disk"); eoValueParam<bool>& eraseParam = _parser.createParam(true, "eraseDir", "erase files in dirName if any", '\0', "Output - Disk");
bool dirOK = false; // not tested yet bool dirOK = false; // not tested yet
///////////////////////////////////////// /////////////////////////////////////////
// now some statistics on the population: // now some statistics on the population:
///////////////////////////////////////// /////////////////////////////////////////
/** /**
* existing stats as of today, April 10. 2001 * existing stats as of today, April 10. 2001
* *
* eoBestFitnessStat : best value in pop - type EOT::Fitness * eoBestFitnessStat : best value in pop - type EOT::Fitness
* eoAverageStat : average value in pop - type EOT::Fitness * eoAverageStat : average value in pop - type EOT::Fitness
* eoSecondMomentStat: average + stdev - type std::pair<double, double> * eoSecondMomentStat: average + stdev - type std::pair<double, double>
* eoSortedPopStat : whole population - type std::string (!!) * eoSortedPopStat : whole population - type std::string (!!)
* eoScalarFitnessStat: the fitnesses - type std::vector<double> * eoScalarFitnessStat: the fitnesses - type std::vector<double>
*/ */
// Best fitness in population // Best fitness in population
//--------------------------- //---------------------------
eoValueParam<bool>& printBestParam = _parser.createParam(true, "printBestStat", "Print Best/avg/stdev every gen.", '\0', "Output"); 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>& 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"); eoValueParam<bool>& fileBestParam = _parser.createParam(false, "fileBestStat", "Output bes/avg/std to file", '\0', "Output - Disk");
eoBestFitnessStat<EOT> *bestStat = NULL; eoBestFitnessStat<EOT> *bestStat = NULL;
if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() ) if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() )
// we need the bestStat for at least one of the 3 above // we need the bestStat for at least one of the 3 above
{ {
bestStat = new eoBestFitnessStat<EOT>; bestStat = new eoBestFitnessStat<EOT>;
// store it // store it
_state.storeFunctor(bestStat); _state.storeFunctor(bestStat);
// add it to the checkpoint // add it to the checkpoint
checkpoint->add(*bestStat); checkpoint->add(*bestStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*bestStat);
} }
// Average fitness alone // Average fitness alone
//---------------------- //----------------------
eoAverageStat<EOT> *averageStat = NULL; // do we need averageStat? eoAverageStat<EOT> *averageStat = NULL; // do we need averageStat?
if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() ) // we need it for gnuplot output
if ( plotBestParam.value() ) // we need it for gnuplot output
{ {
averageStat = new eoAverageStat<EOT>; averageStat = new eoAverageStat<EOT>;
// store it // store it
_state.storeFunctor(averageStat); _state.storeFunctor(averageStat);
// add it to the checkpoint // add it to the checkpoint
checkpoint->add(*averageStat); checkpoint->add(*averageStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*averageStat);
} }
// Second moment stats: average and stdev // Second moment stats: average and stdev
//--------------------------------------- //---------------------------------------
eoSecondMomentStats<EOT> *secondStat = NULL; eoSecondMomentStats<EOT> *secondStat = NULL;
if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output
{ {
secondStat = new eoSecondMomentStats<EOT>; secondStat = new eoSecondMomentStats<EOT>;
// store it // store it
_state.storeFunctor(secondStat); _state.storeFunctor(secondStat);
// add it to the checkpoint // add it to the checkpoint
checkpoint->add(*secondStat); checkpoint->add(*secondStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*secondStat);
} }
// Dump of the whole population // Dump of the whole population
//----------------------------- //-----------------------------
eoSortedPopStat<EOT> *popStat = NULL; eoSortedPopStat<EOT> *popStat = NULL;
eoValueParam<bool>& printPopParam = _parser.createParam(false, "printPop", "Print sorted pop. every gen.", '\0', "Output"); eoValueParam<bool>& printPopParam = _parser.createParam(false, "printPop", "Print sorted pop. every gen.", '\0', "Output");
if ( printPopParam.value() ) // we do want pop dump if ( printPopParam.value() ) // we do want pop dump
{ {
popStat = new eoSortedPopStat<EOT>; popStat = new eoSortedPopStat<EOT>;
// store it // store it
_state.storeFunctor(popStat); _state.storeFunctor(popStat);
// add it to the checkpoint // add it to the checkpoint
checkpoint->add(*popStat); checkpoint->add(*popStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*popStat);
} }
// do we wnat some histogram of fitnesses snpashots? // do we wnat some histogram of fitnesses snpashots?
eoValueParam<bool> plotHistogramParam = _parser.createParam(false, "plotHisto", "Plot histogram of fitnesses", '\0', "Output - Graphical"); eoValueParam<bool> plotHistogramParam = _parser.createParam(false, "plotHisto", "Plot histogram of fitnesses", '\0', "Output - Graphical");
/////////////// ///////////////
// The monitors // The monitors
/////////////// ///////////////
// do we want an eoStdoutMonitor? // do we want an eoStdoutMonitor?
bool needStdoutMonitor = printBestParam.value() bool needStdoutMonitor = printBestParam.value()
|| printPopParam.value() ; || printPopParam.value() ;
// The Stdout monitor will print parameters to the screen ... // The Stdout monitor will print parameters to the screen ...
if ( needStdoutMonitor ) if ( needStdoutMonitor )
{ {
eoStdoutMonitor *monitor = new eoStdoutMonitor(false); eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
_state.storeFunctor(monitor); _state.storeFunctor(monitor);
// when called by the checkpoint (i.e. at every generation) // when called by the checkpoint (i.e. at every generation)
// check if monitoring with signal
if ( ! mon_ctrlCParam.value() )
checkpoint->add(*monitor); checkpoint->add(*monitor);
else
mon_ctrlCCont->add(*monitor);
// the monitor will output a series of parameters: add them // the monitor will output a series of parameters: add them
monitor->add(*generationCounter); monitor->add(*generationCounter);
if (useEvalParam.value()) // we want nb of evaluations if (useEvalParam.value()) // we want nb of evaluations
monitor->add(_eval); monitor->add(_eval);
if (useTimeParam.value()) // we want time if (useTimeParam.value()) // we want time
{ {
tCounter = new eoTimeCounter; tCounter = new eoTimeCounter;
_state.storeFunctor(tCounter); _state.storeFunctor(tCounter);
// check if monitoring with signal
if ( ! mon_ctrlCParam.value() )
checkpoint->add(*tCounter); checkpoint->add(*tCounter);
else
mon_ctrlCCont->add(*tCounter);
monitor->add(*tCounter); monitor->add(*tCounter);
} }
if (printBestParam.value()) if (printBestParam.value())
{ {
monitor->add(*bestStat); monitor->add(*bestStat);
monitor->add(*secondStat); monitor->add(*secondStat);
} }
if ( printPopParam.value()) if ( printPopParam.value())
monitor->add(*popStat); monitor->add(*popStat);
} }
// first handle the dir test - if we need at least one file // first handle the dir test - if we need at least one file
if ( ( fileBestParam.value() || plotBestParam.value() || if ( ( fileBestParam.value() || plotBestParam.value() ||
plotHistogramParam.value() ) plotHistogramParam.value() )
&& !dirOK ) // just in case we add something before && !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 if (fileBestParam.value()) // A file monitor for best & secondMoment
{ {
#ifdef _MSVC #ifdef _MSVC
std::string stmp = dirNameParam.value() + "\best.xg"; std::string stmp = dirNameParam.value() + "\best.xg";
#else #else
std::string stmp = dirNameParam.value() + "/best.xg"; std::string stmp = dirNameParam.value() + "/best.xg";
#endif #endif
eoFileMonitor *fileMonitor = new eoFileMonitor(stmp); eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
// save and give to checkpoint // save and give to checkpoint
_state.storeFunctor(fileMonitor); _state.storeFunctor(fileMonitor);
checkpoint->add(*fileMonitor); checkpoint->add(*fileMonitor);
// and feed with some statistics // and feed with some statistics
fileMonitor->add(*generationCounter); fileMonitor->add(*generationCounter);
fileMonitor->add(_eval); fileMonitor->add(_eval);
if (tCounter) // we want the time as well if (tCounter) // we want the time as well
{ {
// std::cout << "On met timecounter\n"; // std::cout << "On met timecounter\n";
fileMonitor->add(*tCounter); fileMonitor->add(*tCounter);
} }
fileMonitor->add(*bestStat); fileMonitor->add(*bestStat);
fileMonitor->add(*secondStat); fileMonitor->add(*secondStat);
} }
#if defined(HAVE_GNUPLOT) #if defined(HAVE_GNUPLOT)
if (plotBestParam.value()) // an eoGnuplot1DMonitor for best & average if (plotBestParam.value()) // an eoGnuplot1DMonitor for best & average
{ {
std::string stmp = dirNameParam.value() + "/gnu_best.xg"; std::string stmp = dirNameParam.value() + "/gnu_best.xg";
eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>()); eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
// save and give to checkpoint // save and give to checkpoint
_state.storeFunctor(gnuMonitor); _state.storeFunctor(gnuMonitor);
checkpoint->add(*gnuMonitor); checkpoint->add(*gnuMonitor);
// and feed with some statistics // and feed with some statistics
if (useEvalParam.value()) // do we want eval as X coordinate if (useEvalParam.value()) // do we want eval as X coordinate
gnuMonitor->add(_eval); gnuMonitor->add(_eval);
else if (tCounter) // or time? else if (tCounter) // or time?
gnuMonitor->add(*tCounter); gnuMonitor->add(*tCounter);
else // default: generation else // default: generation
gnuMonitor->add(*generationCounter); gnuMonitor->add(*generationCounter);
gnuMonitor->add(*bestStat); gnuMonitor->add(*bestStat);
gnuMonitor->add(*averageStat); gnuMonitor->add(*averageStat);
} }
// historgram? // historgram?
if (plotHistogramParam.value()) // want to see how the fitness is spread? if (plotHistogramParam.value()) // want to see how the fitness is spread?
{ {
eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>; eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
_state.storeFunctor(fitStat); _state.storeFunctor(fitStat);
checkpoint->add(*fitStat); checkpoint->add(*fitStat);
// a gnuplot-based monitor for snapshots: needs a dir name // a gnuplot-based monitor for snapshots: needs a dir name
eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value()); eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
_state.storeFunctor(fitSnapshot); _state.storeFunctor(fitSnapshot);
// add any stat that is a std::vector<double> to it // add any stat that is a std::vector<double> to it
fitSnapshot->add(*fitStat); fitSnapshot->add(*fitStat);
// and of course add it to the checkpoint // and of course add it to the checkpoint
checkpoint->add(*fitSnapshot); checkpoint->add(*fitSnapshot);
} }
#endif #endif
////////////////////////////////// //////////////////////////////////
// State savers // State savers
////////////////////////////// //////////////////////////////
// feed the state to state savers // feed the state to state savers
// save state every N generation // 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" ); eoValueParam<unsigned>& saveFrequencyParam = _parser.createParam(unsigned(0), "saveFrequency", "Save every F generation (0 = only final state, absent = never)", '\0', "Persistence" );
if (_parser.isItThere(saveFrequencyParam)) if (_parser.isItThere(saveFrequencyParam))
{ {
// first make sure dirName is OK // first make sure dirName is OK
if (! dirOK ) if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE 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 #ifdef _MSVC
std::string stmp = dirNameParam.value() + "\generations"; std::string stmp = dirNameParam.value() + "\generations";
#else #else
std::string stmp = dirNameParam.value() + "/generations"; std::string stmp = dirNameParam.value() + "/generations";
#endif #endif
eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp); eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
_state.storeFunctor(stateSaver1); _state.storeFunctor(stateSaver1);
checkpoint->add(*stateSaver1); checkpoint->add(*stateSaver1);
} }
// save state every T seconds // save state every T seconds
eoValueParam<unsigned>& saveTimeIntervalParam = _parser.createParam(unsigned(0), "saveTimeInterval", "Save every T seconds (0 or absent = never)", '\0',"Persistence" ); 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) if (_parser.isItThere(saveTimeIntervalParam) && saveTimeIntervalParam.value()>0)
{ {
// first make sure dirName is OK // first make sure dirName is OK
if (! dirOK ) if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
#ifdef _MSVC #ifdef _MSVC
std::string stmp = dirNameParam.value() + "\time"; std::string stmp = dirNameParam.value() + "\time";
#else #else
std::string stmp = dirNameParam.value() + "/time"; std::string stmp = dirNameParam.value() + "/time";
#endif #endif
eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp); eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
_state.storeFunctor(stateSaver2); _state.storeFunctor(stateSaver2);
checkpoint->add(*stateSaver2); checkpoint->add(*stateSaver2);
} }
// and that's it for the (control and) output // and that's it for the (control and) output
return *checkpoint; return *checkpoint;
} }
#endif #endif

5
eo/src/eoCombinedContinue.h
View file

@ -61,7 +61,9 @@ public:
eoCombinedContinue( eoContinue<EOT>& _cont1, eoContinue<EOT>& _cont2) eoCombinedContinue( eoContinue<EOT>& _cont1, eoContinue<EOT>& _cont2)
: eoContinue<EOT>(), std::vector<eoContinue<EOT>* >() : 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." #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(&_cont1);
this->push_back(&_cont2); this->push_back(&_cont2);
@ -74,7 +76,10 @@ public:
void removeLast(void) 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." #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(); this->pop_back();
} }

2
eo/src/eoCtrlCContinue.h
View file

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

2
eo/src/eoFlight.h
View file

@ -46,7 +46,7 @@ public:
{ {
for (unsigned i = 0; i < _pop.size (); i++) 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> class eoDummyEval : public eoPopEvalFunc<POT>
{ {
public: public:
void operator()(eoPop<POT> &,eoPop<POT> &_pop) void operator()(eoPop<POT> &,eoPop<POT> &/*_pop*/)
{} {}
} }
dummyEval; dummyEval;

2
eo/src/eoParticleBestInit.h
View file

@ -46,7 +46,7 @@ public:
{ {
for (unsigned i = 0; i < _pop.size (); i++) 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 /** It returns 'true' only if the current number of generations modulo
the period doen't equal to zero. */ the period doen't equal to zero. */
bool operator () (const eoPop <EOT> & pop) bool operator () (const eoPop <EOT> & /*pop*/)
{ {
return ((++ counter) % period) != 0 ; 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) 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." #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; 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); add(_op,_rate);
} }

2
eo/src/eoProportionalSelect.h
View file

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

2
eo/src/eoReduceSplit.h
View file

@ -104,7 +104,7 @@ public:
unsigned eliminated = howMany(popSize); unsigned eliminated = howMany(popSize);
if (!eliminated) // nothing to do if (!eliminated) // nothing to do
return ; return ;
unsigned newsize = popSize - eliminated; long newsize = static_cast<long>(popSize) - static_cast<long>(eliminated);
if (newsize < 0) if (newsize < 0)
throw std::logic_error("eoLinearTruncateSplit: Cannot truncate to a larger size!\n"); 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 //! Print term values and descriptions
void printAll(std::ostream& os) const { void printAll(std::ostream& os) const {
for (size_type i=0; i < size(); ++i ) 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 //! Comparison, using less by default

2
eo/src/eoSelectFromWorth.h
View file

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

2
eo/src/eoSyncEasyPSO.h
View file

@ -241,7 +241,7 @@ private:
{ {
public: public:
eoDummyFlight () {} eoDummyFlight () {}
void operator () (POT & _po) {} void operator () (POT & /*_po*/) {}
}dummyFlight; }dummyFlight;
// if the initializer does not need to be used, use the dummy one instead // 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++) 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. * 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) bool operator()(Chrom& chrom)
{ {
unsigned i = eo::rng.random(chrom.size()); unsigned i = eo::rng.random(chrom.size());
chrom[i] = (chrom[i]) ? false : true; chrom[i] = !chrom[i];
return true; return true;
} }
}; };
@ -85,11 +85,11 @@ template<class Chrom> class eoDetBitFlip: public eoMonOp<Chrom>
*/ */
bool operator()(Chrom& 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++) for (unsigned k=0; k<num_bit; k++)
{ {
unsigned i = eo::rng.random(chrom.size()); unsigned i = eo::rng.random(chrom.size());
chrom[i] = (chrom[i]) ? false : true; chrom[i] = !chrom[i];
} }
return true; 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 /** eoBitMutation --> classical mutation
\class eoBitMutation eoBitOp.h ga/eoBitOp.h \class eoBitMutation eoBitOp.h ga/eoBitOp.h
\ingroup bitstring \ingroup bitstring

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

@ -37,7 +37,7 @@
* *
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained * The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in ga.h * 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, * Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations * just declarations

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