From a038586edbe551ac13db8a9754b04e65b992bdb5 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 5 Jul 2010 19:04:35 +0200 Subject: [PATCH 02/74] + do files --- src/CMakeLists.txt | 35 ++++ src/do | 36 ++++ src/doAlgo.h | 16 ++ src/doBounder.h | 27 +++ src/doBounderBound.h | 35 ++++ src/doBounderNo.h | 14 ++ src/doBounderRng.h | 35 ++++ src/doCMASA.h | 395 +++++++++++++++++++++++++++++++++++++ src/doDistrib.h | 14 ++ src/doDistribParams.h | 32 +++ src/doEstimator.h | 16 ++ src/doEstimatorNormal.h | 46 +++++ src/doEstimatorUniform.h | 44 +++++ src/doFileSnapshot.h | 227 +++++++++++++++++++++ src/doModifier.h | 13 ++ src/doModifierDispersion.h | 16 ++ src/doModifierMass.h | 17 ++ src/doNormal.h | 16 ++ src/doNormalCenter.h | 19 ++ src/doNormalParams.h | 24 +++ src/doSampler.h | 58 ++++++ src/doSamplerNormal.h | 60 ++++++ src/doSamplerUniform.h | 55 ++++++ src/doStats.h | 121 ++++++++++++ src/doUniform.h | 16 ++ src/doUniformCenter.h | 28 +++ src/doVectorBounds.h | 24 +++ 27 files changed, 1439 insertions(+) create mode 100644 src/CMakeLists.txt create mode 100644 src/do create mode 100644 src/doAlgo.h create mode 100644 src/doBounder.h create mode 100644 src/doBounderBound.h create mode 100644 src/doBounderNo.h create mode 100644 src/doBounderRng.h create mode 100644 src/doCMASA.h create mode 100644 src/doDistrib.h create mode 100644 src/doDistribParams.h create mode 100644 src/doEstimator.h create mode 100644 src/doEstimatorNormal.h create mode 100644 src/doEstimatorUniform.h create mode 100644 src/doFileSnapshot.h create mode 100644 src/doModifier.h create mode 100644 src/doModifierDispersion.h create mode 100644 src/doModifierMass.h create mode 100644 src/doNormal.h create mode 100644 src/doNormalCenter.h create mode 100644 src/doNormalParams.h create mode 100644 src/doSampler.h create mode 100644 src/doSamplerNormal.h create mode 100644 src/doSamplerUniform.h create mode 100644 src/doStats.h create mode 100644 src/doUniform.h create mode 100644 src/doUniformCenter.h create mode 100644 src/doVectorBounds.h diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt new file mode 100644 index 00000000..a913882b --- /dev/null +++ b/src/CMakeLists.txt @@ -0,0 +1,35 @@ +FIND_PACKAGE(Boost 1.33.0 REQUIRED) + +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +SET(RESOURCES + cma_sa.param + plot.py + ) + +FOREACH(file ${RESOURCES}) + EXECUTE_PROCESS( + COMMAND ${CMAKE_COMMAND} -E copy_if_different + ${CMAKE_CURRENT_SOURCE_DIR}/${file} + ${CMAKE_CURRENT_BINARY_DIR}/${file} + ) +ENDFOREACH(file) + +ADD_EXECUTABLE(cma_sa main.cpp) + +TARGET_LINK_LIBRARIES(cma_sa + ${Boost_LIBRARIES} + BOPO + eoutils + pthread + moeo + eo + peo + rmc_mpi + eometah + nklandscapes + BOPO + #${MPICH2_LIBRARIES} + ${LIBXML2_LIBRARIES} + ${MPI_LIBRARIES} + ) diff --git a/src/do b/src/do new file mode 100644 index 00000000..30289578 --- /dev/null +++ b/src/do @@ -0,0 +1,36 @@ +#ifndef _do_ +#define _do_ + +#include "doAlgo.h" +#include "doCMASA.h" + +#include "doDistrib.h" +#include "doUniform.h" +#include "doNormal.h" + +#include "doEstimator.h" +#include "doEstimatorUniform.h" +#include "doEstimatorNormal.h" + +#include "doModifier.h" +#include "doModifierDispersion.h" +#include "doModifierMass.h" +#include "doUniformCenter.h" +#include "doNormalCenter.h" + +#include "doSampler.h" +#include "doSamplerUniform.h" +#include "doSamplerNormal.h" + +#include "doDistribParams.h" +#include "doVectorBounds.h" +#include "doNormalParams.h" + +#include "doBounder.h" +#include "doBounderNo.h" +#include "doBounderBound.h" +#include "doBounderRng.h" + +#include "doStats.h" + +#endif // !_do_ diff --git a/src/doAlgo.h b/src/doAlgo.h new file mode 100644 index 00000000..54ea1698 --- /dev/null +++ b/src/doAlgo.h @@ -0,0 +1,16 @@ +#ifndef _doAlgo_h +#define _doAlgo_h + +#include + +template < typename D > +class doAlgo : public eoAlgo< typename D::EOType > +{ + //! Alias for the type + typedef typename D::EOType EOT; + +public: + virtual ~doAlgo(){} +}; + +#endif // !_doAlgo_h diff --git a/src/doBounder.h b/src/doBounder.h new file mode 100644 index 00000000..28996474 --- /dev/null +++ b/src/doBounder.h @@ -0,0 +1,27 @@ +#ifndef _doBounder_h +#define _doBounder_h + +#include + +template < typename EOT > +class doBounder : public eoUF< EOT&, void > +{ +public: + doBounder( EOT min = -5, EOT max = 5 ) + : _min(min), _max(max) + { + assert(_min.size() > 0); + assert(_min.size() == _max.size()); + } + + // virtual void operator()( EOT& ) = 0 (provided by eoUF< A1, R >) + + EOT& min(){return _min;} + EOT& max(){return _max;} + +private: + EOT _min; + EOT _max; +}; + +#endif // !_doBounder_h diff --git a/src/doBounderBound.h b/src/doBounderBound.h new file mode 100644 index 00000000..a284d2cb --- /dev/null +++ b/src/doBounderBound.h @@ -0,0 +1,35 @@ +#ifndef _doBounderBound_h +#define _doBounderBound_h + +#include "doBounder.h" + +template < typename EOT > +class doBounderBound : public doBounder< EOT > +{ +public: + doBounderBound( EOT min, EOT max ) + : doBounder< EOT >( min, max ) + {} + + void operator()( EOT& x ) + { + unsigned int size = x.size(); + assert(size > 0); + + for (unsigned int d = 0; d < size; ++d) // browse all dimensions + { + if (x[d] < this->min()[d]) + { + x[d] = this->min()[d]; + continue; + } + + if (x[d] > this->max()[d]) + { + x[d] = this->max()[d]; + } + } + } +}; + +#endif // !_doBounderBound_h diff --git a/src/doBounderNo.h b/src/doBounderNo.h new file mode 100644 index 00000000..36e34451 --- /dev/null +++ b/src/doBounderNo.h @@ -0,0 +1,14 @@ +#ifndef _doBounderNo_h +#define _doBounderNo_h + +#include "doBounder.h" + +template < typename EOT > +class doBounderNo : public doBounder< EOT > +{ +public: + void operator()( EOT& x ) + {} +}; + +#endif // !_doBounderNo_h diff --git a/src/doBounderRng.h b/src/doBounderRng.h new file mode 100644 index 00000000..2f2450bc --- /dev/null +++ b/src/doBounderRng.h @@ -0,0 +1,35 @@ +#ifndef _doBounderRng_h +#define _doBounderRng_h + +#include "doBounder.h" + +template < typename EOT > +class doBounderRng : public doBounder< EOT > +{ +public: + doBounderRng( EOT min, EOT max, eoRndGenerator< double > & rng ) + : doBounder< EOT >( min, max ), _rng(rng) + {} + + void operator()( EOT& x ) + { + unsigned int size = x.size(); + assert(size > 0); + + for (unsigned int d = 0; d < size; ++d) // browse all dimensions + { + + // FIXME: attention: les bornes RNG ont les memes bornes quelque soit les dimensions idealement on voudrait avoir des bornes differentes pour chaque dimensions. + + if (x[d] < this->min()[d] || x[d] > this->max()[d]) + { + x[d] = _rng(); + } + } + } + +private: + eoRndGenerator< double> & _rng; +}; + +#endif // !_doBounderRng_h diff --git a/src/doCMASA.h b/src/doCMASA.h new file mode 100644 index 00000000..cdf446c8 --- /dev/null +++ b/src/doCMASA.h @@ -0,0 +1,395 @@ +#ifndef _doCMASA_h +#define _doCMASA_h + +//----------------------------------------------------------------------------- +// Temporary solution to store populations state at each iteration for plotting. +//----------------------------------------------------------------------------- + +// system header inclusion +#include +// end system header inclusion + +// mkdir headers inclusion +#include +#include +// end mkdir headers inclusion + +#include +#include + +#include + +#include +#include + +//----------------------------------------------------------------------------- + +#include +#include + +#include + +#include "doAlgo.h" +#include "doEstimator.h" +#include "doModifierMass.h" +#include "doSampler.h" + +using namespace boost::numeric::ublas; + +template < typename D > +class doCMASA : public doAlgo< D > +{ +public: + //! Alias for the type + typedef typename D::EOType EOT; + + //! Alias for the fitness + typedef typename EOT::Fitness Fitness; + +public: + + //! doCMASA constructor + /*! + All the boxes used by a CMASA need to be given. + + \param selector The EOT selector + \param estomator The EOT selector + \param selectone SelectOne + \param modifier The D modifier + \param sampler The D sampler + \param evaluation The evaluation function. + \param continue The stopping criterion. + \param cooling_schedule The cooling schedule, describes how the temperature is modified. + \param initial_temperature The initial temperature. + \param replacor The EOT replacor + */ + doCMASA (eoSelect< EOT > & selector, + doEstimator< D > & estimator, + eoSelectOne< EOT > & selectone, + doModifierMass< D > & modifier, + doSampler< D > & sampler, + eoContinue< EOT > & monitoring_continue, + eoEvalFunc < EOT > & evaluation, + moSolContinue < EOT > & continuator, + moCoolingSchedule & cooling_schedule, + double initial_temperature, + eoReplacement< EOT > & replacor + ) + : _selector(selector), + _estimator(estimator), + _selectone(selectone), + _modifier(modifier), + _sampler(sampler), + _monitoring_continue(monitoring_continue), + _evaluation(evaluation), + _continuator(continuator), + _cooling_schedule(cooling_schedule), + _initial_temperature(initial_temperature), + _replacor(replacor) + {} + + //! function that launches the CMASA algorithm. + /*! + As a moTS or a moHC, the CMASA can be used for HYBRIDATION in an evolutionary algorithm. + + \param pop A population to improve. + \return TRUE. + */ + //bool operator ()(eoPop< EOT > & pop) + void operator ()(eoPop< EOT > & pop) + { + assert(pop.size() > 0); + + double temperature = _initial_temperature; + + eoPop< EOT > current_pop = pop; + + eoPop< EOT > selected_pop; + + //------------------------------------------------------------- + // Temporary solution used by plot to enumerate iterations in + // several files. + //------------------------------------------------------------- + + int number_of_iterations = 0; + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Temporary solution to store populations state at each + // iteration for plotting. + //------------------------------------------------------------- + + std::string pop_results_destination("ResPop"); + + { + std::stringstream ss; + ss << "rm -rf " << pop_results_destination; + ::system(ss.str().c_str()); + } + + ::mkdir(pop_results_destination.c_str(), 0755); // create a first time the + // directory where populations state are going to be stored. + std::ofstream ofs_params("ResParams.txt"); + std::ofstream ofs_params_var("ResVars.txt"); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Temporary solution to store bounds valeur for each distribution. + //------------------------------------------------------------- + + std::string bounds_results_destination("ResBounds"); + + { + std::stringstream ss; + ss << "rm -rf " << bounds_results_destination; + ::system(ss.str().c_str()); + } + + ::mkdir(bounds_results_destination.c_str(), 0755); // create a first time the + + //------------------------------------------------------------- + + + { + D distrib = _estimator(pop); + + double size = distrib.size(); + + assert(size > 0); + + double vacc = 1; + + for (int i = 0; i < size; ++i) + { + vacc *= sqrt(distrib.variance()[i]); + } + + assert(vacc <= std::numeric_limits::max()); + + ofs_params_var << vacc << std::endl; + } + + do + { + if (pop != current_pop) + { + _replacor(pop, current_pop); + } + + current_pop.clear(); + selected_pop.clear(); + + + //------------------------------------------------------------- + // (3) Selection of the best points in the population + //------------------------------------------------------------- + + _selector(pop, selected_pop); + + //------------------------------------------------------------- + + + _continuator.init(); + + + //------------------------------------------------------------- + // (4) Estimation of the distribution parameters + //------------------------------------------------------------- + + D distrib = _estimator(selected_pop); + + //------------------------------------------------------------- + + + // TODO: utiliser selected_pop ou pop ??? + + assert(selected_pop.size() > 0); + + + //------------------------------------------------------------- + // Init of a variable contening a point with the bestest fitnesses + //------------------------------------------------------------- + + EOT current_solution = _selectone(selected_pop); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Fit the current solution with the distribution parameters (bounds) + //------------------------------------------------------------- + + // FIXME: si besoin de modifier la dispersion de la distribution + // _modifier_dispersion(distribution, selected_pop); + _modifier(distrib, current_solution); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Building of the sampler in current_pop + //------------------------------------------------------------- + + do + { + EOT candidate_solution = _sampler(distrib); + + EOT& e1 = candidate_solution; + _evaluation( e1 ); + EOT& e2 = current_solution; + _evaluation( e2 ); + + // TODO: verifier le critere d'acceptation + if ( e1.fitness() < e2.fitness() || + rng.uniform() < exp( ::fabs(e1.fitness() - e2.fitness()) / temperature ) ) + { + current_pop.push_back(candidate_solution); + current_solution = candidate_solution; + } + } + while ( _continuator( current_solution) ); + + + //------------------------------------------------------------- + // Temporary solution to store populations state + // at each iteration for plotting. + //------------------------------------------------------------- + + { + std::stringstream ss; + ss << pop_results_destination << "/" << number_of_iterations; + std::ofstream ofs(ss.str().c_str()); + ofs << current_pop; + } + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Temporary solution used by plot to enumerate iterations in + // several files. + //------------------------------------------------------------- + + { + double size = distrib.size(); + + assert(size > 0); + + std::stringstream ss; + ss << bounds_results_destination << "/" << number_of_iterations; + std::ofstream ofs(ss.str().c_str()); + + ofs << size << " "; + std::copy(distrib.param(0).begin(), distrib.param(0).end(), std::ostream_iterator< double >(ofs, " ")); + std::copy(distrib.param(1).begin(), distrib.param(1).end(), std::ostream_iterator< double >(ofs, " ")); + ofs << std::endl; + } + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Temporary saving to get a proof for distribution bounds + // dicreasement + //------------------------------------------------------------- + + { + // double size = distrib.size(); + + // assert(size > 0); + + // vector< double > vmin(size); + // vector< double > vmax(size); + + // std::copy(distrib.param(0).begin(), distrib.param(0).end(), vmin.begin()); + // std::copy(distrib.param(1).begin(), distrib.param(1).end(), vmax.begin()); + + // vector< double > vrange = vmax - vmin; + + // double vacc = 1; + + // for (int i = 0, size = vrange.size(); i < size; ++i) + // { + // vacc *= vrange(i); + // } + + // assert(vacc <= std::numeric_limits::max()); + + // ofs_params << vacc << std::endl; + } + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Temporary saving to get a proof for distribution bounds + // dicreasement + //------------------------------------------------------------- + + { + double size = distrib.size(); + + assert(size > 0); + + double vacc = 1; + + for (int i = 0; i < size; ++i) + { + vacc *= sqrt(distrib.variance()[i]); + } + + assert(vacc <= std::numeric_limits::max()); + + ofs_params_var << vacc << std::endl; + } + + //------------------------------------------------------------- + + ++number_of_iterations; + + } + while ( _cooling_schedule( temperature ) && + _monitoring_continue( selected_pop ) ); + } + +private: + + //! A EOT selector + eoSelect < EOT > & _selector; + + //! A EOT estimator. It is going to estimate distribution parameters. + doEstimator< D > & _estimator; + + //! SelectOne + eoSelectOne< EOT > & _selectone; + + //! A D modifier + doModifierMass< D > & _modifier; + + //! A D sampler + doSampler< D > & _sampler; + + //! A EOT monitoring continuator + eoContinue < EOT > & _monitoring_continue; + + //! A full evaluation function. + eoEvalFunc < EOT > & _evaluation; + + //! Stopping criterion before temperature update + moSolContinue < EOT > & _continuator; + + //! The cooling schedule + moCoolingSchedule & _cooling_schedule; + + //! Initial temperature + double _initial_temperature; + + //! A EOT replacor + eoReplacement < EOT > & _replacor; +}; + +#endif // !_doCMASA_h diff --git a/src/doDistrib.h b/src/doDistrib.h new file mode 100644 index 00000000..71c2f6f1 --- /dev/null +++ b/src/doDistrib.h @@ -0,0 +1,14 @@ +#ifndef _doDistrib_h +#define _doDistrib_h + +template < typename EOT > +class doDistrib +{ +public: + //! Alias for the type + typedef EOT EOType; + + virtual ~doDistrib(){} +}; + +#endif // !_doDistrib_h diff --git a/src/doDistribParams.h b/src/doDistribParams.h new file mode 100644 index 00000000..b895eec9 --- /dev/null +++ b/src/doDistribParams.h @@ -0,0 +1,32 @@ +#ifndef _doDistribParams_h +#define _doDistribParams_h + +#include + +template < typename EOT > +class doDistribParams +{ +public: + doDistribParams(unsigned n = 2) + : _params(n) + {} + + EOT& param(unsigned int i = 0){return _params[i];} + + unsigned int param_size(){return _params.size();} + + unsigned int size() + { + for (unsigned int i = 0, size = param_size(); i < size - 1; ++i) + { + assert(param(i).size() == param(i + 1).size()); + } + + return param(0).size(); + } + +private: + std::vector< EOT > _params; +}; + +#endif // !_doDistribParams_h diff --git a/src/doEstimator.h b/src/doEstimator.h new file mode 100644 index 00000000..682dd3f7 --- /dev/null +++ b/src/doEstimator.h @@ -0,0 +1,16 @@ +#ifndef _doEstimator_h +#define _doEstimator_h + +#include +#include + +template < typename D > +class doEstimator : public eoUF< eoPop< typename D::EOType >&, D > +{ +public: + typedef typename D::EOType EOType; + + // virtual D operator() ( eoPop< EOT >& )=0 (provided by eoUF< A1, R >) +}; + +#endif // !_doEstimator_h diff --git a/src/doEstimatorNormal.h b/src/doEstimatorNormal.h new file mode 100644 index 00000000..133b9803 --- /dev/null +++ b/src/doEstimatorNormal.h @@ -0,0 +1,46 @@ +#ifndef _doEstimatorNormal_h +#define _doEstimatorNormal_h + +#include "doEstimator.h" +#include "doUniform.h" +#include "doStats.h" + +// TODO: calcule de la moyenne + covariance dans une classe derivee + +template < typename EOT > +class doEstimatorNormal : public doEstimator< doNormal< EOT > > +{ +public: + doNormal< EOT > operator()(eoPop& pop) + { + unsigned int popsize = pop.size(); + assert(popsize > 0); + + unsigned int dimsize = pop[0].size(); + assert(dimsize > 0); + + std::vector< Var > var(dimsize); + + for (unsigned int i = 0; i < popsize; ++i) + { + for (unsigned int d = 0; d < dimsize; ++d) + { + var[d].update(pop[i][d]); + } + } + + EOT mean(dimsize); + EOT variance(dimsize); + + for (unsigned int d = 0; d < dimsize; ++d) + { + mean[d] = var[d].get_mean(); + variance[d] = var[d].get_var(); + //variance[d] = var[d].get_std(); // perhaps I should use this !?! + } + + return doNormal< EOT >(mean, variance); + } +}; + +#endif // !_doEstimatorNormal_h diff --git a/src/doEstimatorUniform.h b/src/doEstimatorUniform.h new file mode 100644 index 00000000..8f9b3551 --- /dev/null +++ b/src/doEstimatorUniform.h @@ -0,0 +1,44 @@ +#ifndef _doEstimatorUniform_h +#define _doEstimatorUniform_h + +#include "doEstimator.h" +#include "doUniform.h" + +// TODO: calcule de la moyenne + covariance dans une classe derivee + +template < typename EOT > +class doEstimatorUniform : public doEstimator< doUniform< EOT > > +{ +public: + doUniform< EOT > operator()(eoPop& pop) + { + unsigned int size = pop.size(); + + assert(size > 0); + + EOT min = pop[0]; + EOT max = pop[0]; + + for (unsigned int i = 1; i < size; ++i) + { + unsigned int size = pop[i].size(); + + assert(size > 0); + + // possibilité d'utiliser std::min_element et std::max_element mais exige 2 pass au lieu d'1. + + for (unsigned int d = 0; d < size; ++d) + { + if (pop[i][d] < min[d]) + min[d] = pop[i][d]; + + if (pop[i][d] > max[d]) + max[d] = pop[i][d]; + } + } + + return doUniform< EOT >(min, max); + } +}; + +#endif // !_doEstimatorUniform_h diff --git a/src/doFileSnapshot.h b/src/doFileSnapshot.h new file mode 100644 index 00000000..39a5bb16 --- /dev/null +++ b/src/doFileSnapshot.h @@ -0,0 +1,227 @@ +//----------------------------------------------------------------------------- +// eoFileSnapshot.h +// (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2001 +/* + 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 + Marc.Schoenauer@polytechnique.fr + mkeijzer@dhi.dk + Caner Candan caner@candan.fr + Johann Dréo nojhan@gmail.com + */ +//----------------------------------------------------------------------------- + +#ifndef _doFileSnapshot_h +#define _doFileSnapshot_h + +#include // for mkdir +#include // for mkdir +#include // for unlink + +#include +#include +#include + +#include +#include +#include + +#include + +/** +Prints snapshots of fitnesses to a (new) file every N generations + +Assumes that the parameters that are passed to the monitor +(method add in eoMonitor.h) are eoValueParam > of same size. + +A dir is created and one file per snapshot is created there - +so you can later generate a movie! + +TODO: The counter is handled internally, but this should be changed +so that you can pass e.g. an evalcounter (minor) + +I failed to templatize everything so that it can handle eoParam > +for any type T, simply calling their getValue method ... +*/ + +template < typename EOTParam > +class doFileSnapshot : public eoMonitor +{ +public : + doFileSnapshot(std::string _dirname, unsigned _frequency = 1, + std::string _filename = "gen", + std::string _delim = " ", unsigned _counter = 0, + bool _rmFiles = true): + dirname(_dirname), frequency(_frequency), + filename(_filename), delim(_delim), counter(_counter), boolChanged(true) + { + // FIXME START + // TO REPLACE test command by somethink more gernerical + + std::string s = "test -d " + dirname; + + int res = system(s.c_str()); + // test for (unlikely) errors + if ( (res==-1) || (res==127) ) + throw std::runtime_error("Problem executing test of dir in eoFileSnapshot"); + + // FIXME END + + // now make sure there is a dir without any genXXX file in it + if (res) // no dir present + { + //s = std::string("mkdir ")+dirname; + ::mkdir(dirname.c_str(), 0755); + } + else if (!res && _rmFiles) + { + //s = std::string("/bin/rm ")+dirname+ "/" + filename + "*"; + std::string s = dirname+ "/" + filename + "*"; + ::unlink(s.c_str()); + } + // else + // s = " "; + + //int nothing = system(s.c_str()); + // all done + } + + /** accessor: has something changed (for gnuplot subclass) + */ + virtual bool hasChanged() {return boolChanged;} + + /** accessor to the counter: needed by the gnuplot subclass + */ + unsigned getCounter() {return counter;} + + /** accessor to the current filename: needed by the gnuplot subclass + */ + std::string getFileName() {return currentFileName;} + + /** sets the current filename depending on the counter + */ + void setCurrentFileName() + { + std::ostringstream oscount; + oscount << counter; + currentFileName = dirname + "/" + filename + oscount.str(); + } + + /** The operator(void): opens the std::ostream and calls the write method + */ + eoMonitor& operator()(void) + { + if (counter % frequency) + { + boolChanged = false; // subclass with gnuplot will do nothing + counter++; + return (*this); + } + counter++; + boolChanged = true; + setCurrentFileName(); + std::ofstream os(currentFileName.c_str()); + + if (!os) + { + std::string str = "eoFileSnapshot: Could not open " + currentFileName; + throw std::runtime_error(str); + } + + return operator()(os); + } + + /** The operator(): write on an std::ostream + */ + eoMonitor& operator()(std::ostream& _os) + { + //eo::log << eo::debug << "TOTO" << std::endl; + + //_os << "TOTO" << "\n"; + + //_os << v[0] << "\n"; + + // const eoValueParam > * ptParam = + // static_cast >* >(vec[0]); + + // what's the size of vec ?!? + + eo::log << eo::debug; + + eo::log << "vec size: " << vec.size() << std::endl; + + const eoValueParam< EOTParam > * ptParam = + static_cast< const eoValueParam< EOTParam >* >(vec[0]); + + //const std::vector v = ptParam->value(); + EOTParam v(ptParam->value()); + if (vec.size() == 1) // only one std::vector: -> add number in front + { + eo::log << "I am here..." << std::endl; + + //eo::log << *vec[0] << std::endl; + + for (unsigned k=0; k > vv(vec.size()); + std::vector< EOTParam > vv(vec.size()); + vv[0]=v; + for (unsigned i=1; i >* >(vec[1]); + ptParam = static_cast< const eoValueParam< EOTParam >* >(vec[1]); + vv[i] = ptParam->value(); + if (vv[i].size() != v.size()) + throw std::runtime_error("Dimension error in eoSnapshotMonitor"); + } + for (unsigned k=0; k +class doModifier +{ +public: + virtual ~doModifier(){} + + typedef typename D::EOType EOType; +}; + +#endif // !_doModifier_h diff --git a/src/doModifierDispersion.h b/src/doModifierDispersion.h new file mode 100644 index 00000000..2632757b --- /dev/null +++ b/src/doModifierDispersion.h @@ -0,0 +1,16 @@ +#ifndef _doModifierDispersion_h +#define _doModifierDispersion_h + +#include +#include + +#include "doModifier.h" + +template < typename D > +class doModifierDispersion : public doModifier< D >, public eoBF< D&, eoPop< typename D::EOType >&, void > +{ +public: + // virtual void operator() ( D&, eoPop< D::EOType >& )=0 (provided by eoBF< A1, A2, R >) +}; + +#endif // !_doModifierDispersion_h diff --git a/src/doModifierMass.h b/src/doModifierMass.h new file mode 100644 index 00000000..411c3f29 --- /dev/null +++ b/src/doModifierMass.h @@ -0,0 +1,17 @@ +#ifndef _doModifierMass_h +#define _doModifierMass_h + +#include + +#include "doModifier.h" + +template < typename D > +class doModifierMass : public doModifier< D >, public eoBF< D&, typename D::EOType&, void > +{ +public: + //typedef typename D::EOType::AtomType AtomType; // does not work !!! + + // virtual void operator() ( D&, D::EOType& )=0 (provided by eoBF< A1, A2, R >) +}; + +#endif // !_doModifierMass_h diff --git a/src/doNormal.h b/src/doNormal.h new file mode 100644 index 00000000..6de887fc --- /dev/null +++ b/src/doNormal.h @@ -0,0 +1,16 @@ +#ifndef _doNormal_h +#define _doNormal_h + +#include "doDistrib.h" +#include "doNormalParams.h" + +template < typename EOT > +class doNormal : public doDistrib< EOT >, public doNormalParams< EOT > +{ +public: + doNormal(EOT mean, EOT variance) + : doNormalParams< EOT >(mean, variance) + {} +}; + +#endif // !_doNormal_h diff --git a/src/doNormalCenter.h b/src/doNormalCenter.h new file mode 100644 index 00000000..06113060 --- /dev/null +++ b/src/doNormalCenter.h @@ -0,0 +1,19 @@ +#ifndef _doNormalCenter_h +#define _doNormalCenter_h + +#include "doModifierMass.h" +#include "doNormal.h" + +template < typename EOT > +class doNormalCenter : public doModifierMass< doNormal< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + void operator() ( doNormal< EOT >& distrib, EOT& mass ) + { + distrib.mean() = mass; // vive les references!!! + } +}; + +#endif // !_doNormalCenter_h diff --git a/src/doNormalParams.h b/src/doNormalParams.h new file mode 100644 index 00000000..fbfc88ed --- /dev/null +++ b/src/doNormalParams.h @@ -0,0 +1,24 @@ +#ifndef _doNormalParams_h +#define _doNormalParams_h + +#include "doDistribParams.h" + +template < typename EOT > +class doNormalParams : public doDistribParams< EOT > +{ +public: + doNormalParams(EOT _mean, EOT _variance) + : doDistribParams< EOT >(2) + { + assert(_mean.size() > 0); + assert(_mean.size() == _variance.size()); + + mean() = _mean; + variance() = _variance; + } + + EOT& mean(){return this->param(0);} + EOT& variance(){return this->param(1);} +}; + +#endif // !_doNormalParams_h diff --git a/src/doSampler.h b/src/doSampler.h new file mode 100644 index 00000000..1bb66b44 --- /dev/null +++ b/src/doSampler.h @@ -0,0 +1,58 @@ +#ifndef _doSampler_h +#define _doSampler_h + +#include + +#include "doBounder.h" + +template < typename D > +class doSampler : public eoUF< D&, typename D::EOType > +{ +public: + typedef typename D::EOType EOType; + + doSampler(doBounder< EOType > & bounder) + : _bounder(bounder) + {} + + // virtual EOType operator()( D& ) = 0 (provided by eoUF< A1, R >) + + virtual EOType sample( D& ) = 0; + + EOType operator()( D& distrib ) + { + unsigned int size = distrib.size(); + assert(size > 0); + + + //------------------------------------------------------------- + // Point we want to sample to get higher a set of points + // (coordinates in n dimension) + // x = {x1, x2, ..., xn} + // the sample method is implemented in the derivated class + //------------------------------------------------------------- + + EOType solution(sample(distrib)); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Now we are bounding the distribution thanks to min and max + // parameters. + //------------------------------------------------------------- + + _bounder(solution); + + //------------------------------------------------------------- + + + return solution; + } + +private: + //! Bounder functor + doBounder< EOType > & _bounder; +}; + +#endif // !_doSampler_h diff --git a/src/doSamplerNormal.h b/src/doSamplerNormal.h new file mode 100644 index 00000000..7ba4c2d5 --- /dev/null +++ b/src/doSamplerNormal.h @@ -0,0 +1,60 @@ +#ifndef _doSamplerNormal_h +#define _doSamplerNormal_h + +#include + +#include "doSampler.h" +#include "doNormal.h" +#include "doBounder.h" + +/** + * doSamplerNormal + * This class uses the Normal distribution parameters (bounds) to return + * a random position used for population sampling. + */ +template < typename EOT > +class doSamplerNormal : public doSampler< doNormal< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + doSamplerNormal( doBounder< EOT > & bounder ) + : doSampler< doNormal< EOT > >( bounder ) + {} + + EOT sample( doNormal< EOT >& distrib ) + { + unsigned int size = distrib.size(); + + assert(size > 0); + + //------------------------------------------------------------- + // Point we want to sample to get higher a set of points + // (coordinates in n dimension) + // x = {x1, x2, ..., xn} + //------------------------------------------------------------- + + EOT solution; + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Sampling all dimensions + //------------------------------------------------------------- + + for (unsigned int i = 0; i < size; ++i) + { + solution.push_back( + rng.normal(distrib.mean()[i], + distrib.variance()[i]) + ); + } + + //------------------------------------------------------------- + + return solution; + } +}; + +#endif // !_doSamplerNormal_h diff --git a/src/doSamplerUniform.h b/src/doSamplerUniform.h new file mode 100644 index 00000000..f49b6924 --- /dev/null +++ b/src/doSamplerUniform.h @@ -0,0 +1,55 @@ +#ifndef _doSamplerUniform_h +#define _doSamplerUniform_h + +#include + +#include "doSampler.h" +#include "doUniform.h" + +/** + * doSamplerUniform + * This class uses the Uniform distribution parameters (bounds) to return + * a random position used for population sampling. + */ +template < typename EOT > +class doSamplerUniform : public doSampler< doUniform< EOT > > +{ +public: + EOT sample( doUniform< EOT >& distrib ) + { + unsigned int size = distrib.size(); + assert(size > 0); + + //------------------------------------------------------------- + // Point we want to sample to get higher a population + // x = {x1, x2, ..., xn} + //------------------------------------------------------------- + + EOT solution; + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Sampling all dimensions + //------------------------------------------------------------- + + for (unsigned int i = 0; i < size; ++i) + { + double min = distrib.min()[i]; + double max = distrib.max()[i]; + double random = rng.uniform(min, max); + + assert(min <= random && random <= max); + + solution.push_back(random); + } + + //------------------------------------------------------------- + + + return solution; + } +}; + +#endif // !_doSamplerUniform_h diff --git a/src/doStats.h b/src/doStats.h new file mode 100644 index 00000000..b5ac32b2 --- /dev/null +++ b/src/doStats.h @@ -0,0 +1,121 @@ +/* + * Copyright (C) 2005 Maarten Keijzer + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of version 2 of the GNU General Public License as + * published by the Free Software Foundation. + * + * 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 +#include + +class Mean { + + double n; + double mean; + + public: + Mean() : n(0), mean(0) {} + + void update(double v) { + n++; + double d = v - mean; + mean += 1/n * d; + } + + double get_mean() const { return mean; } +}; + +class Var { + double n; + double mean; + double sumvar; + + public: + Var() : n(0), mean(0), sumvar(0) {} + + void update(double v) { + n++; + double d = v - mean; + mean += 1/n * d; + sumvar += (n-1)/n * d * d; + } + + double get_mean() const { return mean; } + double get_var() const { return sumvar / (n-1); } + double get_std() const { return sqrt(get_var()); } +}; + +/** Single covariance between two variates */ +class Cov { + double n; + double meana; + double meanb; + double sumcov; + + public: + Cov() : n(0), meana(0), meanb(0), sumcov(0) {} + + void update(double a, double b) { + ++n; + double da = a - meana; + double db = b - meanb; + + meana += 1/n * da; + meanb += 1/n * db; + + sumcov += (n-1)/n * da * db; + } + + double get_meana() const { return meana; } + double get_meanb() const { return meanb; } + double get_cov() const { return sumcov / (n-1); } +}; + +class CovMatrix { + double n; + std::vector mean; + std::vector< std::vector > sumcov; + + public: + CovMatrix(unsigned dim) : n(0), mean(dim), sumcov(dim , std::vector(dim)) {} + + void update(const std::vector& v) { + assert(v.size() == mean.size()); + + n++; + + for (unsigned i = 0; i < v.size(); ++i) { + double d = v[i] - mean[i]; + mean[i] += 1/n * d; + + sumcov[i][i] += (n-1)/n * d * d; + + for (unsigned j = i; j < v.size(); ++j) { + double e = v[j] - mean[j]; // mean[j] is not updated yet + + double upd = (n-1)/n * d * e; + + sumcov[i][j] += upd; + sumcov[j][i] += upd; + + } + } + + } + + double get_mean(int i) const { return mean[i]; } + double get_var(int i ) const { return sumcov[i][i] / (n-1); } + double get_std(int i) const { return sqrt(get_var(i)); } + double get_cov(int i, int j) const { return sumcov[i][j] / (n-1); } + +}; diff --git a/src/doUniform.h b/src/doUniform.h new file mode 100644 index 00000000..6bfd9016 --- /dev/null +++ b/src/doUniform.h @@ -0,0 +1,16 @@ +#ifndef _doUniform_h +#define _doUniform_h + +#include "doDistrib.h" +#include "doVectorBounds.h" + +template < typename EOT > +class doUniform : public doDistrib< EOT >, public doVectorBounds< EOT > +{ +public: + doUniform(EOT min, EOT max) + : doVectorBounds< EOT >(min, max) + {} +}; + +#endif // !_doUniform_h diff --git a/src/doUniformCenter.h b/src/doUniformCenter.h new file mode 100644 index 00000000..74864d8b --- /dev/null +++ b/src/doUniformCenter.h @@ -0,0 +1,28 @@ +#ifndef _doUniformCenter_h +#define _doUniformCenter_h + +#include "doModifierMass.h" +#include "doUniform.h" + +template < typename EOT > +class doUniformCenter : public doModifierMass< doUniform< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + void operator() ( doUniform< EOT >& distrib, EOT& mass ) + { + for (unsigned int i = 0, n = mass.size(); i < n; ++i) + { + AtomType& min = distrib.min()[i]; + AtomType& max = distrib.max()[i]; + + AtomType range = (max - min) / 2; + + min = mass[i] - range; + max = mass[i] + range; + } + } +}; + +#endif // !_doUniformCenter_h diff --git a/src/doVectorBounds.h b/src/doVectorBounds.h new file mode 100644 index 00000000..65655c3c --- /dev/null +++ b/src/doVectorBounds.h @@ -0,0 +1,24 @@ +#ifndef _doVectorBounds_h +#define _doVectorBounds_h + +#include "doDistribParams.h" + +template < typename EOT > +class doVectorBounds : public doDistribParams< EOT > +{ +public: + doVectorBounds(EOT _min, EOT _max) + : doDistribParams< EOT >(2) + { + assert(_min.size() > 0); + assert(_min.size() == _max.size()); + + min() = _min; + max() = _max; + } + + EOT& min(){return this->param(0);} + EOT& max(){return this->param(1);} +}; + +#endif // !_doVectorBounds_h From 8ba39921faeb2ae75817a427c7ef1256775bbf06 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 5 Jul 2010 19:06:34 +0200 Subject: [PATCH 03/74] + cma_sa application --- application/cma_sa/CMakeLists.txt | 35 +++++ application/cma_sa/Rosenbrock.h | 42 ++++++ application/cma_sa/Sphere.h | 42 ++++++ application/cma_sa/cma_sa.param | 7 + application/cma_sa/main.cpp | 233 ++++++++++++++++++++++++++++++ application/cma_sa/plot.py | 232 +++++++++++++++++++++++++++++ 6 files changed, 591 insertions(+) create mode 100644 application/cma_sa/CMakeLists.txt create mode 100644 application/cma_sa/Rosenbrock.h create mode 100644 application/cma_sa/Sphere.h create mode 100644 application/cma_sa/cma_sa.param create mode 100644 application/cma_sa/main.cpp create mode 100755 application/cma_sa/plot.py diff --git a/application/cma_sa/CMakeLists.txt b/application/cma_sa/CMakeLists.txt new file mode 100644 index 00000000..a913882b --- /dev/null +++ b/application/cma_sa/CMakeLists.txt @@ -0,0 +1,35 @@ +FIND_PACKAGE(Boost 1.33.0 REQUIRED) + +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +SET(RESOURCES + cma_sa.param + plot.py + ) + +FOREACH(file ${RESOURCES}) + EXECUTE_PROCESS( + COMMAND ${CMAKE_COMMAND} -E copy_if_different + ${CMAKE_CURRENT_SOURCE_DIR}/${file} + ${CMAKE_CURRENT_BINARY_DIR}/${file} + ) +ENDFOREACH(file) + +ADD_EXECUTABLE(cma_sa main.cpp) + +TARGET_LINK_LIBRARIES(cma_sa + ${Boost_LIBRARIES} + BOPO + eoutils + pthread + moeo + eo + peo + rmc_mpi + eometah + nklandscapes + BOPO + #${MPICH2_LIBRARIES} + ${LIBXML2_LIBRARIES} + ${MPI_LIBRARIES} + ) diff --git a/application/cma_sa/Rosenbrock.h b/application/cma_sa/Rosenbrock.h new file mode 100644 index 00000000..c21a8cce --- /dev/null +++ b/application/cma_sa/Rosenbrock.h @@ -0,0 +1,42 @@ +#ifndef _Rosenbrock_h +#define _Rosenbrock_h + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +template < typename EOT > +class Rosenbrock : public eoEvalFunc< EOT > +{ +public: + typedef typename EOT::AtomType AtomType; + + virtual void operator()( EOT& p ) + { + if (!p.invalid()) + return; + + p.fitness( _evaluate( p ) ); + } + +private: + AtomType _evaluate( EOT& p ) + { + AtomType r = 0.0; + + for (unsigned int i = 0; i < p.size() - 1; ++i) + { + r += p[i] * p[i]; + } + + return r; + } +}; + +#endif // !_Rosenbrock_h diff --git a/application/cma_sa/Sphere.h b/application/cma_sa/Sphere.h new file mode 100644 index 00000000..1e73b3ea --- /dev/null +++ b/application/cma_sa/Sphere.h @@ -0,0 +1,42 @@ +#ifndef _Sphere_h +#define _Sphere_h + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +template < typename EOT > +class Sphere : public eoEvalFunc< EOT > +{ +public: + typedef typename EOT::AtomType AtomType; + + virtual void operator()( EOT& p ) + { + if (!p.invalid()) + return; + + p.fitness( _evaluate( p ) ); + } + +private: + AtomType _evaluate( EOT& p ) + { + AtomType r = 0.0; + + for (unsigned int i = 0; i < p.size() - 1; ++i) + { + r += p[i] * p[i]; + } + + return r; + } +}; + +#endif // !_Sphere_h diff --git a/application/cma_sa/cma_sa.param b/application/cma_sa/cma_sa.param new file mode 100644 index 00000000..9aceb230 --- /dev/null +++ b/application/cma_sa/cma_sa.param @@ -0,0 +1,7 @@ +--rho=0 # -p : +// #include + +#ifndef HAVE_GNUPLOT +// FIXME: temporary define to force use of gnuplot without compiling +// again EO. +# define HAVE_GNUPLOT +#endif + +#include +#include + +#include +#include + +#include +#include +#include +#include + +//#include "BopoRosenbrock.h" +#include "Rosenbrock.h" +#include "Sphere.h" + +#include + +typedef eoReal EOT; +//typedef doUniform< EOT > Distrib; +//typedef doNormal< EOT > Distrib; + +int main(int ac, char** av) +{ + eoParserLogger parser(ac, av); + + // Letters used by the following declarations : + // a d i p t + + std::string section("Algorithm parameters"); + + // FIXME: a verifier la valeur par defaut + double initial_temperature = parser.createParam((double)10e5, "temperature", "Initial temperature", 'i', section).value(); // i + + eoState state; + + //----------------------------------------------------------------------------- + // Instantiate all need parameters for CMASA algorithm + //----------------------------------------------------------------------------- + + eoSelect< EOT >* selector = new eoDetSelect< EOT >(0.1); + state.storeFunctor(selector); + + //doEstimator< doUniform< EOT > >* estimator = new doEstimatorUniform< EOT >(); + doEstimator< doNormal< EOT > >* estimator = new doEstimatorNormal< EOT >(); + state.storeFunctor(estimator); + + eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >(); + state.storeFunctor(selectone); + + //doModifierMass< doUniform< EOT > >* modifier = new doUniformCenter< EOT >(); + doModifierMass< doNormal< EOT > >* modifier = new doNormalCenter< EOT >(); + state.storeFunctor(modifier); + + // EOT min(2, 42); + // EOT max(2, 32); + + //eoEvalFunc< EOT >* plainEval = new BopoRosenbrock< EOT, double, const EOT& >(); + eoEvalFunc< EOT >* plainEval = new Sphere< EOT >(); + state.storeFunctor(plainEval); + + eoEvalFuncCounter< EOT > eval(*plainEval); + + eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5); + //eoRndGenerator< double >* gen = new eoNormalGenerator< double >(0, 1); + state.storeFunctor(gen); + + + unsigned int dimension_size = parser.createParam((unsigned int)10, "dimension-size", "Dimension size", 'd', section).value(); // d + + eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( dimension_size, *gen ); + state.storeFunctor(init); + + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (1) Population init and sampler + //----------------------------------------------------------------------------- + + // Generation of population from do_make_pop (creates parameter, manages persistance and so on...) + // ... and creates the parameter letters: L P r S + + // this first sampler creates a uniform distribution independently of our distribution (it doesnot use doUniform). + + eoPop< EOT >& pop = do_make_pop(parser, state, *init); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (2) First evaluation before starting the research algorithm + //----------------------------------------------------------------------------- + + apply(eval, pop); + + //----------------------------------------------------------------------------- + + + //doBounder< EOT >* bounder = new doBounderNo< EOT >(); + doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + EOT(pop[0].size(), 5), + *gen); + state.storeFunctor(bounder); + + //doSampler< doUniform< EOT > >* sampler = new doSamplerUniform< EOT >(); + doSampler< doNormal< EOT > >* sampler = new doSamplerNormal< EOT >( *bounder ); + state.storeFunctor(sampler); + + + unsigned int rho = parser.createParam((unsigned int)0, "rho", "Rho: metropolis sample size", 'p', section).value(); // p + + moGenSolContinue< EOT >* continuator = new moGenSolContinue< EOT >(rho); + state.storeFunctor(continuator); + + double threshold = parser.createParam((double)0.1, "threshold", "Threshold: temperature threshold stopping criteria", 't', section).value(); // t + double alpha = parser.createParam((double)0.1, "alpha", "Alpha: temperature dicrease rate", 'a', section).value(); // a + + moCoolingSchedule* cooling_schedule = new moGeometricCoolingSchedule(threshold, alpha); + state.storeFunctor(cooling_schedule); + + // stopping criteria + // ... and creates the parameter letters: C E g G s T + + eoContinue< EOT >& monitoringContinue = do_make_continue(parser, state, eval); + + // output + + eoCheckPoint< EOT >& checkpoint = do_make_checkpoint(parser, state, eval, monitoringContinue); + + // appends some missing code to checkpoint + + // eoValueParam& plotPopParam = parser.createParam(false, "plotPop", "Plot sorted pop. every gen.", 0, "Graphical Output"); + + // if (plotPopParam.value()) // we do want plot dump + // { + // eoScalarFitnessStat* fitStat = new eoScalarFitnessStat; + // state.storeFunctor(fitStat); + + // checkpoint.add(*fitStat); + + // eoFileSnapshot* snapshot = new eoFileSnapshot("ResPop"); + // state.storeFunctor(snapshot); + + // snapshot->add(*fitStat); + + // checkpoint.add(*snapshot); + // } + + // -------------------------- + + // eoPopStat< EOT >* popStat = new eoPopStat; + // state.storeFunctor(popStat); + + // checkpoint.add(*popStat); + + // eoMonitor* fileSnapshot = new doFileSnapshot< std::vector< std::string > >("ResPop"); + // state.storeFunctor(fileSnapshot); + + // fileSnapshot->add(*popStat); + // checkpoint.add(*fileSnapshot); + + + //----------------------------------------------------------------------------- + // eoEPRemplacement causes the using of the current and previous + // sample for sampling. + //----------------------------------------------------------------------------- + + eoReplacement< EOT >* replacor = new eoEPReplacement< EOT >(pop.size()); + + // Below, use eoGenerationalReplacement to sample only on the current sample + + //eoReplacement< EOT >* replacor = new eoGenerationalReplacement< EOT >(); // FIXME: to define the size + + state.storeFunctor(replacor); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // CMASA algorithm configuration + //----------------------------------------------------------------------------- + + //doAlgo< doUniform< EOT > >* algo = new doCMASA< doUniform< EOT > > + doAlgo< doNormal< EOT > >* algo = new doCMASA< doNormal< EOT > > + (*selector, *estimator, *selectone, *modifier, *sampler, + checkpoint, eval, *continuator, *cooling_schedule, + initial_temperature, *replacor); + + //----------------------------------------------------------------------------- + + + // state.storeFunctor(algo); + + if (parser.userNeedsHelp()) + { + parser.printHelp(std::cout); + exit(1); + } + + // Help + Verbose routines + + make_verbose(parser); + make_help(parser); + + + //----------------------------------------------------------------------------- + // Beginning of the algorithm call + //----------------------------------------------------------------------------- + + try + { + do_run(*algo, pop); + } + catch (std::exception& e) + { + eo::log << eo::errors << "exception: " << e.what() << std::endl; + exit(EXIT_FAILURE); + } + + //----------------------------------------------------------------------------- + + return 0; +} diff --git a/application/cma_sa/plot.py b/application/cma_sa/plot.py new file mode 100755 index 00000000..4fc5924c --- /dev/null +++ b/application/cma_sa/plot.py @@ -0,0 +1,232 @@ +#!/usr/bin/env python + +"""plot.py -- Plot CMA-SA results file""" + +import os, time, math, tempfile +import numpy + +try: + import Gnuplot, Gnuplot.PlotItems, Gnuplot.funcutils +except ImportError: + # kludge in case Gnuplot hasn't been installed as a module yet: + import __init__ + Gnuplot = __init__ + import PlotItems + Gnuplot.PlotItems = PlotItems + import funcutils + Gnuplot.funcutils = funcutils + +def wait(str=None, prompt='Press return to show results...\n'): + if str is not None: + print str + raw_input(prompt) + +def draw2DRect(min=(0,0), max=(1,1), color='black', state=None, g=None): + if g == None: g = Gnuplot.Gnuplot() + if state != None: state.append(g) + + xmin, ymin = min + xmax, ymax = max + + cmd = 'set arrow from %s,%s to %s,%s nohead lc rgb "%s"' + + g(cmd % (xmin, ymin, xmin, ymax, color)) + g(cmd % (xmin, ymax, xmax, ymax, color)) + g(cmd % (xmax, ymax, xmax, ymin, color)) + g(cmd % (xmax, ymin, xmin, ymin, color)) + + return g + +def draw3DRect(min=(0,0,0), max=(1,1,1), state=None, g=None): + if g == None: g = Gnuplot.Gnuplot() + if state != None: state.append(g) + + # TODO + + return g + +def getSortedFiles(path): + assert path != None + + filelist = os.listdir(path) + filelist.sort() + + return filelist + +def plotXPointYFitness(path, fields='3:1', state=None, g=None): + if g == None: g = Gnuplot.Gnuplot() + if state != None: state.append(g) + + g.title('Fitness observation') + g.xlabel('Coordinates') + g.ylabel('Fitness (Quality)') + + files=[] + for filename in getSortedFiles(path): + files.append(Gnuplot.File(path + '/' + filename, using=fields, + with_='points', + title='distribution \'' + filename + '\'')) + + g.plot(*files) + + return g + +def plotXYPointZFitness(path, fields='4:3:1', state=None, g=None): + if g == None: g = Gnuplot.Gnuplot() + if state != None: state.append(g) + + g.title('Fitness observation in 3-D') + g.xlabel('x-axes') + g.ylabel('y-axes') + g.zlabel('Fitness (Quality)') + + files=[] + for filename in getSortedFiles(path): + files.append(Gnuplot.File(path + '/' + filename, using=fields, + with_='points', + title='distribution \'' + filename + '\'')) + + g.splot(*files) + + return g + +def plotXYPoint(path, fields='3:4', state=None, g=None): + if g == None: g = Gnuplot.Gnuplot() + if state != None: state.append(g) + + g.title('Points observation in 2-D') + g.xlabel('x-axes') + g.ylabel('y-axes') + + files=[] + for filename in getSortedFiles(path): + files.append(Gnuplot.File(path + '/' + filename, using=fields, + with_='points', + title='distribution \'' + filename + '\'')) + + g.plot(*files) + + return g + +def plotXYZPoint(path, fields='3:4:5', state=None, g=None): + if g == None: g = Gnuplot.Gnuplot() + if state != None: state.append(g) + + g.title('Points observation in 3-D') + g.xlabel('x-axes') + g.ylabel('y-axes') + g.zlabel('z-axes') + + files=[] + for filename in getSortedFiles(path): + files.append(Gnuplot.File(path + '/' + filename, using=fields, + with_='points', + title='distribution \'' + filename + '\'')) + + g.splot(*files) + + return g + +def plotParams(path, field='1', state=None, g=None): + if g == None: g = Gnuplot.Gnuplot() + if state != None: state.append(g) + + g.title('Hyper-volume comparaison through all dimensions') + g.xlabel('Iterations') + g.ylabel('Hyper-volume') + + g.plot(Gnuplot.File(path, with_='lines', using=field, + title='multivariate distribution narrowing')) + + return g + +def plot2DRectFromFiles(path, state=None, g=None, plot=True): + if g == None: g = Gnuplot.Gnuplot() + if state != None: state.append(g) + + g.title('Rectangle drawing observation') + g.xlabel('x-axes') + g.ylabel('y-axes') + + x1,x2,y1,y2 = 0,0,0,0 + + colors = ['red', 'orange', 'blue', 'green', 'gold', 'yellow', 'gray'] + #colors = open('rgb.txt', 'r').readlines() + colors_size = len(colors) + i = 0 # for color + + for filename in getSortedFiles(path): + line = open(path + '/' + filename, 'r').readline() + + fields = line.split(' ') + + if not fields[0] == '2': + print 'plot2DRectFromFiles: higher than 2 dimensions not possible to draw' + return + + xmin,ymin,xmax,ymax = fields[1:5] + #print xmin,ymin,xmax,ymax + + cur_color = colors[i % colors_size] + + draw2DRect((xmin,ymin), (xmax,ymax), cur_color, g=g) + + g('set obj rect from %s,%s to %s,%s back lw 1.0 fc rgb "%s" fillstyle solid 1.00 border -1' + % (xmin,ymin,xmax,ymax,cur_color) + ) + + if plot: + if float(xmin) < x1: x1 = float(xmin) + if float(ymin) < y1: y1 = float(ymin) + if float(xmax) > x2: x2 = float(xmax) + if float(ymax) > y2: y2 = float(ymax) + + #print x1,y1,x2,y2 + + i += 1 + + #print x1,y1,x2,y2 + + if plot: + g.plot('[%s:%s][%s:%s] -9999 notitle' % (x1, x2, y1, y2)) + + return g + +def main(n): + gstate = [] + + if n >= 1: + plotXPointYFitness('./ResPop', state=gstate) + + if n >= 2: + plotXPointYFitness('./ResPop', '4:1', state=gstate) + + if n >= 2: + plotXYPointZFitness('./ResPop', state=gstate) + + if n >= 3: + plotXYZPoint('./ResPop', state=gstate) + + if n >= 1: + plotParams('./ResParams.txt', state=gstate) + + if n >= 2: + plot2DRectFromFiles('./ResBounds', state=gstate) + plotXYPoint('./ResPop', state=gstate) + + g = plot2DRectFromFiles('./ResBounds', state=gstate, plot=False) + plotXYPoint('./ResPop', g=g) + + wait(prompt='Press return to end the plot.\n') + + pass + +# when executed, just run main(): +if __name__ == '__main__': + from sys import argv, exit + + if len(argv) < 2: + print 'Usage: plot [dimension]' + exit() + + main(int(argv[1])) From 2b9402d3f5aaa813aa35f90fa803b7b4e9b0a31c Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 5 Jul 2010 19:42:34 +0200 Subject: [PATCH 04/74] + packaging + cmake files --- CMakeLists.txt | 77 ++++++++++++++++++++++++++++++++++++++++++++++ Packaging.cmake | 74 ++++++++++++++++++++++++++++++++++++++++++++ src/CMakeLists.txt | 65 +++++++++++++++++++++----------------- 3 files changed, 188 insertions(+), 28 deletions(-) create mode 100644 CMakeLists.txt create mode 100644 Packaging.cmake diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 00000000..ce4a1d85 --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,77 @@ +###################################################################################### +### 1) Set the application properties +###################################################################################### + +# Checks cmake version compatibility +CMAKE_MINIMUM_REQUIRED(VERSION 2.6) + +PROJECT(DO) + +SET(PROJECT_VERSION_MAJOR 1) +SET(PROJECT_VERSION_MINOR 0) +SET(PROJECT_VERSION_PATCH 0) +SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}") + +###################################################################################### + + +###################################################################################### +### 2) Include the install configuration file where are defined the main variables +###################################################################################### + +INCLUDE(${CMAKE_CURRENT_SOURCE_DIR}/install.cmake) + +###################################################################################### + + +##################################################################################### +### 3) Include required modules & utilities +##################################################################################### + +INCLUDE(CMakeBackwardCompatibilityCXX) +#INCLUDE(FindDoxygen) +INCLUDE(CheckLibraryExists) +#INCLUDE(Dart OPTIONAL) + +FIND_PACKAGE(Doxygen) +FIND_PACKAGE(MPI REQUIRED) +FIND_PACKAGE(Gnuplot REQUIRED) + +# Set a special flag if the environment is windows (should do the same in a config.g file) +IF (WIN32) + ADD_DEFINITIONS(-D_WINDOWS=1) +ENDIF (WIN32) + +###################################################################################### + + +##################################################################################### +### 4) Manage the build type +##################################################################################### + +INCLUDE(${CMAKE_SOURCE_DIR}/BuildConfig.cmake) + +###################################################################################### + + +###################################################################################### +### 5) Now where we go ??? +###################################################################################### + +# warning: you have to compile libraries before bopo sources because of dependencies. +ADD_SUBDIRECTORY(lib) +ADD_SUBDIRECTORY(doc) +ADD_SUBDIRECTORY(src) +ADD_SUBDIRECTORY(test) +ADD_SUBDIRECTORY(application) + +###################################################################################### + + +###################################################################################### +### 6) Include packaging +###################################################################################### + +INCLUDE(Packaging.cmake) + +###################################################################################### diff --git a/Packaging.cmake b/Packaging.cmake new file mode 100644 index 00000000..d4d8bbe3 --- /dev/null +++ b/Packaging.cmake @@ -0,0 +1,74 @@ +###################################################################################### +### 1) Check dependencies +###################################################################################### + +IF (NOT DEFINED PROJECT_NAME OR + NOT DEFINED PROJECT_VERSION_MAJOR OR + NOT DEFINED PROJECT_VERSION_MINOR OR + NOT DEFINED PROJECT_VERSION_PATCH OR + NOT DEFINED PROJECT_VERSION) + MESSAGE(FATAL_ERROR "Be sure you have defined PROJECT_NAME and PROJECT_VERSION*.") +ENDIF() + +###################################################################################### + + +###################################################################################### +### 2) Set up components +###################################################################################### + +SET(CPACK_COMPONENTS_ALL libraries) +SET(CPACK_ALL_INSTALL_TYPES Full) + +SET(CPACK_COMPONENT_LIBRARIES_DISPLAY_NAME "Distribution Objects") +SET(CPACK_COMPONENT_LIBRARIES_DESCRIPTION "Distribution Objects library") +SET(CPACK_COMPONENT_LIBRARIES_GROUP "Devel") +SET(CPACK_COMPONENT_LIBRARIES_INSTALL_TYPES Full) + +###################################################################################### + + +###################################################################################### +### 3) Set up general information about packaging +###################################################################################### + +# For more details: http://www.cmake.org/Wiki/CMake:Component_Install_With_CPack + +#cpack package information +SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README") +SET(CPACK_PACKAGE_DESCRIPTION "Distribution Objects") +SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/COPYING") +SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Distribution Objects") +SET(CPACK_PACKAGE_VENDOR "Thales") +SET(CPACK_PACKAGE_CONTACT "caner.candan@thalesgroup.com") +SET(CPACK_PACKAGE_VERSION ${PROJECT_VERSION}) +SET(CPACK_STRIP_FILES ${PROJECT_NAME}) +SET(CPACK_SOURCE_STRIP_FILES "bin/${PROJECT_NAME}") +SET(CPACK_PACKAGE_EXECUTABLES "${PROJECT_NAME}" "${PROJECT_NAME}") +SET(CPACK_PACKAGE_VERSION_MAJOR "${PROJECT_VERSION_MAJOR}") +SET(CPACK_PACKAGE_VERSION_MINOR "${PROJECT_VERSION_MINOR}") +SET(CPACK_PACKAGE_VERSION_PATCH "${PROJECT_VERSION_PATCH}") +SET(CPACK_PACKAGE_INSTALL_DIRECTORY "${PROJECT_NAME} ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}") + +###################################################################################### + + +###################################################################################### +### 4) Set up debian packaging information +###################################################################################### + +SET(CPACK_DEBIAN_PACKAGE_DEPENDS "libstdc++6, libgcc1, libc6, libxml2, libmpich2-1.2") + +SET(CPACK_DEBIAN_PACKAGE_SECTION "devel") +SET(CPACK_DEBIAN_PACKAGE_PRIORITY "optional") + +###################################################################################### + + +###################################################################################### +### 5) And finally, include cpack, this is the last thing to do. +###################################################################################### + +INCLUDE(CPack) + +###################################################################################### diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index a913882b..7ea92512 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,35 +1,44 @@ +###################################################################################### +### 1) Include useful packages +###################################################################################### + FIND_PACKAGE(Boost 1.33.0 REQUIRED) -INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) +###################################################################################### -SET(RESOURCES - cma_sa.param - plot.py + +###################################################################################### +### 2) Include the sources +###################################################################################### + +INCLUDE_DIRECTORIES( + ${PARADISEO_EO_SRC_DIR}/src + ${PARADISEO_MO_SRC_DIR}/src + ${PARADISEO_MOEO_SRC_DIR}/src + ${PARADISEO_PEO_SRC_DIR}/src + ${CMAKE_SOURCE_DIR}/src + ${CMAKE_SOURCE_DIR}/lib/eometah + ${CMAKE_SOURCE_DIR}/lib/nk-landscapes + ${Boost_INCLUDE_DIRS} ) -FOREACH(file ${RESOURCES}) - EXECUTE_PROCESS( - COMMAND ${CMAKE_COMMAND} -E copy_if_different - ${CMAKE_CURRENT_SOURCE_DIR}/${file} - ${CMAKE_CURRENT_BINARY_DIR}/${file} - ) -ENDFOREACH(file) +###################################################################################### -ADD_EXECUTABLE(cma_sa main.cpp) -TARGET_LINK_LIBRARIES(cma_sa - ${Boost_LIBRARIES} - BOPO - eoutils - pthread - moeo - eo - peo - rmc_mpi - eometah - nklandscapes - BOPO - #${MPICH2_LIBRARIES} - ${LIBXML2_LIBRARIES} - ${MPI_LIBRARIES} - ) +###################################################################################### +### 3) Define your target(s) +###################################################################################### + +SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) + +FILE(GLOB SOURCES *.cpp) + +ADD_LIBRARY(${PROJECT_NAME} STATIC ${SOURCES}) + +# INSTALL( +# TARGETS ${LIBRARY_OUTPUT_PATH}/lib${PROJECT_NAME}.a +# DESTINATION lib +# COMPONENT libraries +# ) + +###################################################################################### From 27552a573e13d2a3c34737e512c1498a99c190d7 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 5 Jul 2010 20:31:30 +0200 Subject: [PATCH 05/74] ... --- .gitignore | 23 +++ CMakeLists.txt | 112 ++++++++++----- COPYING | 1 + README | 57 ++++++++ application/CMakeLists.txt | 7 + application/cma_sa/CMakeLists.txt | 22 +-- application/cma_sa/main.cpp | 16 +-- doc/CMakeLists.txt | 26 ++++ doc/doxyfile.cmake | 229 ++++++++++++++++++++++++++++++ doc/index.h | 0 src/CMakeLists.txt | 16 +-- 11 files changed, 426 insertions(+), 83 deletions(-) create mode 100644 .gitignore create mode 100644 COPYING create mode 100644 README create mode 100644 application/CMakeLists.txt create mode 100644 doc/CMakeLists.txt create mode 100644 doc/doxyfile.cmake create mode 100644 doc/index.h diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000..a6f79649 --- /dev/null +++ b/.gitignore @@ -0,0 +1,23 @@ +# ignore html files +*.html + +# ignore all textual files +*.txt + +# ignore object and archive files +*.[oa] + +# ignore auto-saved files +*~ +\#*\# + +# excepted these manually configured files +!CMakeLists.txt +!README.txt +!application/ +!build/ +!doc/ +!lib/ +!src/ +!test/ +build/ diff --git a/CMakeLists.txt b/CMakeLists.txt index ce4a1d85..9bc3de9b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -16,60 +16,96 @@ SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT ###################################################################################### -### 2) Include the install configuration file where are defined the main variables +### 2) Prepare some useful variables ###################################################################################### -INCLUDE(${CMAKE_CURRENT_SOURCE_DIR}/install.cmake) - -###################################################################################### - - -##################################################################################### -### 3) Include required modules & utilities -##################################################################################### - -INCLUDE(CMakeBackwardCompatibilityCXX) -#INCLUDE(FindDoxygen) -INCLUDE(CheckLibraryExists) -#INCLUDE(Dart OPTIONAL) - -FIND_PACKAGE(Doxygen) -FIND_PACKAGE(MPI REQUIRED) -FIND_PACKAGE(Gnuplot REQUIRED) - -# Set a special flag if the environment is windows (should do the same in a config.g file) -IF (WIN32) - ADD_DEFINITIONS(-D_WINDOWS=1) -ENDIF (WIN32) - -###################################################################################### - - -##################################################################################### -### 4) Manage the build type -##################################################################################### - -INCLUDE(${CMAKE_SOURCE_DIR}/BuildConfig.cmake) +SET(DO_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}") +SET(DO_BIN_DIR "${CMAKE_CURRENT_BINARY_DIR}") ###################################################################################### ###################################################################################### -### 5) Now where we go ??? +### 3) Include useful features +###################################################################################### + +INCLUDE(FindDoxygen) + +INCLUDE(FindPkgConfig) + +PKG_CHECK_MODULES(EO eo REQUIRED) + +INCLUDE_DIRECTORIES(${EO_INCLUDE_DIR}) +LINK_DIRECTORIES(${EO_LIBRARY_DIRS}) + +###################################################################################### + + +###################################################################################### +### 4) Include header files path +###################################################################################### + +INCLUDE_DIRECTORIES( + ${CMAKE_CURRENT_SOURCE_DIR}/src + ) + +###################################################################################### + + +###################################################################################### +### 5) Set compiler definitions +###################################################################################### + +IF(UNIX) + # enable warnings + ADD_DEFINITIONS( -Wall -W -Wextra ) + # ADD_DEFINITIONS( -Weffc++) + # ADD_DEFINITIONS( -g3 ) +ENDIF() + +###################################################################################### + + +###################################################################################### +### 6) Prepare some variables for CMAKE usage +###################################################################################### + +SET(SAMPLE_SRCS) + +###################################################################################### + + +###################################################################################### +### 7) Now where we go ? ###################################################################################### -# warning: you have to compile libraries before bopo sources because of dependencies. -ADD_SUBDIRECTORY(lib) -ADD_SUBDIRECTORY(doc) ADD_SUBDIRECTORY(src) -ADD_SUBDIRECTORY(test) ADD_SUBDIRECTORY(application) +ADD_SUBDIRECTORY(test) +ADD_SUBDIRECTORY(doc) ###################################################################################### ###################################################################################### -### 6) Include packaging +### 8) Create executable, link libraries and prepare target +###################################################################################### + +SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) + +LINK_DIRECTORIES(${LIBRARY_OUTPUT_PATH}) + +ADD_LIBRARY(${PROJECT_NAME} STATIC ${SAMPLE_SRCS}) +#ADD_LIBRARY(${PROJECT_NAME} SHARED ${SAMPLE_SRCS}) + +# INSTALL( +# TARGETS ${LIBRARY_OUTPUT_PATH}/lib${PROJECT_NAME}.a +# DESTINATION lib +# COMPONENT libraries +# ) + +###################################################################################### +### 9) Include packaging ###################################################################################### INCLUDE(Packaging.cmake) diff --git a/COPYING b/COPYING new file mode 100644 index 00000000..90cbe47b --- /dev/null +++ b/COPYING @@ -0,0 +1 @@ +Private license diff --git a/README b/README new file mode 100644 index 00000000..64629f58 --- /dev/null +++ b/README @@ -0,0 +1,57 @@ +This package contains the source code for BOPO problems. + +# Step 1 - Configuration +------------------------ +Rename the "install.cmake-dist" file as "install.cmake" and edit it, inserting the FULL PATH +to your ParadisEO distribution. +On Windows write your path with double antislash (ex: C:\\Users\\...) + + +# Step 2 - Build process +------------------------ +ParadisEO is assumed to be compiled. To download ParadisEO, please visit http://paradiseo.gforge.inria.fr/. +Go to the BOPO/build/ directory and lunch cmake: +(Unix) > cmake .. +(Windows) > cmake .. -G"Visual Studio 9 2008" + +Note for windows users: if you don't use VisualStudio 9, enter the name of your generator instead of "VisualStudio 9 2008". + + +# Step 3 - Compilation +---------------------- +In the bopo/build/ directory: +(Unix) > make +(Windows) Open the VisualStudio solution and compile it, compile also the target install. +You can refer to this tutorial if you don't know how to compile a solution: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial + + +# Step 4 - Execution +--------------------- +A toy example is given to test the components. You can run these tests as following. +To define problem-related components for your own problem, please refer to the tutorials available on the website : http://paradiseo.gforge.inria.fr/. +In the bopo/build/ directory: +(Unix) > ctest +Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial + +In the directory "application", there are several directory such as p_eoco which instantiate NSGAII on BOPO problems. + +(Unix) After compilation you can run the script "bopo/run.sh" and see results in "NSGAII.out". Parameters can be modified in the script. + +(Windows) Add argument "NSGAII.param" and execute the corresponding algorithms. +Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial + + +# Documentation +--------------- +The API-documentation is available in doc/html/index.html + + +# Things to keep in mind when using BOPO +---------------------------------------- +* By default, the EO random generator's seed is initialized by the number of seconds since the epoch (with time(0)). It is available in the status file dumped at each execution. Please, keep in mind that if you start two run at the same second without modifying the seed, you will get exactly the same results. + +* Execution times are measured with the boost:timer, that measure wallclock time. Additionaly, it could not measure times larger than approximatively 596.5 hours (or even less). See http://www.boost.org/doc/libs/1_33_1/libs/timer/timer.htm + +* The q-quantile computation use averaging at discontinuities (in R, it correspond to the R-2 method, in SAS, SAS-5). For more explanations, see http://en.wikipedia.org/wiki/Quantile#Estimating_the_quantiles_of_a_population and http://stat.ethz.ch/R-manual/R-devel/library/stats/html/quantile.html + +* You can send a SIGUSR1 to a process to get some information (written down in the log file) on the current state of the search. diff --git a/application/CMakeLists.txt b/application/CMakeLists.txt new file mode 100644 index 00000000..07bcc2d0 --- /dev/null +++ b/application/CMakeLists.txt @@ -0,0 +1,7 @@ +###################################################################################### +### 1) Where do we go now ?!? +###################################################################################### + +ADD_SUBDIRECTORY(cma_sa) + +###################################################################################### diff --git a/application/cma_sa/CMakeLists.txt b/application/cma_sa/CMakeLists.txt index a913882b..10305c28 100644 --- a/application/cma_sa/CMakeLists.txt +++ b/application/cma_sa/CMakeLists.txt @@ -1,5 +1,3 @@ -FIND_PACKAGE(Boost 1.33.0 REQUIRED) - INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) SET(RESOURCES @@ -15,21 +13,7 @@ FOREACH(file ${RESOURCES}) ) ENDFOREACH(file) -ADD_EXECUTABLE(cma_sa main.cpp) +FILE(GLOB SOURCES *.cpp) -TARGET_LINK_LIBRARIES(cma_sa - ${Boost_LIBRARIES} - BOPO - eoutils - pthread - moeo - eo - peo - rmc_mpi - eometah - nklandscapes - BOPO - #${MPICH2_LIBRARIES} - ${LIBXML2_LIBRARIES} - ${MPI_LIBRARIES} - ) +ADD_EXECUTABLE(cma_sa ${SOURCES}) +TARGET_LINK_LIBRARIES(cma_sa DO ${EO_LIBRARIES}) diff --git a/application/cma_sa/main.cpp b/application/cma_sa/main.cpp index e771e649..e15d37f3 100644 --- a/application/cma_sa/main.cpp +++ b/application/cma_sa/main.cpp @@ -1,12 +1,3 @@ -// #include -// #include - -#ifndef HAVE_GNUPLOT -// FIXME: temporary define to force use of gnuplot without compiling -// again EO. -# define HAVE_GNUPLOT -#endif - #include #include @@ -18,15 +9,12 @@ #include #include -//#include "BopoRosenbrock.h" +#include + #include "Rosenbrock.h" #include "Sphere.h" -#include - typedef eoReal EOT; -//typedef doUniform< EOT > Distrib; -//typedef doNormal< EOT > Distrib; int main(int ac, char** av) { diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt new file mode 100644 index 00000000..c44ffc47 --- /dev/null +++ b/doc/CMakeLists.txt @@ -0,0 +1,26 @@ +####################################################################################### +### Doc generation using Doxygen +####################################################################################### + +IF (DOXYGEN_FOUND) + SET(DOC_DIR ${CMAKE_BINARY_DIR}/doc CACHE PATH "documentation directory") + SET(DOC_CONFIG_FILE "doxyfile" CACHE PATH "documentation configuration file") + + # define the doc target + IF (DOXYGEN_EXECUTABLE) + ADD_CUSTOM_TARGET(doc + COMMAND ${DOXYGEN_EXECUTABLE} ${DOC_CONFIG_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + ENDIF (DOXYGEN_EXECUTABLE) + + # configure doxyfile file + CONFIGURE_FILE( + "${CMAKE_CURRENT_SOURCE_DIR}/${DOC_CONFIG_FILE}.cmake" + "${CMAKE_CURRENT_BINARY_DIR}/${DOC_CONFIG_FILE}" + ) +ELSE (DOXYGEN_FOUND) + MESSAGE(STATUS "Unable to generate the documentation, Doxygen package not found") +ENDIF (DOXYGEN_FOUND) + +####################################################################################### diff --git a/doc/doxyfile.cmake b/doc/doxyfile.cmake new file mode 100644 index 00000000..e19b4f28 --- /dev/null +++ b/doc/doxyfile.cmake @@ -0,0 +1,229 @@ +# Doxyfile 1.5.1 + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- +PROJECT_NAME = @PACKAGE_NAME@ +PROJECT_NUMBER = @PACKAGE_VERSION@ +OUTPUT_DIRECTORY = @CMAKE_BINARY_DIR@/doc +CREATE_SUBDIRS = NO +OUTPUT_LANGUAGE = English +BRIEF_MEMBER_DESC = YES +REPEAT_BRIEF = YES +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the +ALWAYS_DETAILED_SEC = NO +INLINE_INHERITED_MEMB = NO +FULL_PATH_NAMES = NO +STRIP_FROM_PATH = @CMAKE_SOURCE_DIR@ +STRIP_FROM_INC_PATH = +SHORT_NAMES = NO +JAVADOC_AUTOBRIEF = YES +MULTILINE_CPP_IS_BRIEF = NO +#DETAILS_AT_TOP = NO +INHERIT_DOCS = YES +SEPARATE_MEMBER_PAGES = NO +TAB_SIZE = 8 +ALIASES = +OPTIMIZE_OUTPUT_FOR_C = NO +OPTIMIZE_OUTPUT_JAVA = NO +BUILTIN_STL_SUPPORT = NO +DISTRIBUTE_GROUP_DOC = NO +SUBGROUPING = YES +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- +EXTRACT_ALL = NO +EXTRACT_PRIVATE = YES +EXTRACT_STATIC = YES +EXTRACT_LOCAL_CLASSES = YES +EXTRACT_LOCAL_METHODS = NO +HIDE_UNDOC_MEMBERS = YES +HIDE_UNDOC_CLASSES = YES +HIDE_FRIEND_COMPOUNDS = NO +HIDE_IN_BODY_DOCS = NO +INTERNAL_DOCS = NO +CASE_SENSE_NAMES = YES +HIDE_SCOPE_NAMES = NO +SHOW_INCLUDE_FILES = YES +INLINE_INFO = YES +SORT_MEMBER_DOCS = NO +SORT_BRIEF_DOCS = NO +SORT_BY_SCOPE_NAME = NO +GENERATE_TODOLIST = YES +GENERATE_TESTLIST = YES +GENERATE_BUGLIST = YES +GENERATE_DEPRECATEDLIST= YES +ENABLED_SECTIONS = +MAX_INITIALIZER_LINES = 30 +SHOW_USED_FILES = YES +SHOW_DIRECTORIES = NO +FILE_VERSION_FILTER = +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- +QUIET = YES +WARNINGS = NO +WARN_IF_UNDOCUMENTED = NO +WARN_IF_DOC_ERROR = YES +WARN_NO_PARAMDOC = NO +WARN_FORMAT = "$file:$line: $text" +WARN_LOGFILE = +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- +INPUT = @CMAKE_SOURCE_DIR@ +FILE_PATTERNS = *.cpp \ + *.h \ + NEWS README +RECURSIVE = YES +EXCLUDE = +EXCLUDE_SYMLINKS = NO +EXCLUDE_PATTERNS = +EXAMPLE_PATH = +EXAMPLE_PATTERNS = * +EXAMPLE_RECURSIVE = NO +IMAGE_PATH = +INPUT_FILTER = +FILTER_PATTERNS = +FILTER_SOURCE_FILES = NO +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- +SOURCE_BROWSER = YES +INLINE_SOURCES = NO +STRIP_CODE_COMMENTS = YES +REFERENCED_BY_RELATION = YES +REFERENCES_RELATION = YES +REFERENCES_LINK_SOURCE = YES +USE_HTAGS = NO +VERBATIM_HEADERS = YES +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- +ALPHABETICAL_INDEX = YES +COLS_IN_ALPHA_INDEX = 3 +IGNORE_PREFIX = moeo +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- +GENERATE_HTML = YES +HTML_OUTPUT = html +HTML_FILE_EXTENSION = .html +HTML_HEADER = +HTML_FOOTER = +HTML_STYLESHEET = +HTML_ALIGN_MEMBERS = YES +GENERATE_HTMLHELP = NO +CHM_FILE = +HHC_LOCATION = +GENERATE_CHI = NO +BINARY_TOC = NO +TOC_EXPAND = NO +DISABLE_INDEX = NO +ENUM_VALUES_PER_LINE = 4 +GENERATE_TREEVIEW = YES +TREEVIEW_WIDTH = 250 +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- +GENERATE_LATEX = YES +LATEX_OUTPUT = latex +LATEX_CMD_NAME = latex +MAKEINDEX_CMD_NAME = makeindex +COMPACT_LATEX = NO +PAPER_TYPE = a4wide +EXTRA_PACKAGES = +LATEX_HEADER = +PDF_HYPERLINKS = NO +USE_PDFLATEX = NO +LATEX_BATCHMODE = NO +LATEX_HIDE_INDICES = NO +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- +GENERATE_RTF = NO +RTF_OUTPUT = rtf +COMPACT_RTF = NO +RTF_HYPERLINKS = NO +RTF_STYLESHEET_FILE = +RTF_EXTENSIONS_FILE = +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- +GENERATE_MAN = YES +MAN_OUTPUT = man +MAN_EXTENSION = .3 +MAN_LINKS = NO +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- +GENERATE_XML = NO +XML_OUTPUT = xml +XML_SCHEMA = +XML_DTD = +XML_PROGRAMLISTING = YES +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- +GENERATE_AUTOGEN_DEF = NO +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- +GENERATE_PERLMOD = NO +PERLMOD_LATEX = NO +PERLMOD_PRETTY = YES +PERLMOD_MAKEVAR_PREFIX = +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- +ENABLE_PREPROCESSING = YES +MACRO_EXPANSION = NO +EXPAND_ONLY_PREDEF = NO +SEARCH_INCLUDES = YES +INCLUDE_PATH = +INCLUDE_FILE_PATTERNS = +PREDEFINED = +EXPAND_AS_DEFINED = +SKIP_FUNCTION_MACROS = YES +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- +CLASS_DIAGRAMS = YES +HIDE_UNDOC_RELATIONS = YES +HAVE_DOT = NO +CLASS_GRAPH = YES +COLLABORATION_GRAPH = YES +GROUP_GRAPHS = YES +UML_LOOK = NO +TEMPLATE_RELATIONS = NO +INCLUDE_GRAPH = YES +INCLUDED_BY_GRAPH = YES +CALL_GRAPH = NO +CALLER_GRAPH = NO +GRAPHICAL_HIERARCHY = YES +DIRECTORY_GRAPH = YES +DOT_IMAGE_FORMAT = png +DOT_PATH = +DOTFILE_DIRS = +MAX_DOT_GRAPH_DEPTH = 0 +DOT_TRANSPARENT = NO +DOT_MULTI_TARGETS = NO +GENERATE_LEGEND = YES +DOT_CLEANUP = YES +#--------------------------------------------------------------------------- +# Configuration::additions related to the search engine +#--------------------------------------------------------------------------- +SEARCHENGINE = YES diff --git a/doc/index.h b/doc/index.h new file mode 100644 index 00000000..e69de29b diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 7ea92512..a9beb5c7 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -2,7 +2,7 @@ ### 1) Include useful packages ###################################################################################### -FIND_PACKAGE(Boost 1.33.0 REQUIRED) +#FIND_PACKAGE(Boost 1.33.0 REQUIRED) ###################################################################################### @@ -11,16 +11,7 @@ FIND_PACKAGE(Boost 1.33.0 REQUIRED) ### 2) Include the sources ###################################################################################### -INCLUDE_DIRECTORIES( - ${PARADISEO_EO_SRC_DIR}/src - ${PARADISEO_MO_SRC_DIR}/src - ${PARADISEO_MOEO_SRC_DIR}/src - ${PARADISEO_PEO_SRC_DIR}/src - ${CMAKE_SOURCE_DIR}/src - ${CMAKE_SOURCE_DIR}/lib/eometah - ${CMAKE_SOURCE_DIR}/lib/nk-landscapes - ${Boost_INCLUDE_DIRS} - ) +#INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) ###################################################################################### @@ -32,8 +23,9 @@ INCLUDE_DIRECTORIES( SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) FILE(GLOB SOURCES *.cpp) +SET(SAMPLE_SRCS ${SOURCES} PARENT_SCOPE) -ADD_LIBRARY(${PROJECT_NAME} STATIC ${SOURCES}) +ADD_LIBRARY(${PROJECT_NAME} STATIC ${SAMPLE_SRCS}) # INSTALL( # TARGETS ${LIBRARY_OUTPUT_PATH}/lib${PROJECT_NAME}.a From 45a9cb88e0968c316051f75ab483bbcff0a5c111 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 5 Jul 2010 20:39:41 +0200 Subject: [PATCH 06/74] + test --- application/cma_sa/CMakeLists.txt | 2 +- test/CMakeLists.txt | 35 +++++++++++++++++++++++++++++++ 2 files changed, 36 insertions(+), 1 deletion(-) create mode 100644 test/CMakeLists.txt diff --git a/application/cma_sa/CMakeLists.txt b/application/cma_sa/CMakeLists.txt index 10305c28..5336cc4c 100644 --- a/application/cma_sa/CMakeLists.txt +++ b/application/cma_sa/CMakeLists.txt @@ -16,4 +16,4 @@ ENDFOREACH(file) FILE(GLOB SOURCES *.cpp) ADD_EXECUTABLE(cma_sa ${SOURCES}) -TARGET_LINK_LIBRARIES(cma_sa DO ${EO_LIBRARIES}) +TARGET_LINK_LIBRARIES(cma_sa ${PROJECT_NAME} ${EO_LIBRARIES}) diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt new file mode 100644 index 00000000..674dac15 --- /dev/null +++ b/test/CMakeLists.txt @@ -0,0 +1,35 @@ +############################################################################### +## +## CMakeLists file for unit test +## +############################################################################### + + +###################################################################################### +### 1) Include the sources +###################################################################################### + +###################################################################################### + + +###################################################################################### +### 2) Specify where CMake can find the libraries +###################################################################################### + +###################################################################################### + + +###################################################################################### +### 3) Define your targets and link the librairies +###################################################################################### + +SET(SOURCES + ) + +FOREACH(current ${SOURCES}) + ADD_EXECUTABLE(${current} ${current}.cpp) + TARGET_LINK_LIBRARIES(${current} ${PROJECT_NAME} ${EO_LIBRARIES}) + ADD_CURRENT(${current} ${current}) +ENDFOREACH() + +###################################################################################### From 7ebb8f405bf852f00520f83d81996abaaf6ce16e Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 6 Jul 2010 01:27:14 +0200 Subject: [PATCH 07/74] config cmake --- CMakeLists.txt | 19 +++++++++---------- application/cma_sa/CMakeLists.txt | 2 +- src/CMakeLists.txt | 31 ++----------------------------- src/doStats.h | 5 +++++ src/test.cpp | 4 ++++ 5 files changed, 21 insertions(+), 40 deletions(-) create mode 100644 src/test.cpp diff --git a/CMakeLists.txt b/CMakeLists.txt index 9bc3de9b..0ce2d1ab 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -30,13 +30,15 @@ SET(DO_BIN_DIR "${CMAKE_CURRENT_BINARY_DIR}") ###################################################################################### INCLUDE(FindDoxygen) - INCLUDE(FindPkgConfig) PKG_CHECK_MODULES(EO eo REQUIRED) +PKG_CHECK_MODULES(MO mo REQUIRED) -INCLUDE_DIRECTORIES(${EO_INCLUDE_DIR}) -LINK_DIRECTORIES(${EO_LIBRARY_DIRS}) +INCLUDE_DIRECTORIES( + ${EO_INCLUDE_DIRS} + ${MO_INCLUDE_DIRS} + ) ###################################################################################### @@ -95,14 +97,11 @@ SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) LINK_DIRECTORIES(${LIBRARY_OUTPUT_PATH}) -ADD_LIBRARY(${PROJECT_NAME} STATIC ${SAMPLE_SRCS}) -#ADD_LIBRARY(${PROJECT_NAME} SHARED ${SAMPLE_SRCS}) +ADD_LIBRARY(do STATIC ${SAMPLE_SRCS}) +INSTALL(TARGETS do ARCHIVE DESTINATION lib COMPONENT libraries) + +###################################################################################### -# INSTALL( -# TARGETS ${LIBRARY_OUTPUT_PATH}/lib${PROJECT_NAME}.a -# DESTINATION lib -# COMPONENT libraries -# ) ###################################################################################### ### 9) Include packaging diff --git a/application/cma_sa/CMakeLists.txt b/application/cma_sa/CMakeLists.txt index 5336cc4c..d4c9092a 100644 --- a/application/cma_sa/CMakeLists.txt +++ b/application/cma_sa/CMakeLists.txt @@ -16,4 +16,4 @@ ENDFOREACH(file) FILE(GLOB SOURCES *.cpp) ADD_EXECUTABLE(cma_sa ${SOURCES}) -TARGET_LINK_LIBRARIES(cma_sa ${PROJECT_NAME} ${EO_LIBRARIES}) +TARGET_LINK_LIBRARIES(cma_sa do ${EO_LIBRARIES} ${MO_LIBRARIES}) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index a9beb5c7..1e45136a 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,36 +1,9 @@ ###################################################################################### -### 1) Include useful packages +### 1) Set all needed source files for the project ###################################################################################### -#FIND_PACKAGE(Boost 1.33.0 REQUIRED) - -###################################################################################### - - -###################################################################################### -### 2) Include the sources -###################################################################################### - -#INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) - -###################################################################################### - - -###################################################################################### -### 3) Define your target(s) -###################################################################################### - -SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) - FILE(GLOB SOURCES *.cpp) + SET(SAMPLE_SRCS ${SOURCES} PARENT_SCOPE) -ADD_LIBRARY(${PROJECT_NAME} STATIC ${SAMPLE_SRCS}) - -# INSTALL( -# TARGETS ${LIBRARY_OUTPUT_PATH}/lib${PROJECT_NAME}.a -# DESTINATION lib -# COMPONENT libraries -# ) - ###################################################################################### diff --git a/src/doStats.h b/src/doStats.h index b5ac32b2..c46a7293 100644 --- a/src/doStats.h +++ b/src/doStats.h @@ -15,6 +15,9 @@ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ +#ifndef _doStats_h +#define _doStats_h + #include #include @@ -119,3 +122,5 @@ class CovMatrix { double get_cov(int i, int j) const { return sumcov[i][j] / (n-1); } }; + +#endif // !_doStats_h diff --git a/src/test.cpp b/src/test.cpp new file mode 100644 index 00000000..97e5ab2c --- /dev/null +++ b/src/test.cpp @@ -0,0 +1,4 @@ +namespace DO +{ + void test(){} +} From 42d780621d970276a8f991b6c883c23c5ea20bf3 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 6 Jul 2010 01:31:44 +0200 Subject: [PATCH 08/74] cpack works --- src/CMakeLists.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 1e45136a..8b6d787a 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -2,6 +2,9 @@ ### 1) Set all needed source files for the project ###################################################################################### +FILE(GLOB HDRS *.h do) +INSTALL(FILES ${HDRS} DESTINATION include/do COMPONENT headers) + FILE(GLOB SOURCES *.cpp) SET(SAMPLE_SRCS ${SOURCES} PARENT_SCOPE) From 011f93da7d96c234f36e59c972574a2c94b35887 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 6 Jul 2010 10:15:47 +0200 Subject: [PATCH 09/74] * fixed some packaging issues --- CMakeLists.txt | 11 ++++++++++- Packaging.cmake | 2 +- 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 0ce2d1ab..a51f4ba7 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -104,7 +104,16 @@ INSTALL(TARGETS do ARCHIVE DESTINATION lib COMPONENT libraries) ###################################################################################### -### 9) Include packaging +### 9) Install pkg-config config file for EO +###################################################################################### + +INSTALL(FILES do.pc DESTINATION lib/pkgconfig COMPONENT headers) + +###################################################################################### + + +###################################################################################### +### 10) Include packaging ###################################################################################### INCLUDE(Packaging.cmake) diff --git a/Packaging.cmake b/Packaging.cmake index d4d8bbe3..d5104c51 100644 --- a/Packaging.cmake +++ b/Packaging.cmake @@ -57,7 +57,7 @@ SET(CPACK_PACKAGE_INSTALL_DIRECTORY "${PROJECT_NAME} ${PROJECT_VERSION_MAJOR}.${ ### 4) Set up debian packaging information ###################################################################################### -SET(CPACK_DEBIAN_PACKAGE_DEPENDS "libstdc++6, libgcc1, libc6, libxml2, libmpich2-1.2") +SET(CPACK_DEBIAN_PACKAGE_DEPENDS "libstdc++6, libgcc1, libc6, libxml2, libmpich2-1.2, eo, mo") SET(CPACK_DEBIAN_PACKAGE_SECTION "devel") SET(CPACK_DEBIAN_PACKAGE_PRIORITY "optional") From d8d8f1268d5661f4f217a1d745e5b0772d76487a Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 6 Jul 2010 11:25:02 +0200 Subject: [PATCH 10/74] + do.pc --- do.pc | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 do.pc diff --git a/do.pc b/do.pc new file mode 100644 index 00000000..44155200 --- /dev/null +++ b/do.pc @@ -0,0 +1,12 @@ +# Package Information for pkg-config + +prefix=/usr +exec_prefix=${prefix} +libdir=${exec_prefix}/lib +includedir=${prefix}/include/do + +Name: Distribution Object +Description: Distribution Object +Version: 1.0 +Libs: -L${libdir} -ldo +Cflags: -I${includedir} From fb83f09b830674d4246a5b5bc91d7eca75fc4dc7 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 6 Jul 2010 15:43:15 +0200 Subject: [PATCH 11/74] ... --- CMakeLists.txt | 26 ++++++++------------------ application/cma_sa/CMakeLists.txt | 6 ++++-- 2 files changed, 12 insertions(+), 20 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index a51f4ba7..715fc0cf 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -16,17 +16,7 @@ SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT ###################################################################################### -### 2) Prepare some useful variables -###################################################################################### - -SET(DO_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}") -SET(DO_BIN_DIR "${CMAKE_CURRENT_BINARY_DIR}") - -###################################################################################### - - -###################################################################################### -### 3) Include useful features +### 2) Include useful features ###################################################################################### INCLUDE(FindDoxygen) @@ -44,7 +34,7 @@ INCLUDE_DIRECTORIES( ###################################################################################### -### 4) Include header files path +### 3) Include header files path ###################################################################################### INCLUDE_DIRECTORIES( @@ -55,7 +45,7 @@ INCLUDE_DIRECTORIES( ###################################################################################### -### 5) Set compiler definitions +### 4) Set compiler definitions ###################################################################################### IF(UNIX) @@ -69,7 +59,7 @@ ENDIF() ###################################################################################### -### 6) Prepare some variables for CMAKE usage +### 5) Prepare some variables for CMAKE usage ###################################################################################### SET(SAMPLE_SRCS) @@ -78,7 +68,7 @@ SET(SAMPLE_SRCS) ###################################################################################### -### 7) Now where we go ? +### 6) Now where we go ? ###################################################################################### ADD_SUBDIRECTORY(src) @@ -90,7 +80,7 @@ ADD_SUBDIRECTORY(doc) ###################################################################################### -### 8) Create executable, link libraries and prepare target +### 7) Create executable, link libraries and prepare target ###################################################################################### SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) @@ -104,7 +94,7 @@ INSTALL(TARGETS do ARCHIVE DESTINATION lib COMPONENT libraries) ###################################################################################### -### 9) Install pkg-config config file for EO +### 8) Install pkg-config config file for EO ###################################################################################### INSTALL(FILES do.pc DESTINATION lib/pkgconfig COMPONENT headers) @@ -113,7 +103,7 @@ INSTALL(FILES do.pc DESTINATION lib/pkgconfig COMPONENT headers) ###################################################################################### -### 10) Include packaging +### 9) Include packaging ###################################################################################### INCLUDE(Packaging.cmake) diff --git a/application/cma_sa/CMakeLists.txt b/application/cma_sa/CMakeLists.txt index d4c9092a..586ba66c 100644 --- a/application/cma_sa/CMakeLists.txt +++ b/application/cma_sa/CMakeLists.txt @@ -1,3 +1,5 @@ +PROJECT(cma_sa) + INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) SET(RESOURCES @@ -15,5 +17,5 @@ ENDFOREACH(file) FILE(GLOB SOURCES *.cpp) -ADD_EXECUTABLE(cma_sa ${SOURCES}) -TARGET_LINK_LIBRARIES(cma_sa do ${EO_LIBRARIES} ${MO_LIBRARIES}) +ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES}) +TARGET_LINK_LIBRARIES(${PROJECT_NAME} do ${EO_LIBRARIES} ${MO_LIBRARIES}) From fc1adfcc78646f7ed8c51c3efcc0f3df8c8cffc6 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 13 Jul 2010 13:20:07 +0200 Subject: [PATCH 12/74] * doStats * doEstimatorNormal: replaced use of Variance by CoMatrix --- src/doCMASA.h | 53 +++++++-------- src/doEstimatorNormal.h | 19 ++++-- src/doStats.h | 147 ++++++++++++++++++---------------------- src/test.cpp | 4 -- 4 files changed, 102 insertions(+), 121 deletions(-) delete mode 100644 src/test.cpp diff --git a/src/doCMASA.h b/src/doCMASA.h index cdf446c8..aa8f5692 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -33,6 +33,7 @@ #include "doEstimator.h" #include "doModifierMass.h" #include "doSampler.h" +#include "doStats.h" using namespace boost::numeric::ublas; @@ -106,6 +107,7 @@ public: eoPop< EOT > selected_pop; + //------------------------------------------------------------- // Temporary solution used by plot to enumerate iterations in // several files. @@ -158,19 +160,16 @@ public: D distrib = _estimator(pop); double size = distrib.size(); - assert(size > 0); - double vacc = 1; + doHyperVolume hv; for (int i = 0; i < size; ++i) { - vacc *= sqrt(distrib.variance()[i]); + hv.update( distrib.variance()[i] ); } - assert(vacc <= std::numeric_limits::max()); - - ofs_params_var << vacc << std::endl; + ofs_params_var << hv << std::endl; } do @@ -297,30 +296,27 @@ public: // dicreasement //------------------------------------------------------------- - { - // double size = distrib.size(); + // { + // double size = distrib.size(); + // assert(size > 0); - // assert(size > 0); + // vector< double > vmin(size); + // vector< double > vmax(size); - // vector< double > vmin(size); - // vector< double > vmax(size); + // std::copy(distrib.param(0).begin(), distrib.param(0).end(), vmin.begin()); + // std::copy(distrib.param(1).begin(), distrib.param(1).end(), vmax.begin()); - // std::copy(distrib.param(0).begin(), distrib.param(0).end(), vmin.begin()); - // std::copy(distrib.param(1).begin(), distrib.param(1).end(), vmax.begin()); + // vector< double > vrange = vmax - vmin; - // vector< double > vrange = vmax - vmin; + // doHyperVolume hv; - // double vacc = 1; + // for (int i = 0, size = vrange.size(); i < size; ++i) + // { + // hv.update( vrange(i) ); + // } - // for (int i = 0, size = vrange.size(); i < size; ++i) - // { - // vacc *= vrange(i); - // } - - // assert(vacc <= std::numeric_limits::max()); - - // ofs_params << vacc << std::endl; - } + // ofs_params << hv << std::endl; + // } //------------------------------------------------------------- @@ -332,19 +328,16 @@ public: { double size = distrib.size(); - assert(size > 0); - double vacc = 1; + doHyperVolume hv; for (int i = 0; i < size; ++i) { - vacc *= sqrt(distrib.variance()[i]); + hv.update( distrib.variance()[i] ); } - assert(vacc <= std::numeric_limits::max()); - - ofs_params_var << vacc << std::endl; + ofs_params_var << hv << std::endl; } //------------------------------------------------------------- diff --git a/src/doEstimatorNormal.h b/src/doEstimatorNormal.h index 133b9803..84430f35 100644 --- a/src/doEstimatorNormal.h +++ b/src/doEstimatorNormal.h @@ -19,14 +19,16 @@ public: unsigned int dimsize = pop[0].size(); assert(dimsize > 0); - std::vector< Var > var(dimsize); + //std::vector< doVar > var(dimsize); + doCovMatrix cov(dimsize); for (unsigned int i = 0; i < popsize; ++i) { - for (unsigned int d = 0; d < dimsize; ++d) - { - var[d].update(pop[i][d]); - } + cov.update(pop[i]); + // for (unsigned int d = 0; d < dimsize; ++d) + // { + // var[d].update(pop[i][d]); + // } } EOT mean(dimsize); @@ -34,9 +36,12 @@ public: for (unsigned int d = 0; d < dimsize; ++d) { - mean[d] = var[d].get_mean(); - variance[d] = var[d].get_var(); + // mean[d] = var[d].get_mean(); + // variance[d] = var[d].get_var(); //variance[d] = var[d].get_std(); // perhaps I should use this !?! + + mean[d] = cov.get_mean(d); + variance[d] = cov.get_var(d); } return doNormal< EOT >(mean, variance); diff --git a/src/doStats.h b/src/doStats.h index c46a7293..27a4b9c4 100644 --- a/src/doStats.h +++ b/src/doStats.h @@ -18,109 +18,96 @@ #ifndef _doStats_h #define _doStats_h -#include -#include +#include -class Mean { +class doStats : public eoPrintable +{ +public: + doStats(); - double n; - double mean; + virtual void printOn(std::ostream&) const; - public: - Mean() : n(0), mean(0) {} - - void update(double v) { - n++; - double d = v - mean; - mean += 1/n * d; - } - - double get_mean() const { return mean; } +protected: + double _n; }; -class Var { - double n; - double mean; - double sumvar; +class doMean : public doStats +{ +public: + doMean(); - public: - Var() : n(0), mean(0), sumvar(0) {} + virtual void update(double); + virtual void printOn(std::ostream&) const; - void update(double v) { - n++; - double d = v - mean; - mean += 1/n * d; - sumvar += (n-1)/n * d * d; - } + double get_mean() const; - double get_mean() const { return mean; } - double get_var() const { return sumvar / (n-1); } - double get_std() const { return sqrt(get_var()); } +protected: + double _mean; +}; + +class doVar : public doMean +{ +public: + doVar(); + + virtual void update(double); + virtual void printOn(std::ostream&) const; + + double get_var() const; + double get_std() const; + +protected: + double _sumvar; }; /** Single covariance between two variates */ -class Cov { - double n; - double meana; - double meanb; - double sumcov; +class doCov : public doStats +{ +public: + doCov(); - public: - Cov() : n(0), meana(0), meanb(0), sumcov(0) {} + virtual void update(double, double); + virtual void printOn(std::ostream&) const; - void update(double a, double b) { - ++n; - double da = a - meana; - double db = b - meanb; + double get_meana() const; + double get_meanb() const; + double get_cov() const; - meana += 1/n * da; - meanb += 1/n * db; - - sumcov += (n-1)/n * da * db; - } - - double get_meana() const { return meana; } - double get_meanb() const { return meanb; } - double get_cov() const { return sumcov / (n-1); } +protected: + double _meana; + double _meanb; + double _sumcov; }; -class CovMatrix { - double n; - std::vector mean; - std::vector< std::vector > sumcov; +class doCovMatrix : public doStats +{ +public: + doCovMatrix(unsigned dim); - public: - CovMatrix(unsigned dim) : n(0), mean(dim), sumcov(dim , std::vector(dim)) {} + virtual void update(const std::vector&); - void update(const std::vector& v) { - assert(v.size() == mean.size()); + double get_mean(int) const; + double get_var(int) const; + double get_std(int) const; + double get_cov(int, int) const; - n++; +protected: + std::vector< double > _mean; + std::vector< std::vector< double > > _sumcov; +}; - for (unsigned i = 0; i < v.size(); ++i) { - double d = v[i] - mean[i]; - mean[i] += 1/n * d; +class doHyperVolume : public doStats +{ +public: + doHyperVolume(); - sumcov[i][i] += (n-1)/n * d * d; + virtual void update(double); + virtual void printOn(std::ostream&) const; - for (unsigned j = i; j < v.size(); ++j) { - double e = v[j] - mean[j]; // mean[j] is not updated yet - - double upd = (n-1)/n * d * e; - - sumcov[i][j] += upd; - sumcov[j][i] += upd; - - } - } - - } - - double get_mean(int i) const { return mean[i]; } - double get_var(int i ) const { return sumcov[i][i] / (n-1); } - double get_std(int i) const { return sqrt(get_var(i)); } - double get_cov(int i, int j) const { return sumcov[i][j] / (n-1); } + double get_hypervolume() const; +protected: + double _hv; }; #endif // !_doStats_h diff --git a/src/test.cpp b/src/test.cpp deleted file mode 100644 index 97e5ab2c..00000000 --- a/src/test.cpp +++ /dev/null @@ -1,4 +0,0 @@ -namespace DO -{ - void test(){} -} From fde64b063bfc170bda84c09a5f736863d22894de Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 23 Jul 2010 13:18:30 +0200 Subject: [PATCH 13/74] * some cleaner updates --- application/cma_sa/CMakeLists.txt | 4 +++- application/cma_sa/main.cpp | 13 +++++-------- src/doDistribParams.h | 12 ++++++++++++ src/doEstimatorNormal.h | 17 +++-------------- src/doFileSnapshot.h | 27 --------------------------- src/doNormalParams.h | 4 ++++ src/doVectorBounds.h | 4 ++++ 7 files changed, 31 insertions(+), 50 deletions(-) diff --git a/application/cma_sa/CMakeLists.txt b/application/cma_sa/CMakeLists.txt index 586ba66c..d68a49c0 100644 --- a/application/cma_sa/CMakeLists.txt +++ b/application/cma_sa/CMakeLists.txt @@ -11,11 +11,13 @@ FOREACH(file ${RESOURCES}) EXECUTE_PROCESS( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/${file} - ${CMAKE_CURRENT_BINARY_DIR}/${file} + ${DO_BINARY_DIR}/${file} ) ENDFOREACH(file) FILE(GLOB SOURCES *.cpp) +SET(EXECUTABLE_OUTPUT_PATH ${DO_BINARY_DIR}) + ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES}) TARGET_LINK_LIBRARIES(${PROJECT_NAME} do ${EO_LIBRARIES} ${MO_LIBRARIES}) diff --git a/application/cma_sa/main.cpp b/application/cma_sa/main.cpp index e15d37f3..f0864a68 100644 --- a/application/cma_sa/main.cpp +++ b/application/cma_sa/main.cpp @@ -48,9 +48,6 @@ int main(int ac, char** av) doModifierMass< doNormal< EOT > >* modifier = new doNormalCenter< EOT >(); state.storeFunctor(modifier); - // EOT min(2, 42); - // EOT max(2, 32); - //eoEvalFunc< EOT >* plainEval = new BopoRosenbrock< EOT, double, const EOT& >(); eoEvalFunc< EOT >* plainEval = new Sphere< EOT >(); state.storeFunctor(plainEval); @@ -119,11 +116,11 @@ int main(int ac, char** av) // stopping criteria // ... and creates the parameter letters: C E g G s T - eoContinue< EOT >& monitoringContinue = do_make_continue(parser, state, eval); + eoContinue< EOT >& monitoring_continue = do_make_continue(parser, state, eval); // output - eoCheckPoint< EOT >& checkpoint = do_make_checkpoint(parser, state, eval, monitoringContinue); + eoCheckPoint< EOT >& checkpoint = do_make_checkpoint(parser, state, eval, monitoring_continue); // appends some missing code to checkpoint @@ -146,10 +143,10 @@ int main(int ac, char** av) // -------------------------- - // eoPopStat< EOT >* popStat = new eoPopStat; - // state.storeFunctor(popStat); + eoPopStat< EOT >* popStat = new eoPopStat; + state.storeFunctor(popStat); - // checkpoint.add(*popStat); + checkpoint.add(*popStat); // eoMonitor* fileSnapshot = new doFileSnapshot< std::vector< std::string > >("ResPop"); // state.storeFunctor(fileSnapshot); diff --git a/src/doDistribParams.h b/src/doDistribParams.h index b895eec9..ef07c151 100644 --- a/src/doDistribParams.h +++ b/src/doDistribParams.h @@ -11,6 +11,18 @@ public: : _params(n) {} + doDistribParams(const doDistribParams& p) { *this = p; } + + doDistribParams& operator=(const doDistribParams& p) + { + if (this != &p) + { + this->_params = p._params; + } + + return *this; + } + EOT& param(unsigned int i = 0){return _params[i];} unsigned int param_size(){return _params.size();} diff --git a/src/doEstimatorNormal.h b/src/doEstimatorNormal.h index 84430f35..3bd2058f 100644 --- a/src/doEstimatorNormal.h +++ b/src/doEstimatorNormal.h @@ -5,8 +5,6 @@ #include "doUniform.h" #include "doStats.h" -// TODO: calcule de la moyenne + covariance dans une classe derivee - template < typename EOT > class doEstimatorNormal : public doEstimator< doNormal< EOT > > { @@ -19,32 +17,23 @@ public: unsigned int dimsize = pop[0].size(); assert(dimsize > 0); - //std::vector< doVar > var(dimsize); doCovMatrix cov(dimsize); for (unsigned int i = 0; i < popsize; ++i) { cov.update(pop[i]); - // for (unsigned int d = 0; d < dimsize; ++d) - // { - // var[d].update(pop[i][d]); - // } } EOT mean(dimsize); - EOT variance(dimsize); + EOT covariance(dimsize); for (unsigned int d = 0; d < dimsize; ++d) { - // mean[d] = var[d].get_mean(); - // variance[d] = var[d].get_var(); - //variance[d] = var[d].get_std(); // perhaps I should use this !?! - mean[d] = cov.get_mean(d); - variance[d] = cov.get_var(d); + covariance[d] = cov.get_var(d); } - return doNormal< EOT >(mean, variance); + return doNormal< EOT >(mean, covariance); } }; diff --git a/src/doFileSnapshot.h b/src/doFileSnapshot.h index 39a5bb16..def9efc2 100644 --- a/src/doFileSnapshot.h +++ b/src/doFileSnapshot.h @@ -83,20 +83,13 @@ public : // now make sure there is a dir without any genXXX file in it if (res) // no dir present { - //s = std::string("mkdir ")+dirname; ::mkdir(dirname.c_str(), 0755); } else if (!res && _rmFiles) { - //s = std::string("/bin/rm ")+dirname+ "/" + filename + "*"; std::string s = dirname+ "/" + filename + "*"; ::unlink(s.c_str()); } - // else - // s = " "; - - //int nothing = system(s.c_str()); - // all done } /** accessor: has something changed (for gnuplot subclass) @@ -148,43 +141,23 @@ public : */ eoMonitor& operator()(std::ostream& _os) { - //eo::log << eo::debug << "TOTO" << std::endl; - - //_os << "TOTO" << "\n"; - - //_os << v[0] << "\n"; - - // const eoValueParam > * ptParam = - // static_cast >* >(vec[0]); - - // what's the size of vec ?!? - - eo::log << eo::debug; - - eo::log << "vec size: " << vec.size() << std::endl; - const eoValueParam< EOTParam > * ptParam = static_cast< const eoValueParam< EOTParam >* >(vec[0]); - //const std::vector v = ptParam->value(); EOTParam v(ptParam->value()); if (vec.size() == 1) // only one std::vector: -> add number in front { eo::log << "I am here..." << std::endl; - //eo::log << *vec[0] << std::endl; - for (unsigned k=0; k > vv(vec.size()); std::vector< EOTParam > vv(vec.size()); vv[0]=v; for (unsigned i=1; i >* >(vec[1]); ptParam = static_cast< const eoValueParam< EOTParam >* >(vec[1]); vv[i] = ptParam->value(); if (vv[i].size() != v.size()) diff --git a/src/doNormalParams.h b/src/doNormalParams.h index fbfc88ed..18d88fb4 100644 --- a/src/doNormalParams.h +++ b/src/doNormalParams.h @@ -17,6 +17,10 @@ public: variance() = _variance; } + doNormalParams(const doNormalParams& p) + : doDistribParams< EOT >( p ) + {} + EOT& mean(){return this->param(0);} EOT& variance(){return this->param(1);} }; diff --git a/src/doVectorBounds.h b/src/doVectorBounds.h index 65655c3c..8a0530db 100644 --- a/src/doVectorBounds.h +++ b/src/doVectorBounds.h @@ -17,6 +17,10 @@ public: max() = _max; } + doVectorBounds(const doVectorBounds& v) + : doDistribParams< EOT >( v ) + {} + EOT& min(){return this->param(0);} EOT& max(){return this->param(1);} }; From 84b1515a56715b8459fd8d875d8c38304652a001 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 23 Jul 2010 13:24:09 +0200 Subject: [PATCH 14/74] + TODO + doStats.cpp --- src/TODO | 2 + src/doStats.cpp | 192 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 194 insertions(+) create mode 100644 src/TODO create mode 100644 src/doStats.cpp diff --git a/src/TODO b/src/TODO new file mode 100644 index 00000000..13785cc8 --- /dev/null +++ b/src/TODO @@ -0,0 +1,2 @@ +* deplacer les ecritures pour gnuplot dans des classes type eoContinue (eoMonitor) +* integrer ACP diff --git a/src/doStats.cpp b/src/doStats.cpp new file mode 100644 index 00000000..80c9869f --- /dev/null +++ b/src/doStats.cpp @@ -0,0 +1,192 @@ +/* + * Copyright (C) 2005 Maarten Keijzer + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of version 2 of the GNU General Public License as + * published by the Free Software Foundation. + * + * 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 +#include + +#include +#include + +#include "doStats.h" + +doStats::doStats() + : _n(0) +{} + +void doStats::printOn(std::ostream& _os) const +{ + _os << "Not implemented yet! "; +} + +doMean::doMean() + : _mean(0) +{} + +void doMean::update(double v) +{ + _n++; + + double d = v - _mean; + + _mean += 1 / _n * d; +} + +double doMean::get_mean() const +{ + return _mean; +} + +void doMean::printOn(std::ostream& _os) const +{ + _os << get_mean(); +} + +doVar::doVar() + : _sumvar(0) +{} + +void doVar::update(double v) +{ + _n++; + + double d = v - _mean; + + _mean += 1 / _n * d; + _sumvar += (_n - 1) / _n * d * d; +} + +double doVar::get_var() const +{ + return _sumvar / (_n - 1); +} + +double doVar::get_std() const +{ + return ::sqrt( get_var() ); +} + +void doVar::printOn(std::ostream& _os) const +{ + _os << get_var(); +} + +doCov::doCov() + : _meana(0), _meanb(0), _sumcov(0) +{} + +void doCov::update(double a, double b) +{ + ++_n; + + double da = a - _meana; + double db = b - _meanb; + + _meana += 1 / _n * da; + _meanb += 1 / _n * db; + + _sumcov += (_n - 1) / _n * da * db; +} + +double doCov::get_meana() const +{ + return _meana; +} + +double doCov::get_meanb() const +{ + return _meanb; +} + +double doCov::get_cov() const +{ + return _sumcov / (_n - 1); +} + +void doCov::printOn(std::ostream& _os) const +{ + _os << get_cov(); +} + +doCovMatrix::doCovMatrix(unsigned dim) + : _mean(dim), _sumcov(dim, std::vector< double >( dim )) +{} + +void doCovMatrix::update(const std::vector& v) +{ + assert(v.size() == _mean.size()); + + _n++; + + for (unsigned int i = 0; i < v.size(); ++i) + { + double d = v[i] - _mean[i]; + + _mean[i] += 1 / _n * d; + _sumcov[i][i] += (_n - 1) / _n * d * d; + + for (unsigned j = i; j < v.size(); ++j) + { + double e = v[j] - _mean[j]; // _mean[j] is not updated yet + + double upd = (_n - 1) / _n * d * e; + + _sumcov[i][j] += upd; + _sumcov[j][i] += upd; + } + } +} + +double doCovMatrix::get_mean(int i) const +{ + return _mean[i]; +} + +double doCovMatrix::get_var(int i) const +{ + return _sumcov[i][i] / (_n - 1); +} + +double doCovMatrix::get_std(int i) const +{ + return ::sqrt( get_var(i) ); +} + +double doCovMatrix::get_cov(int i, int j) const +{ + return _sumcov[i][j] / (_n - 1); +} + +doHyperVolume::doHyperVolume() + : _hv(1) +{} + +void doHyperVolume::update(double v) +{ + _hv *= ::sqrt(v); + + assert( _hv <= std::numeric_limits< double >::max() ); +} + +double doHyperVolume::get_hypervolume() const +{ + return _hv; +} + +void doHyperVolume::printOn(std::ostream& _os) const +{ + _os << get_hypervolume(); +} From 78c68ebf3082e6e959248c7a46f583f74d196c08 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 23 Jul 2010 13:34:42 +0200 Subject: [PATCH 15/74] + added some useful files --- build_gcc_linux_debug | 7 +++++++ build_gcc_linux_release | 7 +++++++ distclean | 4 ++++ package_deb | 5 +++++ package_rpm | 5 +++++ 5 files changed, 28 insertions(+) create mode 100755 build_gcc_linux_debug create mode 100755 build_gcc_linux_release create mode 100755 distclean create mode 100755 package_deb create mode 100755 package_rpm diff --git a/build_gcc_linux_debug b/build_gcc_linux_debug new file mode 100755 index 00000000..da385fdb --- /dev/null +++ b/build_gcc_linux_debug @@ -0,0 +1,7 @@ +#!/usr/bin/env sh + +mkdir debug +cd debug +cmake -DCMAKE_BUILD_TYPE=Debug .. +make +cd .. diff --git a/build_gcc_linux_release b/build_gcc_linux_release new file mode 100755 index 00000000..78a66c55 --- /dev/null +++ b/build_gcc_linux_release @@ -0,0 +1,7 @@ +#!/usr/bin/env sh + +mkdir release +cd release +cmake .. +make +cd .. diff --git a/distclean b/distclean new file mode 100755 index 00000000..e4a02bc4 --- /dev/null +++ b/distclean @@ -0,0 +1,4 @@ +#!/usr/bin/env sh + +rm -rf debug +rm -rf release diff --git a/package_deb b/package_deb new file mode 100755 index 00000000..1a44d021 --- /dev/null +++ b/package_deb @@ -0,0 +1,5 @@ +#!/usr/bin/env sh + +cd release +cpack -G DEB +cd .. diff --git a/package_rpm b/package_rpm new file mode 100755 index 00000000..8d46b7d0 --- /dev/null +++ b/package_rpm @@ -0,0 +1,5 @@ +#!/usr/bin/env sh + +cd release +cpack -G RPM +cd .. From f66efcba04a67006b8aa97c640967307e41e6984 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Thu, 29 Jul 2010 11:22:10 +0200 Subject: [PATCH 16/74] * doc installable --- doc/CMakeLists.txt | 9 + doc/doxyfile.cmake | 1413 +++++++++++++++++++++++++++++++++++++++-- src/do | 1 - src/doCMASA.h | 8 +- src/doDistribParams.h | 44 -- src/doNormalParams.h | 27 +- src/doStats.h | 5 + src/doVectorBounds.h | 28 +- 8 files changed, 1421 insertions(+), 114 deletions(-) delete mode 100644 src/doDistribParams.h diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index c44ffc47..056f3f2f 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -19,6 +19,15 @@ IF (DOXYGEN_FOUND) "${CMAKE_CURRENT_SOURCE_DIR}/${DOC_CONFIG_FILE}.cmake" "${CMAKE_CURRENT_BINARY_DIR}/${DOC_CONFIG_FILE}" ) + + INSTALL( + DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + DESTINATION share/do COMPONENT libraries + PATTERN "CMakeFiles" EXCLUDE + PATTERN "cmake_install.cmake" EXCLUDE + PATTERN "Makefile" EXCLUDE + PATTERN "doxyfile" EXCLUDE + ) ELSE (DOXYGEN_FOUND) MESSAGE(STATUS "Unable to generate the documentation, Doxygen package not found") ENDIF (DOXYGEN_FOUND) diff --git a/doc/doxyfile.cmake b/doc/doxyfile.cmake index e19b4f28..1d610acc 100644 --- a/doc/doxyfile.cmake +++ b/doc/doxyfile.cmake @@ -1,15 +1,91 @@ -# Doxyfile 1.5.1 +# Doxyfile 1.6.3 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + PROJECT_NAME = @PACKAGE_NAME@ + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + PROJECT_NUMBER = @PACKAGE_VERSION@ + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + OUTPUT_DIRECTORY = @CMAKE_BINARY_DIR@/doc + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + ABBREVIATE_BRIEF = "The $name class" \ "The $name widget" \ "The $name file" \ @@ -21,209 +97,1468 @@ ABBREVIATE_BRIEF = "The $name class" \ a \ an \ the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + FULL_PATH_NAMES = NO + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + STRIP_FROM_PATH = @CMAKE_SOURCE_DIR@ -STRIP_FROM_INC_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + JAVADOC_AUTOBRIEF = YES + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + MULTILINE_CPP_IS_BRIEF = NO -#DETAILS_AT_TOP = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + TAB_SIZE = 8 -ALIASES = + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + HIDE_UNDOC_MEMBERS = YES + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + HIDE_UNDOC_CLASSES = YES + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + SHOW_INCLUDE_FILES = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + SORT_MEMBER_DOCS = NO + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + GENERATE_DEPRECATEDLIST= YES -ENABLED_SECTIONS = + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + SHOW_DIRECTORIES = NO -FILE_VERSION_FILTER = + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + QUIET = YES + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + WARNINGS = NO + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + WARN_IF_UNDOCUMENTED = NO + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + WARN_FORMAT = "$file:$line: $text" -WARN_LOGFILE = + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + INPUT = @CMAKE_SOURCE_DIR@ -FILE_PATTERNS = *.cpp \ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = *.cpp \ *.h \ - NEWS README + NEWS \ + README + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + RECURSIVE = YES -EXCLUDE = + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = @CMAKE_BINARY_DIR@ + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + EXCLUDE_PATTERNS = -EXAMPLE_PATH = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + EXAMPLE_RECURSIVE = NO -IMAGE_PATH = -INPUT_FILTER = -FILTER_PATTERNS = + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + FILTER_SOURCE_FILES = NO + #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + VERBATIM_HEADERS = YES + #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + COLS_IN_ALPHA_INDEX = 3 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + IGNORE_PREFIX = moeo + #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + HTML_FILE_EXTENSION = .html -HTML_HEADER = -HTML_FOOTER = -HTML_STYLESHEET = + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = YES + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + GENERATE_HTMLHELP = NO -CHM_FILE = -HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + GENERATE_TREEVIEW = YES + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be implemented using a PHP enabled web server instead of at the web client using Javascript. Doxygen will generate the search PHP script and index +# file to put on the web server. The advantage of the server based approach is that it scales better to large projects and allows full text search. The disadvances is that it is more difficult to setup +# and does not have live searching capabilities. + +SERVER_BASED_SEARCH = NO + #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + GENERATE_LATEX = YES + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + PAPER_TYPE = a4wide -EXTRA_PACKAGES = -LATEX_HEADER = + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + PDF_HYPERLINKS = NO + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + USE_PDFLATEX = NO + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + RTF_HYPERLINKS = NO -RTF_STYLESHEET_FILE = -RTF_EXTENSIONS_FILE = + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + GENERATE_MAN = YES + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + MAN_LINKS = NO + #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + XML_OUTPUT = xml -XML_SCHEMA = -XML_DTD = + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + XML_PROGRAMLISTING = YES + #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + GENERATE_AUTOGEN_DEF = NO + #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + PERLMOD_PRETTY = YES -PERLMOD_MAKEVAR_PREFIX = + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + #--------------------------------------------------------------------------- -# Configuration options related to the preprocessor +# Configuration options related to the preprocessor #--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + SEARCH_INCLUDES = YES -INCLUDE_PATH = -INCLUDE_FILE_PATTERNS = -PREDEFINED = -EXPAND_AS_DEFINED = + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + SKIP_FUNCTION_MACROS = YES + #--------------------------------------------------------------------------- -# Configuration::additions related to external references +# Configuration::additions related to external references #--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + #--------------------------------------------------------------------------- -# Configuration options related to the dot tool +# Configuration options related to the dot tool #--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + HAVE_DOT = NO + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + DOT_IMAGE_FORMAT = png -DOT_PATH = -DOTFILE_DIRS = + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + DOT_CLEANUP = YES -#--------------------------------------------------------------------------- -# Configuration::additions related to the search engine -#--------------------------------------------------------------------------- -SEARCHENGINE = YES diff --git a/src/do b/src/do index 30289578..478a3f21 100644 --- a/src/do +++ b/src/do @@ -22,7 +22,6 @@ #include "doSamplerUniform.h" #include "doSamplerNormal.h" -#include "doDistribParams.h" #include "doVectorBounds.h" #include "doNormalParams.h" diff --git a/src/doCMASA.h b/src/doCMASA.h index aa8f5692..1e28b783 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -140,7 +140,7 @@ public: //------------------------------------------------------------- - // Temporary solution to store bounds valeur for each distribution. + // Temporary solution to store bounds values for each distribution. //------------------------------------------------------------- std::string bounds_results_destination("ResBounds"); @@ -151,7 +151,7 @@ public: ::system(ss.str().c_str()); } - ::mkdir(bounds_results_destination.c_str(), 0755); // create a first time the + ::mkdir(bounds_results_destination.c_str(), 0755); // create once directory //------------------------------------------------------------- @@ -283,8 +283,8 @@ public: std::ofstream ofs(ss.str().c_str()); ofs << size << " "; - std::copy(distrib.param(0).begin(), distrib.param(0).end(), std::ostream_iterator< double >(ofs, " ")); - std::copy(distrib.param(1).begin(), distrib.param(1).end(), std::ostream_iterator< double >(ofs, " ")); + std::copy(distrib.mean().begin(), distrib.mean().end(), std::ostream_iterator< double >(ofs, " ")); + std::copy(distrib.variance().begin(), distrib.variance().end(), std::ostream_iterator< double >(ofs, " ")); ofs << std::endl; } diff --git a/src/doDistribParams.h b/src/doDistribParams.h deleted file mode 100644 index ef07c151..00000000 --- a/src/doDistribParams.h +++ /dev/null @@ -1,44 +0,0 @@ -#ifndef _doDistribParams_h -#define _doDistribParams_h - -#include - -template < typename EOT > -class doDistribParams -{ -public: - doDistribParams(unsigned n = 2) - : _params(n) - {} - - doDistribParams(const doDistribParams& p) { *this = p; } - - doDistribParams& operator=(const doDistribParams& p) - { - if (this != &p) - { - this->_params = p._params; - } - - return *this; - } - - EOT& param(unsigned int i = 0){return _params[i];} - - unsigned int param_size(){return _params.size();} - - unsigned int size() - { - for (unsigned int i = 0, size = param_size(); i < size - 1; ++i) - { - assert(param(i).size() == param(i + 1).size()); - } - - return param(0).size(); - } - -private: - std::vector< EOT > _params; -}; - -#endif // !_doDistribParams_h diff --git a/src/doNormalParams.h b/src/doNormalParams.h index 18d88fb4..87a3a65a 100644 --- a/src/doNormalParams.h +++ b/src/doNormalParams.h @@ -1,28 +1,29 @@ #ifndef _doNormalParams_h #define _doNormalParams_h -#include "doDistribParams.h" - template < typename EOT > -class doNormalParams : public doDistribParams< EOT > +class doNormalParams { public: - doNormalParams(EOT _mean, EOT _variance) - : doDistribParams< EOT >(2) + doNormalParams(EOT mean, EOT variance) + : _mean(mean), _variance(variance) { assert(_mean.size() > 0); assert(_mean.size() == _variance.size()); - - mean() = _mean; - variance() = _variance; } - doNormalParams(const doNormalParams& p) - : doDistribParams< EOT >( p ) - {} + EOT& mean(){return _mean;} + EOT& variance(){return _variance;} - EOT& mean(){return this->param(0);} - EOT& variance(){return this->param(1);} + unsigned int size() + { + assert(_mean.size() == _variance.size()); + return _mean.size(); + } + +private: + EOT _mean; + EOT _variance; }; #endif // !_doNormalParams_h diff --git a/src/doStats.h b/src/doStats.h index 27a4b9c4..94756fa3 100644 --- a/src/doStats.h +++ b/src/doStats.h @@ -110,4 +110,9 @@ protected: double _hv; }; +class doCholesky : public doStats +{ + +}; + #endif // !_doStats_h diff --git a/src/doVectorBounds.h b/src/doVectorBounds.h index 8a0530db..07e4e2cf 100644 --- a/src/doVectorBounds.h +++ b/src/doVectorBounds.h @@ -1,28 +1,30 @@ #ifndef _doVectorBounds_h #define _doVectorBounds_h -#include "doDistribParams.h" - template < typename EOT > -class doVectorBounds : public doDistribParams< EOT > +class doVectorBounds { public: - doVectorBounds(EOT _min, EOT _max) - : doDistribParams< EOT >(2) + doVectorBounds(EOT min, EOT max) + : _min(min), _max(max) { assert(_min.size() > 0); assert(_min.size() == _max.size()); - - min() = _min; - max() = _max; } - doVectorBounds(const doVectorBounds& v) - : doDistribParams< EOT >( v ) - {} + EOT& min(){return _min;} + EOT& max(){return _max;} - EOT& min(){return this->param(0);} - EOT& max(){return this->param(1);} + + unsigned int size() + { + assert(_min.size() == _max.size()); + return _min.size(); + } + +private: + EOT _min; + EOT _max; }; #endif // !_doVectorBounds_h From 8d18acb81d0f87d7402c6ae79a7e48607e6d56d1 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 3 Aug 2010 10:26:15 +0200 Subject: [PATCH 17/74] + some useful files added --- application/cma_sa/main.cpp | 36 +- application/cma_sa/plot.py | 0 build_gcc_linux_debug | 7 + build_gcc_linux_release | 7 + copying | 1 + distclean | 4 + doc/CMakeLists.txt | 9 + doc/doxyfile.cmake | 1413 ++++++++++++++++++++++++++++++++++- matrix.hpp | 560 ++++++++++++++ package_deb | 5 + package_rpm | 5 + readme | 57 ++ src/do | 1 - src/doCMASA.h | 115 +-- src/doNormalParams.h | 27 +- src/doStats.h | 5 + src/doVectorBounds.h | 28 +- src/todo | 2 + 18 files changed, 2149 insertions(+), 133 deletions(-) mode change 100755 => 100644 application/cma_sa/plot.py create mode 100644 build_gcc_linux_debug create mode 100644 build_gcc_linux_release create mode 100644 copying create mode 100644 distclean create mode 100644 matrix.hpp create mode 100644 package_deb create mode 100644 package_rpm create mode 100644 readme create mode 100644 src/todo diff --git a/application/cma_sa/main.cpp b/application/cma_sa/main.cpp index f0864a68..872636e7 100644 --- a/application/cma_sa/main.cpp +++ b/application/cma_sa/main.cpp @@ -52,7 +52,8 @@ int main(int ac, char** av) eoEvalFunc< EOT >* plainEval = new Sphere< EOT >(); state.storeFunctor(plainEval); - eoEvalFuncCounter< EOT > eval(*plainEval); + unsigned long max_eval = parser.getORcreateParam((unsigned long)0, "maxEval", "Maximum number of evaluations (0 = none)", 'E', "Stopping criterion").value(); // E + eoEvalFuncCounter< EOT > eval(*plainEval, max_eval); eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5); //eoRndGenerator< double >* gen = new eoNormalGenerator< double >(0, 1); @@ -122,31 +123,20 @@ int main(int ac, char** av) eoCheckPoint< EOT >& checkpoint = do_make_checkpoint(parser, state, eval, monitoring_continue); - // appends some missing code to checkpoint + // eoPopStat< EOT >* popStat = new eoPopStat; + // state.storeFunctor(popStat); - // eoValueParam& plotPopParam = parser.createParam(false, "plotPop", "Plot sorted pop. every gen.", 0, "Graphical Output"); + // checkpoint.add(*popStat); - // if (plotPopParam.value()) // we do want plot dump - // { - // eoScalarFitnessStat* fitStat = new eoScalarFitnessStat; - // state.storeFunctor(fitStat); + // eoGnuplot1DMonitor* gnuplot = new eoGnuplot1DMonitor("gnuplot.txt"); + // state.storeFunctor(gnuplot); - // checkpoint.add(*fitStat); + // gnuplot->add(eval); + // gnuplot->add(*popStat); - // eoFileSnapshot* snapshot = new eoFileSnapshot("ResPop"); - // state.storeFunctor(snapshot); + //gnuplot->gnuplotCommand("set yrange [0:500]"); - // snapshot->add(*fitStat); - - // checkpoint.add(*snapshot); - // } - - // -------------------------- - - eoPopStat< EOT >* popStat = new eoPopStat; - state.storeFunctor(popStat); - - checkpoint.add(*popStat); + // checkpoint.add(*gnuplot); // eoMonitor* fileSnapshot = new doFileSnapshot< std::vector< std::string > >("ResPop"); // state.storeFunctor(fileSnapshot); @@ -206,6 +196,10 @@ int main(int ac, char** av) { do_run(*algo, pop); } + catch (eoReachedThresholdException& e) + { + eo::log << eo::warnings << e.what() << std::endl; + } catch (std::exception& e) { eo::log << eo::errors << "exception: " << e.what() << std::endl; diff --git a/application/cma_sa/plot.py b/application/cma_sa/plot.py old mode 100755 new mode 100644 diff --git a/build_gcc_linux_debug b/build_gcc_linux_debug new file mode 100644 index 00000000..da385fdb --- /dev/null +++ b/build_gcc_linux_debug @@ -0,0 +1,7 @@ +#!/usr/bin/env sh + +mkdir debug +cd debug +cmake -DCMAKE_BUILD_TYPE=Debug .. +make +cd .. diff --git a/build_gcc_linux_release b/build_gcc_linux_release new file mode 100644 index 00000000..78a66c55 --- /dev/null +++ b/build_gcc_linux_release @@ -0,0 +1,7 @@ +#!/usr/bin/env sh + +mkdir release +cd release +cmake .. +make +cd .. diff --git a/copying b/copying new file mode 100644 index 00000000..90cbe47b --- /dev/null +++ b/copying @@ -0,0 +1 @@ +Private license diff --git a/distclean b/distclean new file mode 100644 index 00000000..e4a02bc4 --- /dev/null +++ b/distclean @@ -0,0 +1,4 @@ +#!/usr/bin/env sh + +rm -rf debug +rm -rf release diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index c44ffc47..056f3f2f 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -19,6 +19,15 @@ IF (DOXYGEN_FOUND) "${CMAKE_CURRENT_SOURCE_DIR}/${DOC_CONFIG_FILE}.cmake" "${CMAKE_CURRENT_BINARY_DIR}/${DOC_CONFIG_FILE}" ) + + INSTALL( + DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + DESTINATION share/do COMPONENT libraries + PATTERN "CMakeFiles" EXCLUDE + PATTERN "cmake_install.cmake" EXCLUDE + PATTERN "Makefile" EXCLUDE + PATTERN "doxyfile" EXCLUDE + ) ELSE (DOXYGEN_FOUND) MESSAGE(STATUS "Unable to generate the documentation, Doxygen package not found") ENDIF (DOXYGEN_FOUND) diff --git a/doc/doxyfile.cmake b/doc/doxyfile.cmake index e19b4f28..1d610acc 100644 --- a/doc/doxyfile.cmake +++ b/doc/doxyfile.cmake @@ -1,15 +1,91 @@ -# Doxyfile 1.5.1 +# Doxyfile 1.6.3 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + PROJECT_NAME = @PACKAGE_NAME@ + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + PROJECT_NUMBER = @PACKAGE_VERSION@ + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + OUTPUT_DIRECTORY = @CMAKE_BINARY_DIR@/doc + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + ABBREVIATE_BRIEF = "The $name class" \ "The $name widget" \ "The $name file" \ @@ -21,209 +97,1468 @@ ABBREVIATE_BRIEF = "The $name class" \ a \ an \ the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + FULL_PATH_NAMES = NO + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + STRIP_FROM_PATH = @CMAKE_SOURCE_DIR@ -STRIP_FROM_INC_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + JAVADOC_AUTOBRIEF = YES + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + MULTILINE_CPP_IS_BRIEF = NO -#DETAILS_AT_TOP = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + TAB_SIZE = 8 -ALIASES = + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + HIDE_UNDOC_MEMBERS = YES + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + HIDE_UNDOC_CLASSES = YES + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + SHOW_INCLUDE_FILES = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + SORT_MEMBER_DOCS = NO + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + GENERATE_DEPRECATEDLIST= YES -ENABLED_SECTIONS = + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + SHOW_DIRECTORIES = NO -FILE_VERSION_FILTER = + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + QUIET = YES + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + WARNINGS = NO + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + WARN_IF_UNDOCUMENTED = NO + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + WARN_FORMAT = "$file:$line: $text" -WARN_LOGFILE = + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + INPUT = @CMAKE_SOURCE_DIR@ -FILE_PATTERNS = *.cpp \ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = *.cpp \ *.h \ - NEWS README + NEWS \ + README + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + RECURSIVE = YES -EXCLUDE = + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = @CMAKE_BINARY_DIR@ + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + EXCLUDE_PATTERNS = -EXAMPLE_PATH = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + EXAMPLE_RECURSIVE = NO -IMAGE_PATH = -INPUT_FILTER = -FILTER_PATTERNS = + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + FILTER_SOURCE_FILES = NO + #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + VERBATIM_HEADERS = YES + #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + COLS_IN_ALPHA_INDEX = 3 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + IGNORE_PREFIX = moeo + #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + HTML_FILE_EXTENSION = .html -HTML_HEADER = -HTML_FOOTER = -HTML_STYLESHEET = + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = YES + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + GENERATE_HTMLHELP = NO -CHM_FILE = -HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + GENERATE_TREEVIEW = YES + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be implemented using a PHP enabled web server instead of at the web client using Javascript. Doxygen will generate the search PHP script and index +# file to put on the web server. The advantage of the server based approach is that it scales better to large projects and allows full text search. The disadvances is that it is more difficult to setup +# and does not have live searching capabilities. + +SERVER_BASED_SEARCH = NO + #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + GENERATE_LATEX = YES + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + PAPER_TYPE = a4wide -EXTRA_PACKAGES = -LATEX_HEADER = + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + PDF_HYPERLINKS = NO + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + USE_PDFLATEX = NO + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + RTF_HYPERLINKS = NO -RTF_STYLESHEET_FILE = -RTF_EXTENSIONS_FILE = + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + GENERATE_MAN = YES + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + MAN_LINKS = NO + #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + XML_OUTPUT = xml -XML_SCHEMA = -XML_DTD = + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + XML_PROGRAMLISTING = YES + #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + GENERATE_AUTOGEN_DEF = NO + #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + PERLMOD_PRETTY = YES -PERLMOD_MAKEVAR_PREFIX = + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + #--------------------------------------------------------------------------- -# Configuration options related to the preprocessor +# Configuration options related to the preprocessor #--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + SEARCH_INCLUDES = YES -INCLUDE_PATH = -INCLUDE_FILE_PATTERNS = -PREDEFINED = -EXPAND_AS_DEFINED = + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + SKIP_FUNCTION_MACROS = YES + #--------------------------------------------------------------------------- -# Configuration::additions related to external references +# Configuration::additions related to external references #--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + #--------------------------------------------------------------------------- -# Configuration options related to the dot tool +# Configuration options related to the dot tool #--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + HAVE_DOT = NO + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. 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This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + DOT_CLEANUP = YES -#--------------------------------------------------------------------------- -# Configuration::additions related to the search engine -#--------------------------------------------------------------------------- -SEARCHENGINE = YES diff --git a/matrix.hpp b/matrix.hpp new file mode 100644 index 00000000..89b77d85 --- /dev/null +++ b/matrix.hpp @@ -0,0 +1,560 @@ +/*************************************************************************** + * $Id: matrix.hpp,v 1.11 2006/05/13 10:05:53 nojhan Exp $ + * Copyright : Free Software Foundation + * Author : Johann Dréo + ****************************************************************************/ + +/* + * This program 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 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 Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser 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 MATRIX +#define MATRIX + +#include +#include + +#include "Exception_oMetah.hpp" + +using namespace std; + +namespace ometah { + +//! Test if a vector is comprised in bounds +template +bool isInBounds( T aVector, T mins, T maxs) +{ + unsigned int i; + for(i=0; i maxs[i] ){ + return false; + } + } + return true; +} + + +//! Force a vector to be in bounds +template +T forceBounds( T aVector, T mins, T maxs) +{ + T CastedVector=aVector; + + unsigned int i; + for(i=0; i maxs[i] ){ + CastedVector[i]=maxs[i]; + } + } + return CastedVector; +} + +//! Create a 2D matrix filled with values +/* + if we want a vector > : + T stand for double + V stand for vector > +*/ +template +U matrixFilled( unsigned int dimL, unsigned int dimC, T fillValue ) +{ + unsigned int i; + + // make the vector possible at this step + typename U::value_type vec(dimC, fillValue); + + U mat; + for(i=0; i +vector > matrixFilled( unsigned int dimL, unsigned int dimC, T fillValue ) +{ + unsigned int i; + + // make the vector possible at this step + vector< T > vec(dimC, fillValue); + + vector > mat; + for(i=0; i +T multiply( T matA, T matB) +{ + + T newMat; + + unsigned int Al=matA.size(); + unsigned int Ac=matA[0].size(); + unsigned int Bl=matB.size(); + unsigned int Bc=matB[0].size(); + + newMat=matrixFilled( Al,Bc,0.0); + + if(Ac!=Bl) { + throw Exception_Size_Match("Cannot multiply matrices, sizes does not match", EXCEPTION_INFOS ); + } + + for( unsigned int i=0; i +U multiply(U aVector, T aNb) +{ + U res; + + res.reserve( aVector.size() ); + + unsigned int i; + for(i=0; i +T cholesky( T A) +{ + + // FIXME : vérifier que A est symétrique définie positive + + T B; + unsigned int Al=A.size(); + unsigned int Ac=A[0].size(); + B = matrixFilled(Al, Ac, 0.0); + + unsigned int i,j,k; + + // first column + i=0; + + // diagonal + j=0; + B[0][0]=sqrt(A[0][0]); + + // end of the column + for(j=1;j +T transpose( T &mat) +{ + unsigned int iSize=mat.size(); + unsigned int jSize=mat[0].size(); + + if ( iSize == 0 || jSize == 0 ) { + ostringstream msg; + msg << "ErrorSize: matrix not defined " + << "(iSize:" << iSize << ", jSize:" << jSize << ")"; + throw Exception_Size( msg.str(), EXCEPTION_INFOS ); + } + + typename T::value_type aVector; + T newMat; + + unsigned int i, j; + + for (j=0; j +vector mean( vector > mat) +{ + vector moyDim; + moyDim.reserve(mat.size()); + + unsigned int i,a; + a=mat.size(); + + for(i=0;i +T mean( vector aVector, unsigned int begin=0, unsigned int during=0) +{ + if (during==0) { + during = aVector.size() - begin; // if no end : take all + } + + T aSum, aMean; + + aSum = sum(aVector, begin, during); // Sum + aMean = aSum / (during - begin); // Mean + + return aMean; +} + +//! Calculate a variance-covariance matrix from a list of vector +/*! + For a population of p points on n dimensions : + if onRow==true, the matrix should have p rows and n columns. + if onRow==false, the matrix should have n rows and p columns. +*/ +template +U varianceCovariance( U pop, bool onRow = true) +{ +/* + // vector of means + typename U::value_type vecMeanCentered; + if(onRow) { + vecMeanCentered = mean( transpose(pop) ); // p rows and n columns => means of p + } else { + vecMeanCentered = mean( pop ); // n rows and p columns => means of n + } + + // centered population + // same size as the initial matrix + U popMeanCentered = matrixFilled(pop.size(),pop[0].size(), 0.0); + + // centering + // rows + for(unsigned int i=0;i covariance of p + } else { + popVar = multiply( popMeanCentered, popMeanCenteredT ); // if n rows and p columns => covariance of n + } + + // multiplication by 1/n : + for(unsigned int i=0;i +T sum(vector aVector, unsigned int begin=0, unsigned int during=0) +{ + if ( begin > aVector.size() || during > aVector.size() ) { + ostringstream msg; + msg << "ErrorSize: parameters are out of vector bounds " + << "(begin:" << begin << ", during:" << during + << ", size:" << aVector.size() << ")"; + throw Exception_Size_Index( msg.str(), EXCEPTION_INFOS ); + } + + if (during==0) { + during = aVector.size() - begin; + } + + T aSum=0; + + for (unsigned int j=begin; j +T stdev(vector aVector, unsigned int begin=0, unsigned int during=0) +{ + if ( begin > aVector.size() || during > aVector.size() ) { + ostringstream msg; + msg << "ErrorSize: parameters are out of vector bounds " + << "(begin:" << begin << ", during:" << during + << ", size:" << aVector.size() << ")"; + throw Exception_Size_Index( msg.str(), EXCEPTION_INFOS ); + } + + if (during==0) { + during = aVector.size() - begin; + } + + vector deviation; + T aMean, aDev, aStd; + + aMean = mean(aVector, begin, during); // mean + + for (unsigned int j=begin; j +typename T::value_type min(T aVector, unsigned int begin=0, unsigned int during=0) +{ + if ( begin > aVector.size() || during > aVector.size() ) { + ostringstream msg; + msg << "ErrorSize: parameters are out of vector bounds " + << "(begin:" << begin << ", during:" << during + << ", size:" << aVector.size() << ")"; + throw Exception_Size_Index( msg.str(), EXCEPTION_INFOS ); + } + + if (during==0) { + during = aVector.size() - begin; + } + + typename T::value_type aMin = aVector[begin]; + + for (unsigned int i=begin+1; i +vector mins(vector > aMatrix) +{ + vector mins; + + for( unsigned int i=0; i < aMatrix.size(); i++ ) { + mins.push_back( min(aMatrix[i]) ); + } + + return mins; +} + +//! Find the maximums values of a matrix, for each row +template +vector maxs(vector > aMatrix) +{ + vector maxs; + + for( unsigned int i=0; i < aMatrix.size(); i++ ) { + maxs.push_back( max(aMatrix[i]) ); + } + + return maxs; +} + +//! Find the maximum value of a vector +template +typename T::value_type max(T aVector, unsigned int begin=0, unsigned int during=0) +{ + if ( begin > aVector.size() || during > aVector.size() ) { + ostringstream msg; + msg << "ErrorSize: parameters are out of vector bounds " + << "(begin:" << begin << ", during:" << during + << ", size:" << aVector.size() << ")"; + throw Exception_Size_Index( msg.str(), EXCEPTION_INFOS ); + } + + if (during==0) { + during = aVector.size() - begin; + } + + typename T::value_type aMax = aVector[begin]; + + for (unsigned int i=begin+1; i aMax ) { + aMax = aVector[i]; + } + } + + return aMax; +} + +//! Substraction of two vectors, terms by terms +template +T substraction(T from, T that) +{ + T res; + + res.reserve(from.size()); + + for(unsigned int i=0; i +T addition(T from, T that) +{ + T res; + + res.reserve( from.size() ); + + for(unsigned int i=0; i +T absolute(T aVector) +{ + for(unsigned int i=0; i +vector gravityCenter( vector > points, vector weights ) +{ + + // if we have only one weight, we use it for all items + if ( weights.size() == 1 ) { + for ( unsigned int i=1; i < points.size(); i++ ) { + weights.push_back( weights[0] ); + } + } + + // if sizes does not match : error + if ( points.size() != weights.size() ) { + ostringstream msg; + msg << "ErrorSize: " + << "points size (" << points.size() << ")" + << " does not match weights size (" << weights.size() << ")"; + throw Exception_Size_Match( msg.str(), EXCEPTION_INFOS ); + } + + T weightsSum = sum(weights); + + vector > pointsT = transpose( points ); + + vector gravity; + + for ( unsigned int i=0; i < pointsT.size(); i++ ) { // dimensions + T g = 0; + for ( unsigned int j=0; j < pointsT[i].size(); j++ ) { // points + g += ( pointsT[i][j] * weights[j] ) / weightsSum; + } + gravity.push_back( g ); + } + + return gravity; +} + +} // ometah + +#endif // MATRIX diff --git a/package_deb b/package_deb new file mode 100644 index 00000000..1a44d021 --- /dev/null +++ b/package_deb @@ -0,0 +1,5 @@ +#!/usr/bin/env sh + +cd release +cpack -G DEB +cd .. diff --git a/package_rpm b/package_rpm new file mode 100644 index 00000000..8d46b7d0 --- /dev/null +++ b/package_rpm @@ -0,0 +1,5 @@ +#!/usr/bin/env sh + +cd release +cpack -G RPM +cd .. diff --git a/readme b/readme new file mode 100644 index 00000000..64629f58 --- /dev/null +++ b/readme @@ -0,0 +1,57 @@ +This package contains the source code for BOPO problems. + +# Step 1 - Configuration +------------------------ +Rename the "install.cmake-dist" file as "install.cmake" and edit it, inserting the FULL PATH +to your ParadisEO distribution. +On Windows write your path with double antislash (ex: C:\\Users\\...) + + +# Step 2 - Build process +------------------------ +ParadisEO is assumed to be compiled. To download ParadisEO, please visit http://paradiseo.gforge.inria.fr/. +Go to the BOPO/build/ directory and lunch cmake: +(Unix) > cmake .. +(Windows) > cmake .. -G"Visual Studio 9 2008" + +Note for windows users: if you don't use VisualStudio 9, enter the name of your generator instead of "VisualStudio 9 2008". + + +# Step 3 - Compilation +---------------------- +In the bopo/build/ directory: +(Unix) > make +(Windows) Open the VisualStudio solution and compile it, compile also the target install. +You can refer to this tutorial if you don't know how to compile a solution: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial + + +# Step 4 - Execution +--------------------- +A toy example is given to test the components. You can run these tests as following. +To define problem-related components for your own problem, please refer to the tutorials available on the website : http://paradiseo.gforge.inria.fr/. +In the bopo/build/ directory: +(Unix) > ctest +Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial + +In the directory "application", there are several directory such as p_eoco which instantiate NSGAII on BOPO problems. + +(Unix) After compilation you can run the script "bopo/run.sh" and see results in "NSGAII.out". Parameters can be modified in the script. + +(Windows) Add argument "NSGAII.param" and execute the corresponding algorithms. +Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial + + +# Documentation +--------------- +The API-documentation is available in doc/html/index.html + + +# Things to keep in mind when using BOPO +---------------------------------------- +* By default, the EO random generator's seed is initialized by the number of seconds since the epoch (with time(0)). It is available in the status file dumped at each execution. Please, keep in mind that if you start two run at the same second without modifying the seed, you will get exactly the same results. + +* Execution times are measured with the boost:timer, that measure wallclock time. Additionaly, it could not measure times larger than approximatively 596.5 hours (or even less). See http://www.boost.org/doc/libs/1_33_1/libs/timer/timer.htm + +* The q-quantile computation use averaging at discontinuities (in R, it correspond to the R-2 method, in SAS, SAS-5). For more explanations, see http://en.wikipedia.org/wiki/Quantile#Estimating_the_quantiles_of_a_population and http://stat.ethz.ch/R-manual/R-devel/library/stats/html/quantile.html + +* You can send a SIGUSR1 to a process to get some information (written down in the log file) on the current state of the search. diff --git a/src/do b/src/do index 30289578..478a3f21 100644 --- a/src/do +++ b/src/do @@ -22,7 +22,6 @@ #include "doSamplerUniform.h" #include "doSamplerNormal.h" -#include "doDistribParams.h" #include "doVectorBounds.h" #include "doNormalParams.h" diff --git a/src/doCMASA.h b/src/doCMASA.h index aa8f5692..c2a3cf8e 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -86,8 +86,48 @@ public: _continuator(continuator), _cooling_schedule(cooling_schedule), _initial_temperature(initial_temperature), - _replacor(replacor) - {} + _replacor(replacor), + + _pop_results_destination("ResPop"), + + // directory where populations state are going to be stored. + _ofs_params("ResParams.txt"), + _ofs_params_var("ResVars.txt"), + + _bounds_results_destination("ResBounds") + { + + //------------------------------------------------------------- + // Temporary solution to store populations state at each + // iteration for plotting. + //------------------------------------------------------------- + + { + std::stringstream ss; + ss << "rm -rf " << _pop_results_destination; + ::system(ss.str().c_str()); + } + + ::mkdir(_pop_results_destination.c_str(), 0755); // create a first time the + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Temporary solution to store bounds values for each distribution. + //------------------------------------------------------------- + + { + std::stringstream ss; + ss << "rm -rf " << _bounds_results_destination; + ::system(ss.str().c_str()); + } + + ::mkdir(_bounds_results_destination.c_str(), 0755); // create once directory + + //------------------------------------------------------------- + + } //! function that launches the CMASA algorithm. /*! @@ -118,44 +158,6 @@ public: //------------------------------------------------------------- - //------------------------------------------------------------- - // Temporary solution to store populations state at each - // iteration for plotting. - //------------------------------------------------------------- - - std::string pop_results_destination("ResPop"); - - { - std::stringstream ss; - ss << "rm -rf " << pop_results_destination; - ::system(ss.str().c_str()); - } - - ::mkdir(pop_results_destination.c_str(), 0755); // create a first time the - // directory where populations state are going to be stored. - std::ofstream ofs_params("ResParams.txt"); - std::ofstream ofs_params_var("ResVars.txt"); - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // Temporary solution to store bounds valeur for each distribution. - //------------------------------------------------------------- - - std::string bounds_results_destination("ResBounds"); - - { - std::stringstream ss; - ss << "rm -rf " << bounds_results_destination; - ::system(ss.str().c_str()); - } - - ::mkdir(bounds_results_destination.c_str(), 0755); // create a first time the - - //------------------------------------------------------------- - - { D distrib = _estimator(pop); @@ -169,7 +171,7 @@ public: hv.update( distrib.variance()[i] ); } - ofs_params_var << hv << std::endl; + _ofs_params_var << hv << std::endl; } do @@ -260,7 +262,7 @@ public: { std::stringstream ss; - ss << pop_results_destination << "/" << number_of_iterations; + ss << _pop_results_destination << "/" << number_of_iterations; std::ofstream ofs(ss.str().c_str()); ofs << current_pop; } @@ -279,12 +281,12 @@ public: assert(size > 0); std::stringstream ss; - ss << bounds_results_destination << "/" << number_of_iterations; + ss << _bounds_results_destination << "/" << number_of_iterations; std::ofstream ofs(ss.str().c_str()); ofs << size << " "; - std::copy(distrib.param(0).begin(), distrib.param(0).end(), std::ostream_iterator< double >(ofs, " ")); - std::copy(distrib.param(1).begin(), distrib.param(1).end(), std::ostream_iterator< double >(ofs, " ")); + std::copy(distrib.mean().begin(), distrib.mean().end(), std::ostream_iterator< double >(ofs, " ")); + std::copy(distrib.variance().begin(), distrib.variance().end(), std::ostream_iterator< double >(ofs, " ")); ofs << std::endl; } @@ -337,7 +339,7 @@ public: hv.update( distrib.variance()[i] ); } - ofs_params_var << hv << std::endl; + _ofs_params_var << hv << std::endl; } //------------------------------------------------------------- @@ -383,6 +385,27 @@ private: //! A EOT replacor eoReplacement < EOT > & _replacor; + + + //------------------------------------------------------------- + // Temporary solution to store populations state at each + // iteration for plotting. + //------------------------------------------------------------- + + std::string _pop_results_destination; + std::ofstream _ofs_params; + std::ofstream _ofs_params_var; + + //------------------------------------------------------------- + + //------------------------------------------------------------- + // Temporary solution to store bounds values for each distribution. + //------------------------------------------------------------- + + std::string _bounds_results_destination; + + //------------------------------------------------------------- + }; #endif // !_doCMASA_h diff --git a/src/doNormalParams.h b/src/doNormalParams.h index 18d88fb4..87a3a65a 100644 --- a/src/doNormalParams.h +++ b/src/doNormalParams.h @@ -1,28 +1,29 @@ #ifndef _doNormalParams_h #define _doNormalParams_h -#include "doDistribParams.h" - template < typename EOT > -class doNormalParams : public doDistribParams< EOT > +class doNormalParams { public: - doNormalParams(EOT _mean, EOT _variance) - : doDistribParams< EOT >(2) + doNormalParams(EOT mean, EOT variance) + : _mean(mean), _variance(variance) { assert(_mean.size() > 0); assert(_mean.size() == _variance.size()); - - mean() = _mean; - variance() = _variance; } - doNormalParams(const doNormalParams& p) - : doDistribParams< EOT >( p ) - {} + EOT& mean(){return _mean;} + EOT& variance(){return _variance;} - EOT& mean(){return this->param(0);} - EOT& variance(){return this->param(1);} + unsigned int size() + { + assert(_mean.size() == _variance.size()); + return _mean.size(); + } + +private: + EOT _mean; + EOT _variance; }; #endif // !_doNormalParams_h diff --git a/src/doStats.h b/src/doStats.h index 27a4b9c4..94756fa3 100644 --- a/src/doStats.h +++ b/src/doStats.h @@ -110,4 +110,9 @@ protected: double _hv; }; +class doCholesky : public doStats +{ + +}; + #endif // !_doStats_h diff --git a/src/doVectorBounds.h b/src/doVectorBounds.h index 8a0530db..07e4e2cf 100644 --- a/src/doVectorBounds.h +++ b/src/doVectorBounds.h @@ -1,28 +1,30 @@ #ifndef _doVectorBounds_h #define _doVectorBounds_h -#include "doDistribParams.h" - template < typename EOT > -class doVectorBounds : public doDistribParams< EOT > +class doVectorBounds { public: - doVectorBounds(EOT _min, EOT _max) - : doDistribParams< EOT >(2) + doVectorBounds(EOT min, EOT max) + : _min(min), _max(max) { assert(_min.size() > 0); assert(_min.size() == _max.size()); - - min() = _min; - max() = _max; } - doVectorBounds(const doVectorBounds& v) - : doDistribParams< EOT >( v ) - {} + EOT& min(){return _min;} + EOT& max(){return _max;} - EOT& min(){return this->param(0);} - EOT& max(){return this->param(1);} + + unsigned int size() + { + assert(_min.size() == _max.size()); + return _min.size(); + } + +private: + EOT _min; + EOT _max; }; #endif // !_doVectorBounds_h diff --git a/src/todo b/src/todo new file mode 100644 index 00000000..13785cc8 --- /dev/null +++ b/src/todo @@ -0,0 +1,2 @@ +* deplacer les ecritures pour gnuplot dans des classes type eoContinue (eoMonitor) +* integrer ACP From 897d0b051d61f3e12e8d202273089003053984fa Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 3 Aug 2010 10:35:25 +0200 Subject: [PATCH 18/74] - doDistribParams --- src/doDistribParams.h | 44 ------------------------------------------- 1 file changed, 44 deletions(-) delete mode 100644 src/doDistribParams.h diff --git a/src/doDistribParams.h b/src/doDistribParams.h deleted file mode 100644 index ef07c151..00000000 --- a/src/doDistribParams.h +++ /dev/null @@ -1,44 +0,0 @@ -#ifndef _doDistribParams_h -#define _doDistribParams_h - -#include - -template < typename EOT > -class doDistribParams -{ -public: - doDistribParams(unsigned n = 2) - : _params(n) - {} - - doDistribParams(const doDistribParams& p) { *this = p; } - - doDistribParams& operator=(const doDistribParams& p) - { - if (this != &p) - { - this->_params = p._params; - } - - return *this; - } - - EOT& param(unsigned int i = 0){return _params[i];} - - unsigned int param_size(){return _params.size();} - - unsigned int size() - { - for (unsigned int i = 0, size = param_size(); i < size - 1; ++i) - { - assert(param(i).size() == param(i + 1).size()); - } - - return param(0).size(); - } - -private: - std::vector< EOT > _params; -}; - -#endif // !_doDistribParams_h From 22602154fc50f9214732d2bba097e223caf54071 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 3 Aug 2010 18:54:41 +0200 Subject: [PATCH 19/74] * cholesky --- CMakeLists.txt | 4 + application/cma_sa/CMakeLists.txt | 7 +- src/doCMASA.h | 6 +- src/doEstimatorNormal.h | 21 ++--- src/doNormal.h | 6 +- src/doNormalParams.h | 21 +++-- src/doSamplerNormal.h | 15 ++- src/doStats.h | 148 +++++++++++++++++++++++++++++- 8 files changed, 195 insertions(+), 33 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 715fc0cf..da961550 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -25,9 +25,13 @@ INCLUDE(FindPkgConfig) PKG_CHECK_MODULES(EO eo REQUIRED) PKG_CHECK_MODULES(MO mo REQUIRED) +FIND_PACKAGE(Boost 1.33.0) + INCLUDE_DIRECTORIES( ${EO_INCLUDE_DIRS} ${MO_INCLUDE_DIRS} + ${Boost_INCLUDE_DIRS} + /Dev/ometah-0.3/common ) ###################################################################################### diff --git a/application/cma_sa/CMakeLists.txt b/application/cma_sa/CMakeLists.txt index d68a49c0..c67ab0dd 100644 --- a/application/cma_sa/CMakeLists.txt +++ b/application/cma_sa/CMakeLists.txt @@ -1,7 +1,12 @@ PROJECT(cma_sa) +FIND_PACKAGE(Boost 1.33.0) + INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) +LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) + SET(RESOURCES cma_sa.param plot.py @@ -20,4 +25,4 @@ FILE(GLOB SOURCES *.cpp) SET(EXECUTABLE_OUTPUT_PATH ${DO_BINARY_DIR}) ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES}) -TARGET_LINK_LIBRARIES(${PROJECT_NAME} do ${EO_LIBRARIES} ${MO_LIBRARIES}) +TARGET_LINK_LIBRARIES(${PROJECT_NAME} do ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) diff --git a/src/doCMASA.h b/src/doCMASA.h index c2a3cf8e..31d1411a 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -168,7 +168,7 @@ public: for (int i = 0; i < size; ++i) { - hv.update( distrib.variance()[i] ); + //hv.update( distrib.varcovar()[i] ); } _ofs_params_var << hv << std::endl; @@ -286,7 +286,7 @@ public: ofs << size << " "; std::copy(distrib.mean().begin(), distrib.mean().end(), std::ostream_iterator< double >(ofs, " ")); - std::copy(distrib.variance().begin(), distrib.variance().end(), std::ostream_iterator< double >(ofs, " ")); + //std::copy(distrib.varcovar().begin(), distrib.varcovar().end(), std::ostream_iterator< double >(ofs, " ")); ofs << std::endl; } @@ -336,7 +336,7 @@ public: for (int i = 0; i < size; ++i) { - hv.update( distrib.variance()[i] ); + //hv.update( distrib.varcovar()[i] ); } _ofs_params_var << hv << std::endl; diff --git a/src/doEstimatorNormal.h b/src/doEstimatorNormal.h index 3bd2058f..b3cc1f3e 100644 --- a/src/doEstimatorNormal.h +++ b/src/doEstimatorNormal.h @@ -9,6 +9,8 @@ template < typename EOT > class doEstimatorNormal : public doEstimator< doNormal< EOT > > { public: + typedef typename EOT::AtomType AtomType; + doNormal< EOT > operator()(eoPop& pop) { unsigned int popsize = pop.size(); @@ -17,23 +19,12 @@ public: unsigned int dimsize = pop[0].size(); assert(dimsize > 0); - doCovMatrix cov(dimsize); + //doCovMatrix cov(dimsize); + doUblasCovMatrix< EOT > cov; - for (unsigned int i = 0; i < popsize; ++i) - { - cov.update(pop[i]); - } + cov.update(pop); - EOT mean(dimsize); - EOT covariance(dimsize); - - for (unsigned int d = 0; d < dimsize; ++d) - { - mean[d] = cov.get_mean(d); - covariance[d] = cov.get_var(d); - } - - return doNormal< EOT >(mean, covariance); + return doNormal< EOT >(cov.get_mean(), cov.get_varcovar()); } }; diff --git a/src/doNormal.h b/src/doNormal.h index 6de887fc..dd869fce 100644 --- a/src/doNormal.h +++ b/src/doNormal.h @@ -8,8 +8,10 @@ template < typename EOT > class doNormal : public doDistrib< EOT >, public doNormalParams< EOT > { public: - doNormal(EOT mean, EOT variance) - : doNormalParams< EOT >(mean, variance) + typedef typename EOT::AtomType AtomType; + + doNormal( const EOT& mean, const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar ) + : doNormalParams< EOT >( mean, varcovar ) {} }; diff --git a/src/doNormalParams.h b/src/doNormalParams.h index 87a3a65a..4a240957 100644 --- a/src/doNormalParams.h +++ b/src/doNormalParams.h @@ -1,29 +1,38 @@ #ifndef _doNormalParams_h #define _doNormalParams_h +#include +#include + +namespace ublas = boost::numeric::ublas; + template < typename EOT > class doNormalParams { public: - doNormalParams(EOT mean, EOT variance) - : _mean(mean), _variance(variance) + typedef typename EOT::AtomType AtomType; + + doNormalParams(const EOT& mean, const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar) + : _mean(mean), _varcovar(varcovar) { assert(_mean.size() > 0); - assert(_mean.size() == _variance.size()); + assert(_mean.size() == _varcovar.size1()); + assert(_mean.size() == _varcovar.size2()); } EOT& mean(){return _mean;} - EOT& variance(){return _variance;} + ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar(){return _varcovar;} unsigned int size() { - assert(_mean.size() == _variance.size()); + assert(_mean.size() == _varcovar.size1()); + assert(_mean.size() == _varcovar.size2()); return _mean.size(); } private: EOT _mean; - EOT _variance; + ublas::symmetric_matrix< AtomType, ublas::lower > _varcovar; }; #endif // !_doNormalParams_h diff --git a/src/doSamplerNormal.h b/src/doSamplerNormal.h index 7ba4c2d5..21c0fafc 100644 --- a/src/doSamplerNormal.h +++ b/src/doSamplerNormal.h @@ -6,6 +6,7 @@ #include "doSampler.h" #include "doNormal.h" #include "doBounder.h" +#include "doStats.h" /** * doSamplerNormal @@ -45,10 +46,16 @@ public: for (unsigned int i = 0; i < size; ++i) { - solution.push_back( - rng.normal(distrib.mean()[i], - distrib.variance()[i]) - ); + Cholesky< EOT > cholesky; + + cholesky.update( distrib.varcovar() ); + + // solution.push_back( + // rng.normal(distrib.mean()[i], + // distrib.varcovar()[i]) + // ); + + //rng.normal() + } //------------------------------------------------------------- diff --git a/src/doStats.h b/src/doStats.h index 94756fa3..27bef334 100644 --- a/src/doStats.h +++ b/src/doStats.h @@ -18,7 +18,14 @@ #ifndef _doStats_h #define _doStats_h +#include +#include +#include + #include +#include + +namespace ublas = boost::numeric::ublas; class doStats : public eoPrintable { @@ -110,9 +117,146 @@ protected: double _hv; }; -class doCholesky : public doStats +template < typename EOT > +class doUblasCovMatrix : public doStats { - +public: + typedef typename EOT::AtomType AtomType; + + virtual void update( const eoPop< EOT >& pop ) + { + unsigned int p_size = pop.size(); // population size + + assert(p_size > 0); + + unsigned int s_size = pop[0].size(); // solution size + + assert(s_size > 0); + + ublas::matrix< AtomType > sample( p_size, s_size ); + + for (unsigned int i = 0; i < p_size; ++i) + { + for (unsigned int j = 0; j < s_size; ++j) + { + sample(i, j) = pop[i][j]; + } + } + + _varcovar.resize(s_size, s_size); + + // variance-covariance matrix are symmetric (and semi-definite positive), + // thus a triangular storage is sufficient + ublas::symmetric_matrix< AtomType, ublas::lower > var(s_size, s_size); + + // variance-covariance matrix computation : A * transpose(A) + var = ublas::prod( sample, ublas::trans( sample ) ); + + for (unsigned int i = 0; i < s_size; ++i) + { + // triangular LOWER matrix, thus j is not going further than i + for (unsigned int j = 0; j <= i; ++j) + { + // we want a reducted covariance matrix + _varcovar(i, j) = var(i, j) / p_size; + } + } + + //_varcovar = varcovar; + + _mean.resize(s_size); + + // unit vector + ublas::scalar_vector< AtomType > u( p_size, 1 ); + + // sum over columns + ublas::vector< AtomType > mean = ublas::prod( ublas::trans( sample ), u ); + + // division by n + mean /= p_size; + + // copy results in the params std::vector + std::copy(mean.begin(), mean.end(), _mean.begin()); + } + + const ublas::symmetric_matrix< AtomType, ublas::lower >& get_varcovar() const {return _varcovar;} + + const EOT& get_mean() const {return _mean;} + +private: + ublas::symmetric_matrix< AtomType, ublas::lower > _varcovar; + EOT _mean; +}; + +template < typename EOT > +class Cholesky : public doStats +{ +public: + typedef typename EOT::AtomType AtomType; + + virtual void update( const ublas::symmetric_matrix< AtomType, ublas::lower >& V) + { + unsigned int Vl = V.size1(); + + assert(Vl > 0); + + unsigned int Vc = V.size2(); + + assert(Vc > 0); + + _L.resize(Vl, Vc); + + unsigned int i,j,k; + + // first column + i=0; + + // diagonal + j=0; + _L(0, 0) = sqrt( V(0, 0) ); + + // end of the column + for ( j = 1; j < Vc; ++j ) + { + _L(j, 0) = V(0, j) / _L(0, 0); + } + + // end of the matrix + for ( i = 1; i < Vl; ++i ) + { // each column + + // diagonal + double sum = 0.0; + + for ( k = 0; k < i; ++k) + { + sum += _L(i, k) * _L(i, k); + } + + assert( ( V(i, i) - sum ) > 0 ); + + _L(i, i) = sqrt( V(i, i) - sum ); + + for ( j = i + 1; j < Vl; ++j ) + { // rows + + // one element + sum = 0.0; + + for ( k = 0; k < i; ++k ) + { + sum += _L(j, k) * _L(i, k); + } + + _L(j, i) = (V(j, i) - sum) / _L(i, i); + } + } + } + + const ublas::symmetric_matrix< AtomType, ublas::lower >& get_L() const {return _L;} + +private: + ublas::symmetric_matrix< AtomType, ublas::lower > _L; }; #endif // !_doStats_h From 9ac22d7515772c86b0cb730ee374ecac5cbe7a17 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 4 Aug 2010 13:05:28 +0200 Subject: [PATCH 20/74] commit with an issue at runtime: Assertion failed in file /usr/include/boost/numeric/ublas/symmetric.hpp at line 163 --- src/doEstimatorNormal.h | 2 +- src/doNormal.h | 2 +- src/doNormalCenter.h | 4 ++- src/doNormalParams.h | 10 +++++--- src/doSamplerNormal.h | 57 +++++++++++++++++++++++++++++------------ src/doSamplerUniform.h | 4 ++- src/doStats.h | 11 +++----- 7 files changed, 60 insertions(+), 30 deletions(-) diff --git a/src/doEstimatorNormal.h b/src/doEstimatorNormal.h index b3cc1f3e..010008a8 100644 --- a/src/doEstimatorNormal.h +++ b/src/doEstimatorNormal.h @@ -24,7 +24,7 @@ public: cov.update(pop); - return doNormal< EOT >(cov.get_mean(), cov.get_varcovar()); + return doNormal< EOT >( cov.get_mean(), cov.get_varcovar() ); } }; diff --git a/src/doNormal.h b/src/doNormal.h index dd869fce..f857da75 100644 --- a/src/doNormal.h +++ b/src/doNormal.h @@ -10,7 +10,7 @@ class doNormal : public doDistrib< EOT >, public doNormalParams< EOT > public: typedef typename EOT::AtomType AtomType; - doNormal( const EOT& mean, const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar ) + doNormal( const ublas::vector< AtomType >& mean, const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar ) : doNormalParams< EOT >( mean, varcovar ) {} }; diff --git a/src/doNormalCenter.h b/src/doNormalCenter.h index 06113060..ff379ba2 100644 --- a/src/doNormalCenter.h +++ b/src/doNormalCenter.h @@ -12,7 +12,9 @@ public: void operator() ( doNormal< EOT >& distrib, EOT& mass ) { - distrib.mean() = mass; // vive les references!!! + ublas::vector< AtomType > mean( distrib.size() ); + std::copy( mass.begin(), mass.end(), mean.begin() ); + distrib.mean() = mean; } }; diff --git a/src/doNormalParams.h b/src/doNormalParams.h index 4a240957..c1f2d15b 100644 --- a/src/doNormalParams.h +++ b/src/doNormalParams.h @@ -12,7 +12,11 @@ class doNormalParams public: typedef typename EOT::AtomType AtomType; - doNormalParams(const EOT& mean, const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar) + doNormalParams + ( + const ublas::vector< AtomType >& mean, + const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar + ) : _mean(mean), _varcovar(varcovar) { assert(_mean.size() > 0); @@ -20,7 +24,7 @@ public: assert(_mean.size() == _varcovar.size2()); } - EOT& mean(){return _mean;} + ublas::vector< AtomType >& mean(){return _mean;} ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar(){return _varcovar;} unsigned int size() @@ -31,7 +35,7 @@ public: } private: - EOT _mean; + ublas::vector< AtomType > _mean; ublas::symmetric_matrix< AtomType, ublas::lower > _varcovar; }; diff --git a/src/doSamplerNormal.h b/src/doSamplerNormal.h index 21c0fafc..413f7ada 100644 --- a/src/doSamplerNormal.h +++ b/src/doSamplerNormal.h @@ -30,36 +30,61 @@ public: assert(size > 0); //------------------------------------------------------------- - // Point we want to sample to get higher a set of points - // (coordinates in n dimension) - // x = {x1, x2, ..., xn} + // Cholesky factorisation gererating matrix L from covariance + // matrix V. + // We must use cholesky.get_L() to get the resulting matrix. + // + // L = cholesky decomposition of varcovar //------------------------------------------------------------- - EOT solution; + Cholesky< EOT > cholesky; + cholesky.update( distrib.varcovar() ); + ublas::symmetric_matrix< AtomType, ublas::lower > L = cholesky.get_L(); //------------------------------------------------------------- //------------------------------------------------------------- - // Sampling all dimensions + // T = vector of size elements drawn in N(0,1) rng.normal(1.0) //------------------------------------------------------------- - for (unsigned int i = 0; i < size; ++i) + ublas::vector< AtomType > T( size ); + + for ( unsigned int i = 0; i < size; ++i ) { - Cholesky< EOT > cholesky; - - cholesky.update( distrib.varcovar() ); - - // solution.push_back( - // rng.normal(distrib.mean()[i], - // distrib.varcovar()[i]) - // ); - - //rng.normal() + + T( i ) = rng.normal( 1.0 ); } //------------------------------------------------------------- + + //------------------------------------------------------------- + // LT = prod( L, trans(T) ) ? + // LT = prod( L, T ) + //------------------------------------------------------------- + + //ublas::symmetric_matrix< AtomType, ublas::lower > LT = ublas::prod( L, ublas::trans( T ) ); + ublas::vector< AtomType > LT = ublas::prod( L, T ); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // solution = means + trans( LT ) ? + // solution = means + LT + //------------------------------------------------------------- + + ublas::vector< AtomType > mean = distrib.mean(); + + ublas::vector< AtomType > ublas_solution = mean + LT; + //ublas::vector< AtomType > ublas_solution = mean + ublas::trans( LT ); + + EOT solution( size ); + + std::copy( ublas_solution.begin(), ublas_solution.end(), solution.begin() ); + + //------------------------------------------------------------- + return solution; } }; diff --git a/src/doSamplerUniform.h b/src/doSamplerUniform.h index f49b6924..374d7a8e 100644 --- a/src/doSamplerUniform.h +++ b/src/doSamplerUniform.h @@ -20,8 +20,10 @@ public: unsigned int size = distrib.size(); assert(size > 0); + //------------------------------------------------------------- - // Point we want to sample to get higher a population + // Point we want to sample to get higher a set of points + // (coordinates in n dimension) // x = {x1, x2, ..., xn} //------------------------------------------------------------- diff --git a/src/doStats.h b/src/doStats.h index 27bef334..8e79562b 100644 --- a/src/doStats.h +++ b/src/doStats.h @@ -170,22 +170,19 @@ public: ublas::scalar_vector< AtomType > u( p_size, 1 ); // sum over columns - ublas::vector< AtomType > mean = ublas::prod( ublas::trans( sample ), u ); + _mean = ublas::prod( ublas::trans( sample ), u ); // division by n - mean /= p_size; - - // copy results in the params std::vector - std::copy(mean.begin(), mean.end(), _mean.begin()); + _mean /= p_size; } const ublas::symmetric_matrix< AtomType, ublas::lower >& get_varcovar() const {return _varcovar;} - const EOT& get_mean() const {return _mean;} + const ublas::vector< AtomType >& get_mean() const {return _mean;} private: ublas::symmetric_matrix< AtomType, ublas::lower > _varcovar; - EOT _mean; + ublas::vector< AtomType > _mean; }; template < typename EOT > From 36ec42d36204631eb4c25ae7b31a8728903697f8 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 4 Aug 2010 14:05:42 +0200 Subject: [PATCH 21/74] * changed some comments sentences --- src/doStats.h | 28 +++++++++++++++++++--------- 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/src/doStats.h b/src/doStats.h index 8e79562b..cc17643b 100644 --- a/src/doStats.h +++ b/src/doStats.h @@ -145,13 +145,26 @@ public: _varcovar.resize(s_size, s_size); - // variance-covariance matrix are symmetric (and semi-definite positive), - // thus a triangular storage is sufficient + + //------------------------------------------------------------- + // variance-covariance matrix are symmetric (and semi-definite + // positive), thus a triangular storage is sufficient + //------------------------------------------------------------- + ublas::symmetric_matrix< AtomType, ublas::lower > var(s_size, s_size); + //------------------------------------------------------------- + + + //------------------------------------------------------------- // variance-covariance matrix computation : A * transpose(A) + //------------------------------------------------------------- + var = ublas::prod( sample, ublas::trans( sample ) ); + //------------------------------------------------------------- + + for (unsigned int i = 0; i < s_size; ++i) { // triangular LOWER matrix, thus j is not going further than i @@ -162,8 +175,6 @@ public: } } - //_varcovar = varcovar; - _mean.resize(s_size); // unit vector @@ -219,8 +230,8 @@ public: } // end of the matrix - for ( i = 1; i < Vl; ++i ) - { // each column + for ( i = 1; i < Vl; ++i ) // each column + { // diagonal double sum = 0.0; @@ -234,9 +245,8 @@ public: _L(i, i) = sqrt( V(i, i) - sum ); - for ( j = i + 1; j < Vl; ++j ) - { // rows - + for ( j = i + 1; j < Vl; ++j ) // rows + { // one element sum = 0.0; From 94dd8e16eb8c56b07653f2a4cea3241dbd4ae84d Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 6 Aug 2010 10:19:50 +0200 Subject: [PATCH 22/74] replace doNormal by doNormalMulti --- src/doCMASA.h | 8 ----- src/doNormal.h | 18 ---------- src/{doNormalParams.h => doNormalMulti.h} | 42 ++++++----------------- 3 files changed, 10 insertions(+), 58 deletions(-) delete mode 100644 src/doNormal.h rename src/{doNormalParams.h => doNormalMulti.h} (57%) diff --git a/src/doCMASA.h b/src/doCMASA.h index 7454f37c..31d1411a 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -123,9 +123,6 @@ public: ::system(ss.str().c_str()); } -<<<<<<< HEAD - ::mkdir(bounds_results_destination.c_str(), 0755); // create once directory -======= ::mkdir(_bounds_results_destination.c_str(), 0755); // create once directory //------------------------------------------------------------- @@ -157,7 +154,6 @@ public: //------------------------------------------------------------- int number_of_iterations = 0; ->>>>>>> 36ec42d36204631eb4c25ae7b31a8728903697f8 //------------------------------------------------------------- @@ -290,11 +286,7 @@ public: ofs << size << " "; std::copy(distrib.mean().begin(), distrib.mean().end(), std::ostream_iterator< double >(ofs, " ")); -<<<<<<< HEAD - std::copy(distrib.variance().begin(), distrib.variance().end(), std::ostream_iterator< double >(ofs, " ")); -======= //std::copy(distrib.varcovar().begin(), distrib.varcovar().end(), std::ostream_iterator< double >(ofs, " ")); ->>>>>>> 36ec42d36204631eb4c25ae7b31a8728903697f8 ofs << std::endl; } diff --git a/src/doNormal.h b/src/doNormal.h deleted file mode 100644 index f857da75..00000000 --- a/src/doNormal.h +++ /dev/null @@ -1,18 +0,0 @@ -#ifndef _doNormal_h -#define _doNormal_h - -#include "doDistrib.h" -#include "doNormalParams.h" - -template < typename EOT > -class doNormal : public doDistrib< EOT >, public doNormalParams< EOT > -{ -public: - typedef typename EOT::AtomType AtomType; - - doNormal( const ublas::vector< AtomType >& mean, const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar ) - : doNormalParams< EOT >( mean, varcovar ) - {} -}; - -#endif // !_doNormal_h diff --git a/src/doNormalParams.h b/src/doNormalMulti.h similarity index 57% rename from src/doNormalParams.h rename to src/doNormalMulti.h index 557c5443..9c89c8d3 100644 --- a/src/doNormalParams.h +++ b/src/doNormalMulti.h @@ -1,36 +1,20 @@ -#ifndef _doNormalParams_h -#define _doNormalParams_h +#ifndef _doNormalMulti_h +#define _doNormalMulti_h -<<<<<<< HEAD -======= #include #include +#include "doDistrib.h" + namespace ublas = boost::numeric::ublas; ->>>>>>> 36ec42d36204631eb4c25ae7b31a8728903697f8 template < typename EOT > -class doNormalParams +class doNormalMulti : public doDistrib< EOT > { public: -<<<<<<< HEAD - doNormalParams(EOT mean, EOT variance) - : _mean(mean), _variance(variance) - { - assert(_mean.size() > 0); - assert(_mean.size() == _variance.size()); - } - - EOT& mean(){return _mean;} - EOT& variance(){return _variance;} - - unsigned int size() - { - assert(_mean.size() == _variance.size()); -======= typedef typename EOT::AtomType AtomType; - doNormalParams + doNormalMulti ( const ublas::vector< AtomType >& mean, const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar @@ -42,25 +26,19 @@ public: assert(_mean.size() == _varcovar.size2()); } - ublas::vector< AtomType >& mean(){return _mean;} - ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar(){return _varcovar;} - unsigned int size() { assert(_mean.size() == _varcovar.size1()); assert(_mean.size() == _varcovar.size2()); ->>>>>>> 36ec42d36204631eb4c25ae7b31a8728903697f8 return _mean.size(); } + ublas::vector< AtomType >& mean(){return _mean;} + ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar(){return _varcovar;} + private: -<<<<<<< HEAD - EOT _mean; - EOT _variance; -======= ublas::vector< AtomType > _mean; ublas::symmetric_matrix< AtomType, ublas::lower > _varcovar; ->>>>>>> 36ec42d36204631eb4c25ae7b31a8728903697f8 }; -#endif // !_doNormalParams_h +#endif // !_doNormalMulti_h From 1070ec8a32e173b450b82f45751177e0cfc24b89 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 6 Aug 2010 10:24:45 +0200 Subject: [PATCH 23/74] added doNormalMono --- src/doNormalMono.h | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 src/doNormalMono.h diff --git a/src/doNormalMono.h b/src/doNormalMono.h new file mode 100644 index 00000000..aa334085 --- /dev/null +++ b/src/doNormalMono.h @@ -0,0 +1,31 @@ +#ifndef _doNormalMono_h +#define _doNormalMono_h + +#include "doDistrib.h" + +template < typename EOT > +class doNormalMono : public doDistrib< EOT > +{ +public: + doNormalMono( const EOT& mean, const EOT& variance ) + : _mean(mean), _variance(variance) + { + assert(_mean.size() > 0); + assert(_mean.size() == _variance.size()); + } + + unsigned int size() + { + assert(_mean.size() == _variance.size()); + return _mean.size(); + } + + EOT& mean(){return _mean;} + EOT& variance(){return _variance;} + +private: + EOT _mean; + EOT _variance; +}; + +#endif // !_doNormalMono_h From 963d59e706ea34b342043985a3d3162b65644b6f Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 16 Aug 2010 07:52:30 +0200 Subject: [PATCH 24/74] an intermediate commit to keep updates --- application/cma_sa/main.cpp | 40 ++- src/do | 16 +- src/do.cpp | 1 + src/doCMASA.h | 20 +- src/doCheckPoint.h | 78 +++++ src/doContinue.h | 27 ++ src/doEstimatorNormal.h | 31 -- src/doEstimatorNormalMono.h | 70 +++++ src/doEstimatorNormalMulti.h | 109 +++++++ src/doHyperVolume.h | 25 ++ src/doNormalCenter.h | 21 -- src/doNormalMonoCenter.h | 19 ++ src/doNormalMultiCenter.h | 21 ++ src/doSamplerNormalMono.h | 65 +++++ ...SamplerNormal.h => doSamplerNormalMulti.h} | 96 +++++- src/doStat.h | 33 +++ src/doStatNormalMono.h | 21 ++ src/doStatNormalMulti.h | 24 ++ src/doStatUniform.h | 21 ++ src/doStats.cpp | 192 ------------ src/doStats.h | 275 ------------------ 21 files changed, 649 insertions(+), 556 deletions(-) create mode 100644 src/do.cpp create mode 100644 src/doCheckPoint.h create mode 100644 src/doContinue.h delete mode 100644 src/doEstimatorNormal.h create mode 100644 src/doEstimatorNormalMono.h create mode 100644 src/doEstimatorNormalMulti.h create mode 100644 src/doHyperVolume.h delete mode 100644 src/doNormalCenter.h create mode 100644 src/doNormalMonoCenter.h create mode 100644 src/doNormalMultiCenter.h create mode 100644 src/doSamplerNormalMono.h rename src/{doSamplerNormal.h => doSamplerNormalMulti.h} (54%) create mode 100644 src/doStat.h create mode 100644 src/doStatNormalMono.h create mode 100644 src/doStatNormalMulti.h create mode 100644 src/doStatUniform.h delete mode 100644 src/doStats.cpp delete mode 100644 src/doStats.h diff --git a/application/cma_sa/main.cpp b/application/cma_sa/main.cpp index 872636e7..a452ead8 100644 --- a/application/cma_sa/main.cpp +++ b/application/cma_sa/main.cpp @@ -14,9 +14,13 @@ #include "Rosenbrock.h" #include "Sphere.h" -typedef eoReal EOT; +typedef eoReal EOT; -int main(int ac, char** av) +//typedef doUniform< EOT > Distrib; +//typedef doNormalMono< EOT > Distrib; +typedef doNormalMulti< EOT > Distrib; + +int main(int ac, char** av) { eoParserLogger parser(ac, av); @@ -37,19 +41,24 @@ int main(int ac, char** av) eoSelect< EOT >* selector = new eoDetSelect< EOT >(0.1); state.storeFunctor(selector); - //doEstimator< doUniform< EOT > >* estimator = new doEstimatorUniform< EOT >(); - doEstimator< doNormal< EOT > >* estimator = new doEstimatorNormal< EOT >(); + doEstimator< Distrib >* estimator = + //new doEstimatorUniform< EOT >(); + //new doEstimatorNormalMono< EOT >(); + new doEstimatorNormalMulti< EOT >(); state.storeFunctor(estimator); eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >(); state.storeFunctor(selectone); - //doModifierMass< doUniform< EOT > >* modifier = new doUniformCenter< EOT >(); - doModifierMass< doNormal< EOT > >* modifier = new doNormalCenter< EOT >(); + doModifierMass< Distrib >* modifier = + //new doUniformCenter< EOT >(); + //new doNormalMonoCenter< EOT >(); + new doNormalMultiCenter< EOT >(); state.storeFunctor(modifier); - //eoEvalFunc< EOT >* plainEval = new BopoRosenbrock< EOT, double, const EOT& >(); - eoEvalFunc< EOT >* plainEval = new Sphere< EOT >(); + eoEvalFunc< EOT >* plainEval = + //new BopoRosenbrock< EOT, typename EOT::AtomType, const EOT& >(); + new Sphere< EOT >(); state.storeFunctor(plainEval); unsigned long max_eval = parser.getORcreateParam((unsigned long)0, "maxEval", "Maximum number of evaluations (0 = none)", 'E', "Stopping criterion").value(); // E @@ -66,6 +75,12 @@ int main(int ac, char** av) state.storeFunctor(init); + doStats< Distrib >* stats = + //new doStatsUniform< EOT >(); + //new doStatsNormalMono< EOT >(); + new doStatsNormalMulti< EOT >(); + state.storeFunctor(stats); + //----------------------------------------------------------------------------- @@ -98,8 +113,10 @@ int main(int ac, char** av) *gen); state.storeFunctor(bounder); - //doSampler< doUniform< EOT > >* sampler = new doSamplerUniform< EOT >(); - doSampler< doNormal< EOT > >* sampler = new doSamplerNormal< EOT >( *bounder ); + doSampler< Distrib >* sampler = + //new doSamplerUniform< EOT >(); + //new doSamplerNormalMono< EOT >( *bounder ); + new doSamplerNormalMulti< EOT >( *bounder ); state.storeFunctor(sampler); @@ -165,8 +182,7 @@ int main(int ac, char** av) // CMASA algorithm configuration //----------------------------------------------------------------------------- - //doAlgo< doUniform< EOT > >* algo = new doCMASA< doUniform< EOT > > - doAlgo< doNormal< EOT > >* algo = new doCMASA< doNormal< EOT > > + doAlgo< Distrib >* algo = new doCMASA< Distrib > (*selector, *estimator, *selectone, *modifier, *sampler, checkpoint, eval, *continuator, *cooling_schedule, initial_temperature, *replacor); diff --git a/src/do b/src/do index 478a3f21..10248481 100644 --- a/src/do +++ b/src/do @@ -6,24 +6,27 @@ #include "doDistrib.h" #include "doUniform.h" -#include "doNormal.h" +#include "doNormalMono.h" +#include "doNormalMulti.h" #include "doEstimator.h" #include "doEstimatorUniform.h" -#include "doEstimatorNormal.h" +#include "doEstimatorNormalMono.h" +#include "doEstimatorNormalMulti.h" #include "doModifier.h" #include "doModifierDispersion.h" #include "doModifierMass.h" #include "doUniformCenter.h" -#include "doNormalCenter.h" +#include "doNormalMonoCenter.h" +#include "doNormalMultiCenter.h" #include "doSampler.h" #include "doSamplerUniform.h" -#include "doSamplerNormal.h" +#include "doSamplerNormalMono.h" +#include "doSamplerNormalMulti.h" #include "doVectorBounds.h" -#include "doNormalParams.h" #include "doBounder.h" #include "doBounderNo.h" @@ -31,5 +34,8 @@ #include "doBounderRng.h" #include "doStats.h" +#include "doStatsUniform.h" +#include "doStatsNormalMono.h" +#include "doStatsNormalMulti.h" #endif // !_do_ diff --git a/src/do.cpp b/src/do.cpp new file mode 100644 index 00000000..b33d98fe --- /dev/null +++ b/src/do.cpp @@ -0,0 +1 @@ +#include "do" diff --git a/src/doCMASA.h b/src/doCMASA.h index 31d1411a..ec7de9d8 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -33,6 +33,7 @@ #include "doEstimator.h" #include "doModifierMass.h" #include "doSampler.h" +#include "doHyperVolume.h" #include "doStats.h" using namespace boost::numeric::ublas; @@ -41,9 +42,12 @@ template < typename D > class doCMASA : public doAlgo< D > { public: - //! Alias for the type + //! Alias for the type EOT typedef typename D::EOType EOT; + //! Alias for the atom type + typedef typename EOT::AtomType AtomType; + //! Alias for the fitness typedef typename EOT::Fitness Fitness; @@ -74,7 +78,8 @@ public: moSolContinue < EOT > & continuator, moCoolingSchedule & cooling_schedule, double initial_temperature, - eoReplacement< EOT > & replacor + eoReplacement< EOT > & replacor, + doStats< D > & stats ) : _selector(selector), _estimator(estimator), @@ -87,6 +92,7 @@ public: _cooling_schedule(cooling_schedule), _initial_temperature(initial_temperature), _replacor(replacor), + _stats(stats), _pop_results_destination("ResPop"), @@ -164,14 +170,14 @@ public: double size = distrib.size(); assert(size > 0); - doHyperVolume hv; + doHyperVolume< EOT > hv; for (int i = 0; i < size; ++i) { //hv.update( distrib.varcovar()[i] ); } - _ofs_params_var << hv << std::endl; + // _ofs_params_var << hv << std::endl; } do @@ -332,14 +338,14 @@ public: double size = distrib.size(); assert(size > 0); - doHyperVolume hv; + doHyperVolume< EOT > hv; for (int i = 0; i < size; ++i) { //hv.update( distrib.varcovar()[i] ); } - _ofs_params_var << hv << std::endl; + //_ofs_params_var << hv << std::endl; } //------------------------------------------------------------- @@ -386,6 +392,8 @@ private: //! A EOT replacor eoReplacement < EOT > & _replacor; + //! Stats to print distrib parameters out + doStats< D > & _stats; //------------------------------------------------------------- // Temporary solution to store populations state at each diff --git a/src/doCheckPoint.h b/src/doCheckPoint.h new file mode 100644 index 00000000..e569e08d --- /dev/null +++ b/src/doCheckPoint.h @@ -0,0 +1,78 @@ +#ifndef _doCheckPoint_h +#define _doCheckPoint_h + +#include "doContinue.h" +#include "doStat.h" + +//! eoCheckPoint< EOT > classe fitted to Distribution Object library + +template < typename D > +class doCheckPoint : public doContinue< D > +{ +public: + typedef typename D::EOType EOType; + + doCheckPoint(doContinue< D >& _cont) + { + _continuators.push_back( &_cont ); + } + + bool operator()(const D& distrib) + { + for ( unsigned int i = 0, size = _stats.size(); i < size; ++i ) + { + (*_stats[i])( distrib ); + } + + bool bContinue = true; + for ( unsigned int i = 0, size = _continuators.size(); i < size; ++i ) + { + if ( !(*_continuators[i]( distrib )) ) + { + bContinue = false; + } + } + + if ( !bContinue ) + { + for ( unsigned int i = 0, size = _stats.size(); i < size; ++i ) + { + _stats[i]->lastCall( distrib ); + } + } + + return bContinue; + } + + void add(doContinue< D >& cont) { _continuators.push_back( &cont ); } + void add(doStatBase< D >& stat) { _stats.push_back( &stat ); } + + virtual std::string className(void) const { return "doCheckPoint"; } + + std::string allClassNames() const + { + std::string s("\n" + className() + "\n"); + + s += "Stats\n"; + for ( unsigned int i = 0, size = _stats.size(); i < size; ++i ) + { + s += _stats[i]->className() + "\n"; + } + s += "\n"; + + s += "Continuators\n"; + for ( unsigned int i = 0, size = _continuators.size(); i < size; ++i ) + { + s += _continuators[i]->className() + "\n"; + } + s += "\n"; + + return s; + } + +private: + std::vector< doContinue< D >* > _continuators; + std::vector< doStatBase< D >* > _stats; +}; + +#endif // !_doCheckPoint_h diff --git a/src/doContinue.h b/src/doContinue.h new file mode 100644 index 00000000..f7a7448d --- /dev/null +++ b/src/doContinue.h @@ -0,0 +1,27 @@ +#ifndef _doContinue_h +#define _doContinue_h + +#include +#include +#include + +//! eoContinue< EOT > classe fitted to Distribution Object library + +template < typename D > +class doContinue : public eoUF< const D&, bool >, public eoPersistent +{ +public: + virtual std::string className(void) const { return "doContinue"; } + + void readFrom(std::istream&) + { + /* It should be implemented by subclasses ! */ + } + + void printOn(std::ostream&) const + { + /* It should be implemented by subclasses ! */ + } +}; + +#endif // !_doContinue_h diff --git a/src/doEstimatorNormal.h b/src/doEstimatorNormal.h deleted file mode 100644 index 010008a8..00000000 --- a/src/doEstimatorNormal.h +++ /dev/null @@ -1,31 +0,0 @@ -#ifndef _doEstimatorNormal_h -#define _doEstimatorNormal_h - -#include "doEstimator.h" -#include "doUniform.h" -#include "doStats.h" - -template < typename EOT > -class doEstimatorNormal : public doEstimator< doNormal< EOT > > -{ -public: - typedef typename EOT::AtomType AtomType; - - doNormal< EOT > operator()(eoPop& pop) - { - unsigned int popsize = pop.size(); - assert(popsize > 0); - - unsigned int dimsize = pop[0].size(); - assert(dimsize > 0); - - //doCovMatrix cov(dimsize); - doUblasCovMatrix< EOT > cov; - - cov.update(pop); - - return doNormal< EOT >( cov.get_mean(), cov.get_varcovar() ); - } -}; - -#endif // !_doEstimatorNormal_h diff --git a/src/doEstimatorNormalMono.h b/src/doEstimatorNormalMono.h new file mode 100644 index 00000000..c6e168b7 --- /dev/null +++ b/src/doEstimatorNormalMono.h @@ -0,0 +1,70 @@ +#ifndef _doEstimatorNormalMono_h +#define _doEstimatorNormalMono_h + +#include "doEstimator.h" +#include "doNormalMono.h" + +template < typename EOT > +class doEstimatorNormalMono : public doEstimator< doNormalMono< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + class Variance + { + public: + Variance() : _sumvar(0){} + + void update(AtomType v) + { + _n++; + + AtomType d = v - _mean; + + _mean += 1 / _n * d; + _sumvar += (_n - 1) / _n * d * d; + } + + AtomType get_mean() const {return _mean;} + AtomType get_var() const {return _sumvar / (_n - 1);} + AtomType get_std() const {return sqrt( get_var() );} + + private: + AtomType _n; + AtomType _mean; + AtomType _sumvar; + }; + +public: + doNormalMono< EOT > operator()(eoPop& pop) + { + unsigned int popsize = pop.size(); + assert(popsize > 0); + + unsigned int dimsize = pop[0].size(); + assert(dimsize > 0); + + std::vector< Variance > var( dimsize ); + + for (unsigned int i = 0; i < popsize; ++i) + { + for (unsigned int d = 0; d < dimsize; ++d) + { + var[d].update( pop[i][d] ); + } + } + + EOT mean( dimsize ); + EOT variance( dimsize ); + + for (unsigned int d = 0; d < dimsize; ++d) + { + mean[d] = var[d].get_mean(); + variance[d] = var[d].get_var(); + } + + return doNormalMono< EOT >( mean, variance ); + } +}; + +#endif // !_doEstimatorNormalMono_h diff --git a/src/doEstimatorNormalMulti.h b/src/doEstimatorNormalMulti.h new file mode 100644 index 00000000..404a71d2 --- /dev/null +++ b/src/doEstimatorNormalMulti.h @@ -0,0 +1,109 @@ +#ifndef _doEstimatorNormalMulti_h +#define _doEstimatorNormalMulti_h + +#include "doEstimator.h" +#include "doUniform.h" +#include "doStats.h" + +template < typename EOT > +class doEstimatorNormalMulti : public doEstimator< doNormalMulti< EOT > > +{ +public: + class CovMatrix + { + public: + typedef typename EOT::AtomType AtomType; + + void update( const eoPop< EOT >& pop ) + { + unsigned int p_size = pop.size(); // population size + + assert(p_size > 0); + + unsigned int s_size = pop[0].size(); // solution size + + assert(s_size > 0); + + ublas::matrix< AtomType > sample( p_size, s_size ); + + for (unsigned int i = 0; i < p_size; ++i) + { + for (unsigned int j = 0; j < s_size; ++j) + { + sample(i, j) = pop[i][j]; + } + } + + _varcovar.resize(s_size, s_size); + + + //------------------------------------------------------------- + // variance-covariance matrix are symmetric (and semi-definite + // positive), thus a triangular storage is sufficient + //------------------------------------------------------------- + + ublas::symmetric_matrix< AtomType, ublas::lower > var(s_size, s_size); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // variance-covariance matrix computation : A * transpose(A) + //------------------------------------------------------------- + + var = ublas::prod( sample, ublas::trans( sample ) ); + + //------------------------------------------------------------- + + + for (unsigned int i = 0; i < s_size; ++i) + { + // triangular LOWER matrix, thus j is not going further than i + for (unsigned int j = 0; j <= i; ++j) + { + // we want a reducted covariance matrix + _varcovar(i, j) = var(i, j) / p_size; + } + } + + _mean.resize(s_size); + + // unit vector + ublas::scalar_vector< AtomType > u( p_size, 1 ); + + // sum over columns + _mean = ublas::prod( ublas::trans( sample ), u ); + + // division by n + _mean /= p_size; + } + + const ublas::symmetric_matrix< AtomType, ublas::lower >& get_varcovar() const {return _varcovar;} + + const ublas::vector< AtomType >& get_mean() const {return _mean;} + + private: + ublas::symmetric_matrix< AtomType, ublas::lower > _varcovar; + ublas::vector< AtomType > _mean; + }; + +public: + typedef typename EOT::AtomType AtomType; + + doNormalMulti< EOT > operator()(eoPop& pop) + { + unsigned int popsize = pop.size(); + assert(popsize > 0); + + unsigned int dimsize = pop[0].size(); + assert(dimsize > 0); + + CovMatrix cov; + + cov.update(pop); + + return doNormalMulti< EOT >( cov.get_mean(), cov.get_varcovar() ); + } +}; + +#endif // !_doEstimatorNormalMulti_h diff --git a/src/doHyperVolume.h b/src/doHyperVolume.h new file mode 100644 index 00000000..c47f457b --- /dev/null +++ b/src/doHyperVolume.h @@ -0,0 +1,25 @@ +#ifndef _doHyperVolume_h +#define _doHyperVolume_h + +template < typename EOT > +class doHyperVolume +{ +public: + typedef typename EOT::AtomType AtomType; + + doHyperVolume() : _hv(1) {} + + void update(AtomType v) + { + _hv *= ::sqrt( v ); + + assert( _hv <= std::numeric_limits< AtomType >::max() ); + } + + AtomType get_hypervolume() const { return _hv; } + +protected: + AtomType _hv; +}; + +#endif // !_doHyperVolume_h diff --git a/src/doNormalCenter.h b/src/doNormalCenter.h deleted file mode 100644 index ff379ba2..00000000 --- a/src/doNormalCenter.h +++ /dev/null @@ -1,21 +0,0 @@ -#ifndef _doNormalCenter_h -#define _doNormalCenter_h - -#include "doModifierMass.h" -#include "doNormal.h" - -template < typename EOT > -class doNormalCenter : public doModifierMass< doNormal< EOT > > -{ -public: - typedef typename EOT::AtomType AtomType; - - void operator() ( doNormal< EOT >& distrib, EOT& mass ) - { - ublas::vector< AtomType > mean( distrib.size() ); - std::copy( mass.begin(), mass.end(), mean.begin() ); - distrib.mean() = mean; - } -}; - -#endif // !_doNormalCenter_h diff --git a/src/doNormalMonoCenter.h b/src/doNormalMonoCenter.h new file mode 100644 index 00000000..48b448a4 --- /dev/null +++ b/src/doNormalMonoCenter.h @@ -0,0 +1,19 @@ +#ifndef _doNormalMonoCenter_h +#define _doNormalMonoCenter_h + +#include "doModifierMass.h" +#include "doNormalMono.h" + +template < typename EOT > +class doNormalMonoCenter : public doModifierMass< doNormalMono< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + void operator() ( doNormalMono< EOT >& distrib, EOT& mass ) + { + distrib.mean() = mass; + } +}; + +#endif // !_doNormalMonoCenter_h diff --git a/src/doNormalMultiCenter.h b/src/doNormalMultiCenter.h new file mode 100644 index 00000000..65e9ec7c --- /dev/null +++ b/src/doNormalMultiCenter.h @@ -0,0 +1,21 @@ +#ifndef _doNormalMultiCenter_h +#define _doNormalMultiCenter_h + +#include "doModifierMass.h" +#include "doNormalMulti.h" + +template < typename EOT > +class doNormalMultiCenter : public doModifierMass< doNormalMulti< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + void operator() ( doNormalMulti< EOT >& distrib, EOT& mass ) + { + ublas::vector< AtomType > mean( distrib.size() ); + std::copy( mass.begin(), mass.end(), mean.begin() ); + distrib.mean() = mean; + } +}; + +#endif // !_doNormalMultiCenter_h diff --git a/src/doSamplerNormalMono.h b/src/doSamplerNormalMono.h new file mode 100644 index 00000000..fa45b2e8 --- /dev/null +++ b/src/doSamplerNormalMono.h @@ -0,0 +1,65 @@ +#ifndef _doSamplerNormalMono_h +#define _doSamplerNormalMono_h + +#include + +#include "doSampler.h" +#include "doNormalMono.h" +#include "doBounder.h" +#include "doStats.h" + +/** + * doSamplerNormalMono + * This class uses the NormalMono distribution parameters (bounds) to return + * a random position used for population sampling. + */ +template < typename EOT > +class doSamplerNormalMono : public doSampler< doNormalMono< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + doSamplerNormalMono( doBounder< EOT > & bounder ) + : doSampler< doNormalMono< EOT > >( bounder ) + {} + + EOT sample( doNormalMono< EOT >& distrib ) + { + unsigned int size = distrib.size(); + assert(size > 0); + + + //------------------------------------------------------------- + // Point we want to sample to get higher a set of points + // (coordinates in n dimension) + // x = {x1, x2, ..., xn} + //------------------------------------------------------------- + + EOT solution; + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Sampling all dimensions + //------------------------------------------------------------- + + for (unsigned int i = 0; i < size; ++i) + { + AtomType mean = distrib.mean()[i]; + AtomType variance = distrib.variance()[i]; + AtomType random = rng.normal(mean, variance); + + assert(variance >= 0); + + solution.push_back(random); + } + + //------------------------------------------------------------- + + + return solution; + } +}; + +#endif // !_doSamplerNormalMono_h diff --git a/src/doSamplerNormal.h b/src/doSamplerNormalMulti.h similarity index 54% rename from src/doSamplerNormal.h rename to src/doSamplerNormalMulti.h index 413f7ada..ae54945b 100644 --- a/src/doSamplerNormal.h +++ b/src/doSamplerNormalMulti.h @@ -1,34 +1,106 @@ -#ifndef _doSamplerNormal_h -#define _doSamplerNormal_h +#ifndef _doSamplerNormalMulti_h +#define _doSamplerNormalMulti_h + +#include +#include +#include #include #include "doSampler.h" -#include "doNormal.h" +#include "doNormalMulti.h" #include "doBounder.h" #include "doStats.h" /** - * doSamplerNormal + * doSamplerNormalMulti * This class uses the Normal distribution parameters (bounds) to return * a random position used for population sampling. */ template < typename EOT > -class doSamplerNormal : public doSampler< doNormal< EOT > > +class doSamplerNormalMulti : public doSampler< doNormalMulti< EOT > > { public: typedef typename EOT::AtomType AtomType; - doSamplerNormal( doBounder< EOT > & bounder ) - : doSampler< doNormal< EOT > >( bounder ) + class Cholesky + { + public: + virtual void update( const ublas::symmetric_matrix< AtomType, ublas::lower >& V) + { + unsigned int Vl = V.size1(); + + assert(Vl > 0); + + unsigned int Vc = V.size2(); + + assert(Vc > 0); + + _L.resize(Vl, Vc); + + unsigned int i,j,k; + + // first column + i=0; + + // diagonal + j=0; + _L(0, 0) = sqrt( V(0, 0) ); + + // end of the column + for ( j = 1; j < Vc; ++j ) + { + _L(j, 0) = V(0, j) / _L(0, 0); + } + + // end of the matrix + for ( i = 1; i < Vl; ++i ) // each column + { + + // diagonal + double sum = 0.0; + + for ( k = 0; k < i; ++k) + { + sum += _L(i, k) * _L(i, k); + } + + assert( ( V(i, i) - sum ) > 0 ); + + _L(i, i) = sqrt( V(i, i) - sum ); + + for ( j = i + 1; j < Vl; ++j ) // rows + { + // one element + sum = 0.0; + + for ( k = 0; k < i; ++k ) + { + sum += _L(j, k) * _L(i, k); + } + + _L(j, i) = (V(j, i) - sum) / _L(i, i); + } + } + } + + const ublas::symmetric_matrix< AtomType, ublas::lower >& get_L() const {return _L;} + + private: + ublas::symmetric_matrix< AtomType, ublas::lower > _L; + }; + + doSamplerNormalMulti( doBounder< EOT > & bounder ) + : doSampler< doNormalMulti< EOT > >( bounder ) {} - EOT sample( doNormal< EOT >& distrib ) + EOT sample( doNormalMulti< EOT >& distrib ) { unsigned int size = distrib.size(); assert(size > 0); + //------------------------------------------------------------- // Cholesky factorisation gererating matrix L from covariance // matrix V. @@ -37,7 +109,7 @@ public: // L = cholesky decomposition of varcovar //------------------------------------------------------------- - Cholesky< EOT > cholesky; + Cholesky cholesky; cholesky.update( distrib.varcovar() ); ublas::symmetric_matrix< AtomType, ublas::lower > L = cholesky.get_L(); @@ -59,25 +131,21 @@ public: //------------------------------------------------------------- - // LT = prod( L, trans(T) ) ? // LT = prod( L, T ) //------------------------------------------------------------- - //ublas::symmetric_matrix< AtomType, ublas::lower > LT = ublas::prod( L, ublas::trans( T ) ); ublas::vector< AtomType > LT = ublas::prod( L, T ); //------------------------------------------------------------- //------------------------------------------------------------- - // solution = means + trans( LT ) ? // solution = means + LT //------------------------------------------------------------- ublas::vector< AtomType > mean = distrib.mean(); ublas::vector< AtomType > ublas_solution = mean + LT; - //ublas::vector< AtomType > ublas_solution = mean + ublas::trans( LT ); EOT solution( size ); @@ -89,4 +157,4 @@ public: } }; -#endif // !_doSamplerNormal_h +#endif // !_doSamplerNormalMulti_h diff --git a/src/doStat.h b/src/doStat.h new file mode 100644 index 00000000..46b213ba --- /dev/null +++ b/src/doStat.h @@ -0,0 +1,33 @@ +#ifndef _doStat_h +#define _doStat_h + +#include + +template < typename D > +class doStatBase : public eoUF< const D&, void > +{ +public: + // virtual void operator()( const D& ) = 0 (provided by eoUF< A1, R >) + + virtual void lastCall( const D& ) {} + virtual std::string className() const { return "doStatBase"; } +}; + +template < typename D > +class doStat : doStatBase< D > +{ +public: + typedef typename D::EOType EOType; + typedef typename EOType::AtomType AtomType; + +public: + doStat(){} + + + D& distrib() { return _distrib; } + +private: + D& _distrib; +}; + +#endif // !_doStat_h diff --git a/src/doStatNormalMono.h b/src/doStatNormalMono.h new file mode 100644 index 00000000..bc0a5b60 --- /dev/null +++ b/src/doStatNormalMono.h @@ -0,0 +1,21 @@ +#ifndef _doStatNormalMono_h +#define _doStatNormalMono_h + +#include "doStat.h" +#include "doNormalMono.h" + +template < typename EOT > +class doStatNormalMono : public doStat< doNormalMono< EOT > > +{ +public: + doStatNormalMono( doNormalMono< EOT >& distrib ) + : doStat< doNormalMono< EOT > >( distrib ) + {} + + virtual void printOn(std::ostream& os) const + { + os << this->distrib().mean() << " " << this->distrib().variance(); + } +}; + +#endif // !_doStatNormalMono_h diff --git a/src/doStatNormalMulti.h b/src/doStatNormalMulti.h new file mode 100644 index 00000000..7d57ee5a --- /dev/null +++ b/src/doStatNormalMulti.h @@ -0,0 +1,24 @@ +#ifndef _doStatNormalMulti_h +#define _doStatNormalMulti_h + +#include + +#include "doStat.h" +#include "doNormalMulti.h" +#include "doDistrib.h" + +template < typename EOT > +class doStatNormalMulti : public doStat< doNormalMulti< EOT > > +{ +public: + doStatNormalMulti( doNormalMulti< EOT >& distrib ) + : doStat< doNormalMulti< EOT > >( distrib ) + {} + + virtual void printOn(std::ostream& os) const + { + os << this->distrib().mean() << this->distrib().varcovar(); + } +}; + +#endif // !_doStatNormalMulti_h diff --git a/src/doStatUniform.h b/src/doStatUniform.h new file mode 100644 index 00000000..abeeb11d --- /dev/null +++ b/src/doStatUniform.h @@ -0,0 +1,21 @@ +#ifndef _doStatUniform_h +#define _doStatUniform_h + +#include "doStat.h" +#include "doUniform.h" + +template < typename EOT > +class doStatUniform : public doStat< doUniform< EOT > > +{ +public: + doStatUniform( doUniform< EOT >& distrib ) + : doStat< doUniform< EOT > >( distrib ) + {} + + virtual void printOn(std::ostream& os) const + { + os << this->distrib().min() << " " << this->distrib().max(); + } +}; + +#endif // !_doStatUniform_h diff --git a/src/doStats.cpp b/src/doStats.cpp deleted file mode 100644 index 80c9869f..00000000 --- a/src/doStats.cpp +++ /dev/null @@ -1,192 +0,0 @@ -/* - * Copyright (C) 2005 Maarten Keijzer - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of version 2 of the GNU General Public License as - * published by the Free Software Foundation. - * - * 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 -#include - -#include -#include - -#include "doStats.h" - -doStats::doStats() - : _n(0) -{} - -void doStats::printOn(std::ostream& _os) const -{ - _os << "Not implemented yet! "; -} - -doMean::doMean() - : _mean(0) -{} - -void doMean::update(double v) -{ - _n++; - - double d = v - _mean; - - _mean += 1 / _n * d; -} - -double doMean::get_mean() const -{ - return _mean; -} - -void doMean::printOn(std::ostream& _os) const -{ - _os << get_mean(); -} - -doVar::doVar() - : _sumvar(0) -{} - -void doVar::update(double v) -{ - _n++; - - double d = v - _mean; - - _mean += 1 / _n * d; - _sumvar += (_n - 1) / _n * d * d; -} - -double doVar::get_var() const -{ - return _sumvar / (_n - 1); -} - -double doVar::get_std() const -{ - return ::sqrt( get_var() ); -} - -void doVar::printOn(std::ostream& _os) const -{ - _os << get_var(); -} - -doCov::doCov() - : _meana(0), _meanb(0), _sumcov(0) -{} - -void doCov::update(double a, double b) -{ - ++_n; - - double da = a - _meana; - double db = b - _meanb; - - _meana += 1 / _n * da; - _meanb += 1 / _n * db; - - _sumcov += (_n - 1) / _n * da * db; -} - -double doCov::get_meana() const -{ - return _meana; -} - -double doCov::get_meanb() const -{ - return _meanb; -} - -double doCov::get_cov() const -{ - return _sumcov / (_n - 1); -} - -void doCov::printOn(std::ostream& _os) const -{ - _os << get_cov(); -} - -doCovMatrix::doCovMatrix(unsigned dim) - : _mean(dim), _sumcov(dim, std::vector< double >( dim )) -{} - -void doCovMatrix::update(const std::vector& v) -{ - assert(v.size() == _mean.size()); - - _n++; - - for (unsigned int i = 0; i < v.size(); ++i) - { - double d = v[i] - _mean[i]; - - _mean[i] += 1 / _n * d; - _sumcov[i][i] += (_n - 1) / _n * d * d; - - for (unsigned j = i; j < v.size(); ++j) - { - double e = v[j] - _mean[j]; // _mean[j] is not updated yet - - double upd = (_n - 1) / _n * d * e; - - _sumcov[i][j] += upd; - _sumcov[j][i] += upd; - } - } -} - -double doCovMatrix::get_mean(int i) const -{ - return _mean[i]; -} - -double doCovMatrix::get_var(int i) const -{ - return _sumcov[i][i] / (_n - 1); -} - -double doCovMatrix::get_std(int i) const -{ - return ::sqrt( get_var(i) ); -} - -double doCovMatrix::get_cov(int i, int j) const -{ - return _sumcov[i][j] / (_n - 1); -} - -doHyperVolume::doHyperVolume() - : _hv(1) -{} - -void doHyperVolume::update(double v) -{ - _hv *= ::sqrt(v); - - assert( _hv <= std::numeric_limits< double >::max() ); -} - -double doHyperVolume::get_hypervolume() const -{ - return _hv; -} - -void doHyperVolume::printOn(std::ostream& _os) const -{ - _os << get_hypervolume(); -} diff --git a/src/doStats.h b/src/doStats.h deleted file mode 100644 index 50cc9c95..00000000 --- a/src/doStats.h +++ /dev/null @@ -1,275 +0,0 @@ -/* - * Copyright (C) 2005 Maarten Keijzer - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of version 2 of the GNU General Public License as - * published by the Free Software Foundation. - * - * 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 _doStats_h -#define _doStats_h - -#include -#include -#include - -#include -#include - -namespace ublas = boost::numeric::ublas; - -class doStats : public eoPrintable -{ -public: - doStats(); - - virtual void printOn(std::ostream&) const; - -protected: - double _n; -}; - -class doMean : public doStats -{ -public: - doMean(); - - virtual void update(double); - virtual void printOn(std::ostream&) const; - - double get_mean() const; - -protected: - double _mean; -}; - -class doVar : public doMean -{ -public: - doVar(); - - virtual void update(double); - virtual void printOn(std::ostream&) const; - - double get_var() const; - double get_std() const; - -protected: - double _sumvar; -}; - -/** Single covariance between two variates */ -class doCov : public doStats -{ -public: - doCov(); - - virtual void update(double, double); - virtual void printOn(std::ostream&) const; - - double get_meana() const; - double get_meanb() const; - double get_cov() const; - -protected: - double _meana; - double _meanb; - double _sumcov; -}; - -class doCovMatrix : public doStats -{ -public: - doCovMatrix(unsigned dim); - - virtual void update(const std::vector&); - - double get_mean(int) const; - double get_var(int) const; - double get_std(int) const; - double get_cov(int, int) const; - -protected: - std::vector< double > _mean; - std::vector< std::vector< double > > _sumcov; -}; - -class doHyperVolume : public doStats -{ -public: - doHyperVolume(); - - virtual void update(double); - virtual void printOn(std::ostream&) const; - - double get_hypervolume() const; - -protected: - double _hv; -}; - -<<<<<<< HEAD -class doCholesky : public doStats -{ - -======= -template < typename EOT > -class doUblasCovMatrix : public doStats -{ -public: - typedef typename EOT::AtomType AtomType; - - virtual void update( const eoPop< EOT >& pop ) - { - unsigned int p_size = pop.size(); // population size - - assert(p_size > 0); - - unsigned int s_size = pop[0].size(); // solution size - - assert(s_size > 0); - - ublas::matrix< AtomType > sample( p_size, s_size ); - - for (unsigned int i = 0; i < p_size; ++i) - { - for (unsigned int j = 0; j < s_size; ++j) - { - sample(i, j) = pop[i][j]; - } - } - - _varcovar.resize(s_size, s_size); - - - //------------------------------------------------------------- - // variance-covariance matrix are symmetric (and semi-definite - // positive), thus a triangular storage is sufficient - //------------------------------------------------------------- - - ublas::symmetric_matrix< AtomType, ublas::lower > var(s_size, s_size); - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // variance-covariance matrix computation : A * transpose(A) - //------------------------------------------------------------- - - var = ublas::prod( sample, ublas::trans( sample ) ); - - //------------------------------------------------------------- - - - for (unsigned int i = 0; i < s_size; ++i) - { - // triangular LOWER matrix, thus j is not going further than i - for (unsigned int j = 0; j <= i; ++j) - { - // we want a reducted covariance matrix - _varcovar(i, j) = var(i, j) / p_size; - } - } - - _mean.resize(s_size); - - // unit vector - ublas::scalar_vector< AtomType > u( p_size, 1 ); - - // sum over columns - _mean = ublas::prod( ublas::trans( sample ), u ); - - // division by n - _mean /= p_size; - } - - const ublas::symmetric_matrix< AtomType, ublas::lower >& get_varcovar() const {return _varcovar;} - - const ublas::vector< AtomType >& get_mean() const {return _mean;} - -private: - ublas::symmetric_matrix< AtomType, ublas::lower > _varcovar; - ublas::vector< AtomType > _mean; -}; - -template < typename EOT > -class Cholesky : public doStats -{ -public: - typedef typename EOT::AtomType AtomType; - - virtual void update( const ublas::symmetric_matrix< AtomType, ublas::lower >& V) - { - unsigned int Vl = V.size1(); - - assert(Vl > 0); - - unsigned int Vc = V.size2(); - - assert(Vc > 0); - - _L.resize(Vl, Vc); - - unsigned int i,j,k; - - // first column - i=0; - - // diagonal - j=0; - _L(0, 0) = sqrt( V(0, 0) ); - - // end of the column - for ( j = 1; j < Vc; ++j ) - { - _L(j, 0) = V(0, j) / _L(0, 0); - } - - // end of the matrix - for ( i = 1; i < Vl; ++i ) // each column - { - - // diagonal - double sum = 0.0; - - for ( k = 0; k < i; ++k) - { - sum += _L(i, k) * _L(i, k); - } - - assert( ( V(i, i) - sum ) > 0 ); - - _L(i, i) = sqrt( V(i, i) - sum ); - - for ( j = i + 1; j < Vl; ++j ) // rows - { - // one element - sum = 0.0; - - for ( k = 0; k < i; ++k ) - { - sum += _L(j, k) * _L(i, k); - } - - _L(j, i) = (V(j, i) - sum) / _L(i, i); - } - } - } - - const ublas::symmetric_matrix< AtomType, ublas::lower >& get_L() const {return _L;} - -private: - ublas::symmetric_matrix< AtomType, ublas::lower > _L; ->>>>>>> 36ec42d36204631eb4c25ae7b31a8728903697f8 -}; - -#endif // !_doStats_h From 6d9134edbf22ec94f99a8747b770ac40e7561415 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 16 Aug 2010 11:30:06 +0200 Subject: [PATCH 25/74] * added the eo features Continue/CheckOut/Stat to DO in order to dump distribution parameters and to have compatibility with eoMonitor/eoUpdater classes --- application/cma_sa/main.cpp | 44 ++++++++--- src/do | 11 ++- src/doCMASA.h | 148 ++++++++++++++++++++--------------- src/doCheckPoint.h | 43 +++++++++- src/doContinue.h | 8 ++ src/doEstimatorNormalMulti.h | 1 - src/doNormalMono.h | 4 +- src/doNormalMulti.h | 4 +- src/doSamplerNormalMono.h | 1 - src/doSamplerNormalMulti.h | 3 +- src/doStat.h | 34 +++++--- src/doStatNormalMono.h | 17 ++-- src/doStatNormalMulti.h | 29 +++++-- src/doStatUniform.h | 17 ++-- src/doVectorBounds.h | 5 +- 15 files changed, 252 insertions(+), 117 deletions(-) diff --git a/application/cma_sa/main.cpp b/application/cma_sa/main.cpp index a452ead8..556e2e2c 100644 --- a/application/cma_sa/main.cpp +++ b/application/cma_sa/main.cpp @@ -75,11 +75,11 @@ int main(int ac, char** av) state.storeFunctor(init); - doStats< Distrib >* stats = - //new doStatsUniform< EOT >(); - //new doStatsNormalMono< EOT >(); - new doStatsNormalMulti< EOT >(); - state.storeFunctor(stats); + // doStats< Distrib >* stats = + // //new doStatsUniform< EOT >(); + // //new doStatsNormalMono< EOT >(); + // new doStatsNormalMulti< EOT >(); + // state.storeFunctor(stats); //----------------------------------------------------------------------------- @@ -122,8 +122,8 @@ int main(int ac, char** av) unsigned int rho = parser.createParam((unsigned int)0, "rho", "Rho: metropolis sample size", 'p', section).value(); // p - moGenSolContinue< EOT >* continuator = new moGenSolContinue< EOT >(rho); - state.storeFunctor(continuator); + moGenSolContinue< EOT >* sa_continue = new moGenSolContinue< EOT >(rho); + state.storeFunctor(sa_continue); double threshold = parser.createParam((double)0.1, "threshold", "Threshold: temperature threshold stopping criteria", 't', section).value(); // t double alpha = parser.createParam((double)0.1, "alpha", "Alpha: temperature dicrease rate", 'a', section).value(); // a @@ -134,11 +134,11 @@ int main(int ac, char** av) // stopping criteria // ... and creates the parameter letters: C E g G s T - eoContinue< EOT >& monitoring_continue = do_make_continue(parser, state, eval); + eoContinue< EOT >& eo_continue = do_make_continue(parser, state, eval); // output - eoCheckPoint< EOT >& checkpoint = do_make_checkpoint(parser, state, eval, monitoring_continue); + eoCheckPoint< EOT >& monitoring_continue = do_make_checkpoint(parser, state, eval, eo_continue); // eoPopStat< EOT >* popStat = new eoPopStat; // state.storeFunctor(popStat); @@ -162,6 +162,29 @@ int main(int ac, char** av) // checkpoint.add(*fileSnapshot); + doDummyContinue< Distrib >* dummy_continue = new doDummyContinue< Distrib >(); + state.storeFunctor(dummy_continue); + + doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue ); + state.storeFunctor(distribution_continue); + + doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); + state.storeFunctor(distrib_stat); + + distribution_continue->add( *distrib_stat ); + + eoMonitor* stdout_monitor = new eoStdoutMonitor(); + state.storeFunctor(stdout_monitor); + + stdout_monitor->add(*distrib_stat); + distribution_continue->add( *stdout_monitor ); + + eoFileMonitor* file_monitor = new eoFileMonitor("distribution.txt"); + state.storeFunctor(file_monitor); + + file_monitor->add(*distrib_stat); + distribution_continue->add( *file_monitor ); + //----------------------------------------------------------------------------- // eoEPRemplacement causes the using of the current and previous // sample for sampling. @@ -184,7 +207,8 @@ int main(int ac, char** av) doAlgo< Distrib >* algo = new doCMASA< Distrib > (*selector, *estimator, *selectone, *modifier, *sampler, - checkpoint, eval, *continuator, *cooling_schedule, + monitoring_continue, *distribution_continue, + eval, *sa_continue, *cooling_schedule, initial_temperature, *replacor); //----------------------------------------------------------------------------- diff --git a/src/do b/src/do index 10248481..b4bf2e8b 100644 --- a/src/do +++ b/src/do @@ -33,9 +33,12 @@ #include "doBounderBound.h" #include "doBounderRng.h" -#include "doStats.h" -#include "doStatsUniform.h" -#include "doStatsNormalMono.h" -#include "doStatsNormalMulti.h" +#include "doContinue.h" +#include "doCheckPoint.h" + +#include "doStat.h" +#include "doStatUniform.h" +#include "doStatNormalMono.h" +#include "doStatNormalMulti.h" #endif // !_do_ diff --git a/src/doCMASA.h b/src/doCMASA.h index ec7de9d8..06f6628f 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -34,7 +34,8 @@ #include "doModifierMass.h" #include "doSampler.h" #include "doHyperVolume.h" -#include "doStats.h" +#include "doStat.h" +#include "doContinue.h" using namespace boost::numeric::ublas; @@ -74,12 +75,12 @@ public: doModifierMass< D > & modifier, doSampler< D > & sampler, eoContinue< EOT > & monitoring_continue, + doContinue< D > & distribution_continue, eoEvalFunc < EOT > & evaluation, - moSolContinue < EOT > & continuator, + moSolContinue < EOT > & sa_continue, moCoolingSchedule & cooling_schedule, double initial_temperature, - eoReplacement< EOT > & replacor, - doStats< D > & stats + eoReplacement< EOT > & replacor ) : _selector(selector), _estimator(estimator), @@ -87,20 +88,22 @@ public: _modifier(modifier), _sampler(sampler), _monitoring_continue(monitoring_continue), + _distribution_continue(distribution_continue), _evaluation(evaluation), - _continuator(continuator), + _sa_continue(sa_continue), _cooling_schedule(cooling_schedule), _initial_temperature(initial_temperature), - _replacor(replacor), - _stats(stats), + _replacor(replacor) - _pop_results_destination("ResPop"), + // , - // directory where populations state are going to be stored. - _ofs_params("ResParams.txt"), - _ofs_params_var("ResVars.txt"), + // _pop_results_destination("ResPop"), - _bounds_results_destination("ResBounds") + // // directory where populations state are going to be stored. + // _ofs_params("ResParams.txt"), + // _ofs_params_var("ResVars.txt"), + + // _bounds_results_destination("ResBounds") { //------------------------------------------------------------- @@ -108,13 +111,13 @@ public: // iteration for plotting. //------------------------------------------------------------- - { - std::stringstream ss; - ss << "rm -rf " << _pop_results_destination; - ::system(ss.str().c_str()); - } + // { + // std::stringstream os; + // os << "rm -rf " << _pop_results_destination; + // ::system(os.str().c_str()); + // } - ::mkdir(_pop_results_destination.c_str(), 0755); // create a first time the + // ::mkdir(_pop_results_destination.c_str(), 0755); // create a first time the //------------------------------------------------------------- @@ -123,13 +126,13 @@ public: // Temporary solution to store bounds values for each distribution. //------------------------------------------------------------- - { - std::stringstream ss; - ss << "rm -rf " << _bounds_results_destination; - ::system(ss.str().c_str()); - } + // { + // std::stringstream os; + // os << "rm -rf " << _bounds_results_destination; + // ::system(os.str().c_str()); + // } - ::mkdir(_bounds_results_destination.c_str(), 0755); // create once directory + //::mkdir(_bounds_results_destination.c_str(), 0755); // create once directory //------------------------------------------------------------- @@ -159,26 +162,39 @@ public: // several files. //------------------------------------------------------------- - int number_of_iterations = 0; + //int number_of_iterations = 0; //------------------------------------------------------------- - { - D distrib = _estimator(pop); + //------------------------------------------------------------- + // Estimating a first time the distribution parameter thanks + // to population. + //------------------------------------------------------------- - double size = distrib.size(); - assert(size > 0); + D distrib = _estimator(pop); - doHyperVolume< EOT > hv; + double size = distrib.size(); + assert(size > 0); - for (int i = 0; i < size; ++i) - { - //hv.update( distrib.varcovar()[i] ); - } + //------------------------------------------------------------- - // _ofs_params_var << hv << std::endl; - } + + // { + // D distrib = _estimator(pop); + + // double size = distrib.size(); + // assert(size > 0); + + // doHyperVolume< EOT > hv; + + // for (int i = 0; i < size; ++i) + // { + // //hv.update( distrib.varcovar()[i] ); + // } + + // // _ofs_params_var << hv << std::endl; + // } do { @@ -200,14 +216,14 @@ public: //------------------------------------------------------------- - _continuator.init(); + _sa_continue.init(); //------------------------------------------------------------- // (4) Estimation of the distribution parameters //------------------------------------------------------------- - D distrib = _estimator(selected_pop); + distrib = _estimator(selected_pop); //------------------------------------------------------------- @@ -258,7 +274,7 @@ public: current_solution = candidate_solution; } } - while ( _continuator( current_solution) ); + while ( _sa_continue( current_solution) ); //------------------------------------------------------------- @@ -266,12 +282,12 @@ public: // at each iteration for plotting. //------------------------------------------------------------- - { - std::stringstream ss; - ss << _pop_results_destination << "/" << number_of_iterations; - std::ofstream ofs(ss.str().c_str()); - ofs << current_pop; - } + // { + // std::ostringstream os; + // os << _pop_results_destination << "/" << number_of_iterations; + // std::ofstream ofs(os.str().c_str()); + // ofs << current_pop; + // } //------------------------------------------------------------- @@ -281,20 +297,21 @@ public: // several files. //------------------------------------------------------------- - { - double size = distrib.size(); + // { + // double size = distrib.size(); - assert(size > 0); + // assert(size > 0); - std::stringstream ss; - ss << _bounds_results_destination << "/" << number_of_iterations; - std::ofstream ofs(ss.str().c_str()); + // std::stringstream os; + // os << _bounds_results_destination << "/" << number_of_iterations; + // std::ofstream ofs(os.str().c_str()); - ofs << size << " "; - std::copy(distrib.mean().begin(), distrib.mean().end(), std::ostream_iterator< double >(ofs, " ")); + // ofs << size << " "; + //ublas::vector< AtomType > mean = distrib.mean(); + //std::copy(mean.begin(), mean.end(), std::ostream_iterator< double >(ofs, " ")); //std::copy(distrib.varcovar().begin(), distrib.varcovar().end(), std::ostream_iterator< double >(ofs, " ")); - ofs << std::endl; - } + // ofs << std::endl; + // } //------------------------------------------------------------- @@ -350,11 +367,12 @@ public: //------------------------------------------------------------- - ++number_of_iterations; + //++number_of_iterations; } while ( _cooling_schedule( temperature ) && - _monitoring_continue( selected_pop ) ); + _monitoring_continue( selected_pop ) && + _distribution_continue( distrib ) ); } private: @@ -377,11 +395,14 @@ private: //! A EOT monitoring continuator eoContinue < EOT > & _monitoring_continue; + //! A D continuator + doContinue < D > & _distribution_continue; + //! A full evaluation function. eoEvalFunc < EOT > & _evaluation; //! Stopping criterion before temperature update - moSolContinue < EOT > & _continuator; + moSolContinue < EOT > & _sa_continue; //! The cooling schedule moCoolingSchedule & _cooling_schedule; @@ -392,17 +413,14 @@ private: //! A EOT replacor eoReplacement < EOT > & _replacor; - //! Stats to print distrib parameters out - doStats< D > & _stats; - //------------------------------------------------------------- // Temporary solution to store populations state at each // iteration for plotting. //------------------------------------------------------------- - std::string _pop_results_destination; - std::ofstream _ofs_params; - std::ofstream _ofs_params_var; + // std::string _pop_results_destination; + // std::ofstream _ofs_params; + // std::ofstream _ofs_params_var; //------------------------------------------------------------- @@ -410,7 +428,7 @@ private: // Temporary solution to store bounds values for each distribution. //------------------------------------------------------------- - std::string _bounds_results_destination; + // std::string _bounds_results_destination; //------------------------------------------------------------- diff --git a/src/doCheckPoint.h b/src/doCheckPoint.h index e569e08d..79a2cfe8 100644 --- a/src/doCheckPoint.h +++ b/src/doCheckPoint.h @@ -1,6 +1,9 @@ #ifndef _doCheckPoint_h #define _doCheckPoint_h +#include +#include + #include "doContinue.h" #include "doStat.h" @@ -24,10 +27,20 @@ public: (*_stats[i])( distrib ); } + for ( unsigned int i = 0, size = _updaters.size(); i < size; ++i ) + { + (*_updaters[i])(); + } + + for ( unsigned int i = 0, size = _monitors.size(); i < size; ++i ) + { + (*_monitors[i])(); + } + bool bContinue = true; for ( unsigned int i = 0, size = _continuators.size(); i < size; ++i ) { - if ( !(*_continuators[i]( distrib )) ) + if ( !(*_continuators[i])( distrib ) ) { bContinue = false; } @@ -39,6 +52,16 @@ public: { _stats[i]->lastCall( distrib ); } + + for ( unsigned int i = 0, size = _updaters.size(); i < size; ++i ) + { + _updaters[i]->lastCall(); + } + + for ( unsigned int i = 0, size = _monitors.size(); i < size; ++i ) + { + _monitors[i]->lastCall(); + } } return bContinue; @@ -46,6 +69,8 @@ public: void add(doContinue< D >& cont) { _continuators.push_back( &cont ); } void add(doStatBase< D >& stat) { _stats.push_back( &stat ); } + void add(eoMonitor& mon) { _monitors.push_back( &mon ); } + void add(eoUpdater& upd) { _updaters.push_back( &upd ); } virtual std::string className(void) const { return "doCheckPoint"; } @@ -60,6 +85,20 @@ public: } s += "\n"; + s += "Updaters\n"; + for ( unsigned int i = 0; i < _updaters.size(); ++i ) + { + s += _updaters[i]->className() + "\n"; + } + s += "\n"; + + s += "Monitors\n"; + for ( unsigned int i = 0; i < _monitors.size(); ++i ) + { + s += _monitors[i]->className() + "\n"; + } + s += "\n"; + s += "Continuators\n"; for ( unsigned int i = 0, size = _continuators.size(); i < size; ++i ) { @@ -73,6 +112,8 @@ public: private: std::vector< doContinue< D >* > _continuators; std::vector< doStatBase< D >* > _stats; + std::vector< eoMonitor* > _monitors; + std::vector< eoUpdater* > _updaters; }; #endif // !_doCheckPoint_h diff --git a/src/doContinue.h b/src/doContinue.h index f7a7448d..f0b56daf 100644 --- a/src/doContinue.h +++ b/src/doContinue.h @@ -24,4 +24,12 @@ public: } }; +template < typename D > +class doDummyContinue : public doContinue< D > +{ + bool operator()(const D&){ return true; } + + virtual std::string className() const { return "doNoContinue"; } +}; + #endif // !_doContinue_h diff --git a/src/doEstimatorNormalMulti.h b/src/doEstimatorNormalMulti.h index 404a71d2..0e7d50ab 100644 --- a/src/doEstimatorNormalMulti.h +++ b/src/doEstimatorNormalMulti.h @@ -3,7 +3,6 @@ #include "doEstimator.h" #include "doUniform.h" -#include "doStats.h" template < typename EOT > class doEstimatorNormalMulti : public doEstimator< doNormalMulti< EOT > > diff --git a/src/doNormalMono.h b/src/doNormalMono.h index aa334085..6fb0b9b7 100644 --- a/src/doNormalMono.h +++ b/src/doNormalMono.h @@ -20,8 +20,8 @@ public: return _mean.size(); } - EOT& mean(){return _mean;} - EOT& variance(){return _variance;} + EOT mean(){return _mean;} + EOT variance(){return _variance;} private: EOT _mean; diff --git a/src/doNormalMulti.h b/src/doNormalMulti.h index 9c89c8d3..50082efb 100644 --- a/src/doNormalMulti.h +++ b/src/doNormalMulti.h @@ -33,8 +33,8 @@ public: return _mean.size(); } - ublas::vector< AtomType >& mean(){return _mean;} - ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar(){return _varcovar;} + ublas::vector< AtomType > mean() const {return _mean;} + ublas::symmetric_matrix< AtomType, ublas::lower > varcovar() const {return _varcovar;} private: ublas::vector< AtomType > _mean; diff --git a/src/doSamplerNormalMono.h b/src/doSamplerNormalMono.h index fa45b2e8..10592682 100644 --- a/src/doSamplerNormalMono.h +++ b/src/doSamplerNormalMono.h @@ -6,7 +6,6 @@ #include "doSampler.h" #include "doNormalMono.h" #include "doBounder.h" -#include "doStats.h" /** * doSamplerNormalMono diff --git a/src/doSamplerNormalMulti.h b/src/doSamplerNormalMulti.h index ae54945b..8c3de541 100644 --- a/src/doSamplerNormalMulti.h +++ b/src/doSamplerNormalMulti.h @@ -10,7 +10,6 @@ #include "doSampler.h" #include "doNormalMulti.h" #include "doBounder.h" -#include "doStats.h" /** * doSamplerNormalMulti @@ -26,7 +25,7 @@ public: class Cholesky { public: - virtual void update( const ublas::symmetric_matrix< AtomType, ublas::lower >& V) + void update( const ublas::symmetric_matrix< AtomType, ublas::lower >& V) { unsigned int Vl = V.size1(); diff --git a/src/doStat.h b/src/doStat.h index 46b213ba..dd32f6a4 100644 --- a/src/doStat.h +++ b/src/doStat.h @@ -13,21 +13,35 @@ public: virtual std::string className() const { return "doStatBase"; } }; -template < typename D > -class doStat : doStatBase< D > +template < typename D > class doCheckPoint; + +template < typename D, typename T > +class doStat : public eoValueParam< T >, public doStatBase< D > { public: - typedef typename D::EOType EOType; - typedef typename EOType::AtomType AtomType; + doStat(T value, std::string description) + : eoValueParam< T >(value, description) + {} + virtual std::string className(void) const { return "doStat"; } + + doStat< D, T >& addTo(doCheckPoint< D >& cp) { cp.add(*this); return *this; } + + // TODO: doStat< D, T >& addTo(doMonitor& mon) { mon.add(*this); return *this; } +}; + + +//! A parent class for any kind of distribution to dump parameter to std::string type + +template < typename D > +class doDistribStat : public doStat< D, std::string > +{ public: - doStat(){} + using doStat< D, std::string >::value; - - D& distrib() { return _distrib; } - -private: - D& _distrib; + doDistribStat(std::string desc) + : doStat< D, std::string >("", desc) + {} }; #endif // !_doStat_h diff --git a/src/doStatNormalMono.h b/src/doStatNormalMono.h index bc0a5b60..7259f294 100644 --- a/src/doStatNormalMono.h +++ b/src/doStatNormalMono.h @@ -5,16 +5,23 @@ #include "doNormalMono.h" template < typename EOT > -class doStatNormalMono : public doStat< doNormalMono< EOT > > +class doStatNormalMono : public doDistribStat< doNormalMono< EOT > > { public: - doStatNormalMono( doNormalMono< EOT >& distrib ) - : doStat< doNormalMono< EOT > >( distrib ) + using doDistribStat< doNormalMono< EOT > >::value; + + doStatNormalMono( std::string desc = "" ) + : doDistribStat< doNormalMono< EOT > >( desc ) {} - virtual void printOn(std::ostream& os) const + void operator()( const doNormalMono< EOT >& distrib ) { - os << this->distrib().mean() << " " << this->distrib().variance(); + value() = "\n# ====== mono normal distribution dump =====\n"; + + std::ostringstream os; + os << distrib.mean() << " " << distrib.variance() << std::endl; + + value() += os.str(); } }; diff --git a/src/doStatNormalMulti.h b/src/doStatNormalMulti.h index 7d57ee5a..7c3cb8e0 100644 --- a/src/doStatNormalMulti.h +++ b/src/doStatNormalMulti.h @@ -5,19 +5,36 @@ #include "doStat.h" #include "doNormalMulti.h" -#include "doDistrib.h" template < typename EOT > -class doStatNormalMulti : public doStat< doNormalMulti< EOT > > +class doStatNormalMulti : public doDistribStat< doNormalMulti< EOT > > { public: - doStatNormalMulti( doNormalMulti< EOT >& distrib ) - : doStat< doNormalMulti< EOT > >( distrib ) + typedef typename EOT::AtomType AtomType; + + using doDistribStat< doNormalMulti< EOT > >::value; + + doStatNormalMulti( std::string desc = "" ) + : doDistribStat< doNormalMulti< EOT > >( desc ) {} - virtual void printOn(std::ostream& os) const + void operator()( const doNormalMulti< EOT >& distrib ) { - os << this->distrib().mean() << this->distrib().varcovar(); + value() = "\n# ====== multi normal distribution dump =====\n"; + + std::ostringstream os; + + os << distrib.mean() << " " << distrib.varcovar() << std::endl; + + // ublas::vector< AtomType > mean = distrib.mean(); + // std::copy(mean.begin(), mean.end(), std::ostream_iterator< std::string >( os, " " )); + + // ublas::symmetric_matrix< AtomType, ublas::lower > varcovar = distrib.varcovar(); + // std::copy(varcovar.begin(), varcovar.end(), std::ostream_iterator< std::string >( os, " " )); + + // os << std::endl; + + value() += os.str(); } }; diff --git a/src/doStatUniform.h b/src/doStatUniform.h index abeeb11d..442ef5f8 100644 --- a/src/doStatUniform.h +++ b/src/doStatUniform.h @@ -5,16 +5,23 @@ #include "doUniform.h" template < typename EOT > -class doStatUniform : public doStat< doUniform< EOT > > +class doStatUniform : public doDistribStat< doUniform< EOT > > { public: - doStatUniform( doUniform< EOT >& distrib ) - : doStat< doUniform< EOT > >( distrib ) + using doDistribStat< doUniform< EOT > >::value; + + doStatUniform( std::string desc = "" ) + : doDistribStat< doUniform< EOT > >( desc ) {} - virtual void printOn(std::ostream& os) const + void operator()( const doUniform< EOT >& distrib ) { - os << this->distrib().min() << " " << this->distrib().max(); + value() = "\n# ====== uniform distribution dump =====\n"; + + std::ostringstream os; + os << distrib.min() << " " << distrib.max() << std::endl; + + value() += os.str(); } }; diff --git a/src/doVectorBounds.h b/src/doVectorBounds.h index 07e4e2cf..02788046 100644 --- a/src/doVectorBounds.h +++ b/src/doVectorBounds.h @@ -12,9 +12,8 @@ public: assert(_min.size() == _max.size()); } - EOT& min(){return _min;} - EOT& max(){return _max;} - + EOT min(){return _min;} + EOT max(){return _max;} unsigned int size() { From 5583208c75ab5d4590b72678529b96fd990a18dd Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 16 Aug 2010 11:45:43 +0200 Subject: [PATCH 26/74] added L(i,i) = sqrt( abs(V(i,i) - sum) ) but the issue still exists --- src/doSamplerNormalMulti.h | 4 +++- src/doStat.h | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/doSamplerNormalMulti.h b/src/doSamplerNormalMulti.h index 8c3de541..94e40758 100644 --- a/src/doSamplerNormalMulti.h +++ b/src/doSamplerNormalMulti.h @@ -66,7 +66,9 @@ public: assert( ( V(i, i) - sum ) > 0 ); - _L(i, i) = sqrt( V(i, i) - sum ); + //_L(i, i) = sqrt( V(i, i) - sum ); + + _L(i,i) = sqrt( fabs( V(i,i) - sum) ); for ( j = i + 1; j < Vl; ++j ) // rows { diff --git a/src/doStat.h b/src/doStat.h index dd32f6a4..a6ac76e5 100644 --- a/src/doStat.h +++ b/src/doStat.h @@ -27,7 +27,7 @@ public: doStat< D, T >& addTo(doCheckPoint< D >& cp) { cp.add(*this); return *this; } - // TODO: doStat< D, T >& addTo(doMonitor& mon) { mon.add(*this); return *this; } + // TODO: doStat< D, T >& addTo(eoMonitor& mon) { mon.add(*this); return *this; } }; From 10d1ebbb9b826ef53d991cc5c94d84c863697233 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 16 Aug 2010 15:38:39 +0200 Subject: [PATCH 27/74] issue to fix --- application/cma_sa/main.cpp | 4 ++-- src/doCMASA.h | 26 ++++++++++++++------------ src/doSamplerNormalMulti.h | 2 ++ 3 files changed, 18 insertions(+), 14 deletions(-) diff --git a/application/cma_sa/main.cpp b/application/cma_sa/main.cpp index 556e2e2c..607997cf 100644 --- a/application/cma_sa/main.cpp +++ b/application/cma_sa/main.cpp @@ -38,7 +38,7 @@ int main(int ac, char** av) // Instantiate all need parameters for CMASA algorithm //----------------------------------------------------------------------------- - eoSelect< EOT >* selector = new eoDetSelect< EOT >(0.1); + eoSelect< EOT >* selector = new eoDetSelect< EOT >(0.5); state.storeFunctor(selector); doEstimator< Distrib >* estimator = @@ -47,7 +47,7 @@ int main(int ac, char** av) new doEstimatorNormalMulti< EOT >(); state.storeFunctor(estimator); - eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >(); + eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >( 2 ); state.storeFunctor(selectone); doModifierMass< Distrib >* modifier = diff --git a/src/doCMASA.h b/src/doCMASA.h index 06f6628f..45b06705 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -162,7 +162,7 @@ public: // several files. //------------------------------------------------------------- - //int number_of_iterations = 0; + int number_of_iterations = 0; //------------------------------------------------------------- @@ -213,6 +213,8 @@ public: _selector(pop, selected_pop); + assert( selected_pop.size() > 0 ); + //------------------------------------------------------------- @@ -351,23 +353,23 @@ public: // dicreasement //------------------------------------------------------------- - { - double size = distrib.size(); - assert(size > 0); + // { + // double size = distrib.size(); + // assert(size > 0); - doHyperVolume< EOT > hv; + // doHyperVolume< EOT > hv; - for (int i = 0; i < size; ++i) - { - //hv.update( distrib.varcovar()[i] ); - } + // for (int i = 0; i < size; ++i) + // { + // //hv.update( distrib.varcovar()[i] ); + // } - //_ofs_params_var << hv << std::endl; - } + // //_ofs_params_var << hv << std::endl; + // } //------------------------------------------------------------- - //++number_of_iterations; + ++number_of_iterations; } while ( _cooling_schedule( temperature ) && diff --git a/src/doSamplerNormalMulti.h b/src/doSamplerNormalMulti.h index 94e40758..36bf6c2e 100644 --- a/src/doSamplerNormalMulti.h +++ b/src/doSamplerNormalMulti.h @@ -35,6 +35,8 @@ public: assert(Vc > 0); + assert( Vl == Vc ); + _L.resize(Vl, Vc); unsigned int i,j,k; From fd413603042a57f41506f0b08c5c5386f2082038 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 17 Aug 2010 17:44:53 +0200 Subject: [PATCH 28/74] bug fixed --- src/doEstimatorNormalMulti.h | 41 +++++++++++++++++++++++------------- src/doSamplerNormalMulti.h | 7 +++--- 2 files changed, 29 insertions(+), 19 deletions(-) diff --git a/src/doEstimatorNormalMulti.h b/src/doEstimatorNormalMulti.h index 0e7d50ab..63df5606 100644 --- a/src/doEstimatorNormalMulti.h +++ b/src/doEstimatorNormalMulti.h @@ -13,7 +13,7 @@ public: public: typedef typename EOT::AtomType AtomType; - void update( const eoPop< EOT >& pop ) + CovMatrix( const eoPop< EOT >& pop ) { unsigned int p_size = pop.size(); // population size @@ -41,7 +41,7 @@ public: // positive), thus a triangular storage is sufficient //------------------------------------------------------------- - ublas::symmetric_matrix< AtomType, ublas::lower > var(s_size, s_size); + //ublas::symmetric_matrix< AtomType, ublas::lower > var; //(s_size, s_size); //------------------------------------------------------------- @@ -50,20 +50,33 @@ public: // variance-covariance matrix computation : A * transpose(A) //------------------------------------------------------------- - var = ublas::prod( sample, ublas::trans( sample ) ); + //ublas::matrix< AtomType > var = ublas::prod( sample, ublas::trans( sample ) ); + //ublas::symmetric_matrix< AtomType, ublas::lower > var = ublas::prod( sample, ublas::trans( sample ) ); + ublas::symmetric_matrix< AtomType, ublas::lower > var = ublas::prod( ublas::trans( sample ), sample ); + + assert(var.size1() == s_size); + assert(var.size2() == s_size); + assert(var.size1() == _varcovar.size1()); + assert(var.size2() == _varcovar.size2()); + + std::cout << "_varcovar: " << _varcovar << std::endl; + std::cout << "var: " << var << std::endl; //------------------------------------------------------------- - for (unsigned int i = 0; i < s_size; ++i) - { - // triangular LOWER matrix, thus j is not going further than i - for (unsigned int j = 0; j <= i; ++j) - { - // we want a reducted covariance matrix - _varcovar(i, j) = var(i, j) / p_size; - } - } + // for (unsigned int i = 0; i < s_size; ++i) + // { + // // triangular LOWER matrix, thus j is not going further than i + // for (unsigned int j = 0; j <= i; ++j) + // { + // // we want a reducted covariance matrix + // std::cout << "i " << i << " j " << j << std::endl; + // _varcovar(i, j) = var(i, j) / p_size; + // } + // } + + _varcovar = var / p_size; _mean.resize(s_size); @@ -97,9 +110,7 @@ public: unsigned int dimsize = pop[0].size(); assert(dimsize > 0); - CovMatrix cov; - - cov.update(pop); + CovMatrix cov( pop ); return doNormalMulti< EOT >( cov.get_mean(), cov.get_varcovar() ); } diff --git a/src/doSamplerNormalMulti.h b/src/doSamplerNormalMulti.h index 36bf6c2e..3164af3f 100644 --- a/src/doSamplerNormalMulti.h +++ b/src/doSamplerNormalMulti.h @@ -25,7 +25,7 @@ public: class Cholesky { public: - void update( const ublas::symmetric_matrix< AtomType, ublas::lower >& V) + Cholesky( const ublas::symmetric_matrix< AtomType, ublas::lower >& V) { unsigned int Vl = V.size1(); @@ -66,7 +66,7 @@ public: sum += _L(i, k) * _L(i, k); } - assert( ( V(i, i) - sum ) > 0 ); + // assert( ( V(i, i) - sum ) > 0 ); //_L(i, i) = sqrt( V(i, i) - sum ); @@ -112,8 +112,7 @@ public: // L = cholesky decomposition of varcovar //------------------------------------------------------------- - Cholesky cholesky; - cholesky.update( distrib.varcovar() ); + Cholesky cholesky( distrib.varcovar() ); ublas::symmetric_matrix< AtomType, ublas::lower > L = cholesky.get_L(); //------------------------------------------------------------- From 29486099051d866fef3211d0b319582e4e34cce4 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 18 Aug 2010 13:37:17 +0200 Subject: [PATCH 29/74] - some useless comments + authors in files header --- src/do | 7 +++++++ src/do.cpp | 7 +++++++ src/doAlgo.h | 7 +++++++ src/doBounder.h | 7 +++++++ src/doBounderBound.h | 7 +++++++ src/doBounderNo.h | 7 +++++++ src/doBounderRng.h | 7 +++++++ src/doCMASA.h | 7 +++++++ src/doCheckPoint.h | 7 +++++++ src/doContinue.h | 7 +++++++ src/doDistrib.h | 7 +++++++ src/doEstimator.h | 7 +++++++ src/doEstimatorNormalMono.h | 7 +++++++ src/doEstimatorNormalMulti.h | 24 +++++++++--------------- src/doEstimatorUniform.h | 7 +++++++ src/doHyperVolume.h | 7 +++++++ src/doModifier.h | 7 +++++++ src/doModifierDispersion.h | 7 +++++++ src/doModifierMass.h | 7 +++++++ src/doNormalMono.h | 7 +++++++ src/doNormalMonoCenter.h | 7 +++++++ src/doNormalMulti.h | 7 +++++++ src/doNormalMultiCenter.h | 7 +++++++ src/doSampler.h | 7 +++++++ src/doSamplerNormalMono.h | 7 +++++++ src/doSamplerNormalMulti.h | 11 +++++++---- src/doSamplerUniform.h | 7 +++++++ src/doStat.h | 7 +++++++ src/doStatNormalMono.h | 7 +++++++ src/doStatNormalMulti.h | 7 +++++++ src/doStatUniform.h | 7 +++++++ src/doUniform.h | 7 +++++++ src/doUniformCenter.h | 7 +++++++ src/doVectorBounds.h | 7 +++++++ src/todo | 2 -- 35 files changed, 240 insertions(+), 21 deletions(-) delete mode 100644 src/todo diff --git a/src/do b/src/do index b4bf2e8b..cd18c140 100644 --- a/src/do +++ b/src/do @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _do_ #define _do_ diff --git a/src/do.cpp b/src/do.cpp index b33d98fe..082374a4 100644 --- a/src/do.cpp +++ b/src/do.cpp @@ -1 +1,8 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #include "do" diff --git a/src/doAlgo.h b/src/doAlgo.h index 54ea1698..0f260d93 100644 --- a/src/doAlgo.h +++ b/src/doAlgo.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doAlgo_h #define _doAlgo_h diff --git a/src/doBounder.h b/src/doBounder.h index 28996474..3ce4a554 100644 --- a/src/doBounder.h +++ b/src/doBounder.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doBounder_h #define _doBounder_h diff --git a/src/doBounderBound.h b/src/doBounderBound.h index a284d2cb..cff765b8 100644 --- a/src/doBounderBound.h +++ b/src/doBounderBound.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doBounderBound_h #define _doBounderBound_h diff --git a/src/doBounderNo.h b/src/doBounderNo.h index 36e34451..94d873a8 100644 --- a/src/doBounderNo.h +++ b/src/doBounderNo.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doBounderNo_h #define _doBounderNo_h diff --git a/src/doBounderRng.h b/src/doBounderRng.h index 2f2450bc..52b95bca 100644 --- a/src/doBounderRng.h +++ b/src/doBounderRng.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doBounderRng_h #define _doBounderRng_h diff --git a/src/doCMASA.h b/src/doCMASA.h index 45b06705..1536f08f 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doCMASA_h #define _doCMASA_h diff --git a/src/doCheckPoint.h b/src/doCheckPoint.h index 79a2cfe8..d424e184 100644 --- a/src/doCheckPoint.h +++ b/src/doCheckPoint.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doCheckPoint_h #define _doCheckPoint_h diff --git a/src/doContinue.h b/src/doContinue.h index f0b56daf..a93de093 100644 --- a/src/doContinue.h +++ b/src/doContinue.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doContinue_h #define _doContinue_h diff --git a/src/doDistrib.h b/src/doDistrib.h index 71c2f6f1..15b051f8 100644 --- a/src/doDistrib.h +++ b/src/doDistrib.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doDistrib_h #define _doDistrib_h diff --git a/src/doEstimator.h b/src/doEstimator.h index 682dd3f7..956bed78 100644 --- a/src/doEstimator.h +++ b/src/doEstimator.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doEstimator_h #define _doEstimator_h diff --git a/src/doEstimatorNormalMono.h b/src/doEstimatorNormalMono.h index c6e168b7..fb9c1f2f 100644 --- a/src/doEstimatorNormalMono.h +++ b/src/doEstimatorNormalMono.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doEstimatorNormalMono_h #define _doEstimatorNormalMono_h diff --git a/src/doEstimatorNormalMulti.h b/src/doEstimatorNormalMulti.h index 63df5606..e1c907b2 100644 --- a/src/doEstimatorNormalMulti.h +++ b/src/doEstimatorNormalMulti.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doEstimatorNormalMulti_h #define _doEstimatorNormalMulti_h @@ -39,19 +46,10 @@ public: //------------------------------------------------------------- // variance-covariance matrix are symmetric (and semi-definite // positive), thus a triangular storage is sufficient + // + // variance-covariance matrix computation : transpose(A) * A //------------------------------------------------------------- - //ublas::symmetric_matrix< AtomType, ublas::lower > var; //(s_size, s_size); - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // variance-covariance matrix computation : A * transpose(A) - //------------------------------------------------------------- - - //ublas::matrix< AtomType > var = ublas::prod( sample, ublas::trans( sample ) ); - //ublas::symmetric_matrix< AtomType, ublas::lower > var = ublas::prod( sample, ublas::trans( sample ) ); ublas::symmetric_matrix< AtomType, ublas::lower > var = ublas::prod( ublas::trans( sample ), sample ); assert(var.size1() == s_size); @@ -59,9 +57,6 @@ public: assert(var.size1() == _varcovar.size1()); assert(var.size2() == _varcovar.size2()); - std::cout << "_varcovar: " << _varcovar << std::endl; - std::cout << "var: " << var << std::endl; - //------------------------------------------------------------- @@ -71,7 +66,6 @@ public: // for (unsigned int j = 0; j <= i; ++j) // { // // we want a reducted covariance matrix - // std::cout << "i " << i << " j " << j << std::endl; // _varcovar(i, j) = var(i, j) / p_size; // } // } diff --git a/src/doEstimatorUniform.h b/src/doEstimatorUniform.h index 8f9b3551..ca361ce0 100644 --- a/src/doEstimatorUniform.h +++ b/src/doEstimatorUniform.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doEstimatorUniform_h #define _doEstimatorUniform_h diff --git a/src/doHyperVolume.h b/src/doHyperVolume.h index c47f457b..2a1be37f 100644 --- a/src/doHyperVolume.h +++ b/src/doHyperVolume.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doHyperVolume_h #define _doHyperVolume_h diff --git a/src/doModifier.h b/src/doModifier.h index 9c28f996..b36106c9 100644 --- a/src/doModifier.h +++ b/src/doModifier.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doModifier_h #define _doModifier_h diff --git a/src/doModifierDispersion.h b/src/doModifierDispersion.h index 2632757b..4d5e42c4 100644 --- a/src/doModifierDispersion.h +++ b/src/doModifierDispersion.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doModifierDispersion_h #define _doModifierDispersion_h diff --git a/src/doModifierMass.h b/src/doModifierMass.h index 411c3f29..4f5df5c0 100644 --- a/src/doModifierMass.h +++ b/src/doModifierMass.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doModifierMass_h #define _doModifierMass_h diff --git a/src/doNormalMono.h b/src/doNormalMono.h index 6fb0b9b7..fa8f8e6f 100644 --- a/src/doNormalMono.h +++ b/src/doNormalMono.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doNormalMono_h #define _doNormalMono_h diff --git a/src/doNormalMonoCenter.h b/src/doNormalMonoCenter.h index 48b448a4..7786d347 100644 --- a/src/doNormalMonoCenter.h +++ b/src/doNormalMonoCenter.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doNormalMonoCenter_h #define _doNormalMonoCenter_h diff --git a/src/doNormalMulti.h b/src/doNormalMulti.h index 50082efb..1b3e3f16 100644 --- a/src/doNormalMulti.h +++ b/src/doNormalMulti.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doNormalMulti_h #define _doNormalMulti_h diff --git a/src/doNormalMultiCenter.h b/src/doNormalMultiCenter.h index 65e9ec7c..bf52ecf1 100644 --- a/src/doNormalMultiCenter.h +++ b/src/doNormalMultiCenter.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doNormalMultiCenter_h #define _doNormalMultiCenter_h diff --git a/src/doSampler.h b/src/doSampler.h index 1bb66b44..63641247 100644 --- a/src/doSampler.h +++ b/src/doSampler.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doSampler_h #define _doSampler_h diff --git a/src/doSamplerNormalMono.h b/src/doSamplerNormalMono.h index 10592682..b790ee6b 100644 --- a/src/doSamplerNormalMono.h +++ b/src/doSamplerNormalMono.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doSamplerNormalMono_h #define _doSamplerNormalMono_h diff --git a/src/doSamplerNormalMulti.h b/src/doSamplerNormalMulti.h index 3164af3f..2378634a 100644 --- a/src/doSamplerNormalMulti.h +++ b/src/doSamplerNormalMulti.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doSamplerNormalMulti_h #define _doSamplerNormalMulti_h @@ -66,10 +73,6 @@ public: sum += _L(i, k) * _L(i, k); } - // assert( ( V(i, i) - sum ) > 0 ); - - //_L(i, i) = sqrt( V(i, i) - sum ); - _L(i,i) = sqrt( fabs( V(i,i) - sum) ); for ( j = i + 1; j < Vl; ++j ) // rows diff --git a/src/doSamplerUniform.h b/src/doSamplerUniform.h index 374d7a8e..e407360d 100644 --- a/src/doSamplerUniform.h +++ b/src/doSamplerUniform.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doSamplerUniform_h #define _doSamplerUniform_h diff --git a/src/doStat.h b/src/doStat.h index a6ac76e5..5a6056a9 100644 --- a/src/doStat.h +++ b/src/doStat.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doStat_h #define _doStat_h diff --git a/src/doStatNormalMono.h b/src/doStatNormalMono.h index 7259f294..1eab0d53 100644 --- a/src/doStatNormalMono.h +++ b/src/doStatNormalMono.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doStatNormalMono_h #define _doStatNormalMono_h diff --git a/src/doStatNormalMulti.h b/src/doStatNormalMulti.h index 7c3cb8e0..d433e40e 100644 --- a/src/doStatNormalMulti.h +++ b/src/doStatNormalMulti.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doStatNormalMulti_h #define _doStatNormalMulti_h diff --git a/src/doStatUniform.h b/src/doStatUniform.h index 442ef5f8..808750f7 100644 --- a/src/doStatUniform.h +++ b/src/doStatUniform.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doStatUniform_h #define _doStatUniform_h diff --git a/src/doUniform.h b/src/doUniform.h index 6bfd9016..624fec1f 100644 --- a/src/doUniform.h +++ b/src/doUniform.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doUniform_h #define _doUniform_h diff --git a/src/doUniformCenter.h b/src/doUniformCenter.h index 74864d8b..8b0016bc 100644 --- a/src/doUniformCenter.h +++ b/src/doUniformCenter.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doUniformCenter_h #define _doUniformCenter_h diff --git a/src/doVectorBounds.h b/src/doVectorBounds.h index 02788046..4e23d486 100644 --- a/src/doVectorBounds.h +++ b/src/doVectorBounds.h @@ -1,3 +1,10 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + #ifndef _doVectorBounds_h #define _doVectorBounds_h diff --git a/src/todo b/src/todo deleted file mode 100644 index 13785cc8..00000000 --- a/src/todo +++ /dev/null @@ -1,2 +0,0 @@ -* deplacer les ecritures pour gnuplot dans des classes type eoContinue (eoMonitor) -* integrer ACP From bd390cd217ffe594e8b83196bb9165a923fce81f Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 18 Aug 2010 18:22:28 +0200 Subject: [PATCH 30/74] - useless comments and files removed --- application/cma_sa/main.cpp | 19 ++++--------- readme | 57 ------------------------------------- src/doCMASA.h | 45 ++++++++++++++--------------- 3 files changed, 27 insertions(+), 94 deletions(-) delete mode 100644 readme diff --git a/application/cma_sa/main.cpp b/application/cma_sa/main.cpp index 607997cf..4fc41bbb 100644 --- a/application/cma_sa/main.cpp +++ b/application/cma_sa/main.cpp @@ -74,13 +74,6 @@ int main(int ac, char** av) eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( dimension_size, *gen ); state.storeFunctor(init); - - // doStats< Distrib >* stats = - // //new doStatsUniform< EOT >(); - // //new doStatsNormalMono< EOT >(); - // new doStatsNormalMulti< EOT >(); - // state.storeFunctor(stats); - //----------------------------------------------------------------------------- @@ -173,15 +166,13 @@ int main(int ac, char** av) distribution_continue->add( *distrib_stat ); - eoMonitor* stdout_monitor = new eoStdoutMonitor(); - state.storeFunctor(stdout_monitor); + // eoMonitor* stdout_monitor = new eoStdoutMonitor(); + // state.storeFunctor(stdout_monitor); + // stdout_monitor->add(*distrib_stat); + // distribution_continue->add( *stdout_monitor ); - stdout_monitor->add(*distrib_stat); - distribution_continue->add( *stdout_monitor ); - - eoFileMonitor* file_monitor = new eoFileMonitor("distribution.txt"); + eoFileMonitor* file_monitor = new eoFileMonitor("distribution_bounds.txt"); state.storeFunctor(file_monitor); - file_monitor->add(*distrib_stat); distribution_continue->add( *file_monitor ); diff --git a/readme b/readme deleted file mode 100644 index 64629f58..00000000 --- a/readme +++ /dev/null @@ -1,57 +0,0 @@ -This package contains the source code for BOPO problems. - -# Step 1 - Configuration ------------------------- -Rename the "install.cmake-dist" file as "install.cmake" and edit it, inserting the FULL PATH -to your ParadisEO distribution. -On Windows write your path with double antislash (ex: C:\\Users\\...) - - -# Step 2 - Build process ------------------------- -ParadisEO is assumed to be compiled. To download ParadisEO, please visit http://paradiseo.gforge.inria.fr/. -Go to the BOPO/build/ directory and lunch cmake: -(Unix) > cmake .. -(Windows) > cmake .. -G"Visual Studio 9 2008" - -Note for windows users: if you don't use VisualStudio 9, enter the name of your generator instead of "VisualStudio 9 2008". - - -# Step 3 - Compilation ----------------------- -In the bopo/build/ directory: -(Unix) > make -(Windows) Open the VisualStudio solution and compile it, compile also the target install. -You can refer to this tutorial if you don't know how to compile a solution: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial - - -# Step 4 - Execution ---------------------- -A toy example is given to test the components. You can run these tests as following. -To define problem-related components for your own problem, please refer to the tutorials available on the website : http://paradiseo.gforge.inria.fr/. -In the bopo/build/ directory: -(Unix) > ctest -Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial - -In the directory "application", there are several directory such as p_eoco which instantiate NSGAII on BOPO problems. - -(Unix) After compilation you can run the script "bopo/run.sh" and see results in "NSGAII.out". Parameters can be modified in the script. - -(Windows) Add argument "NSGAII.param" and execute the corresponding algorithms. -Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial - - -# Documentation ---------------- -The API-documentation is available in doc/html/index.html - - -# Things to keep in mind when using BOPO ----------------------------------------- -* By default, the EO random generator's seed is initialized by the number of seconds since the epoch (with time(0)). It is available in the status file dumped at each execution. Please, keep in mind that if you start two run at the same second without modifying the seed, you will get exactly the same results. - -* Execution times are measured with the boost:timer, that measure wallclock time. Additionaly, it could not measure times larger than approximatively 596.5 hours (or even less). See http://www.boost.org/doc/libs/1_33_1/libs/timer/timer.htm - -* The q-quantile computation use averaging at discontinuities (in R, it correspond to the R-2 method, in SAS, SAS-5). For more explanations, see http://en.wikipedia.org/wiki/Quantile#Estimating_the_quantiles_of_a_population and http://stat.ethz.ch/R-manual/R-devel/library/stats/html/quantile.html - -* You can send a SIGUSR1 to a process to get some information (written down in the log file) on the current state of the search. diff --git a/src/doCMASA.h b/src/doCMASA.h index 1536f08f..c0c0cb86 100644 --- a/src/doCMASA.h +++ b/src/doCMASA.h @@ -100,17 +100,15 @@ public: _sa_continue(sa_continue), _cooling_schedule(cooling_schedule), _initial_temperature(initial_temperature), - _replacor(replacor) + _replacor(replacor), - // , + _pop_results_destination("ResPop")//, - // _pop_results_destination("ResPop"), + // directory where populations state are going to be stored. + // _ofs_params("ResParams.txt"), + // _ofs_params_var("ResVars.txt"), - // // directory where populations state are going to be stored. - // _ofs_params("ResParams.txt"), - // _ofs_params_var("ResVars.txt"), - - // _bounds_results_destination("ResBounds") + // _bounds_results_destination("ResBounds") { //------------------------------------------------------------- @@ -118,13 +116,13 @@ public: // iteration for plotting. //------------------------------------------------------------- - // { - // std::stringstream os; - // os << "rm -rf " << _pop_results_destination; - // ::system(os.str().c_str()); - // } + { + std::stringstream os; + os << "rm -rf " << _pop_results_destination; + ::system(os.str().c_str()); + } - // ::mkdir(_pop_results_destination.c_str(), 0755); // create a first time the + ::mkdir(_pop_results_destination.c_str(), 0755); // create a first time //------------------------------------------------------------- @@ -291,12 +289,12 @@ public: // at each iteration for plotting. //------------------------------------------------------------- - // { - // std::ostringstream os; - // os << _pop_results_destination << "/" << number_of_iterations; - // std::ofstream ofs(os.str().c_str()); - // ofs << current_pop; - // } + { + std::ostringstream os; + os << _pop_results_destination << "/" << number_of_iterations; + std::ofstream ofs(os.str().c_str()); + ofs << current_pop; + } //------------------------------------------------------------- @@ -380,8 +378,9 @@ public: } while ( _cooling_schedule( temperature ) && - _monitoring_continue( selected_pop ) && - _distribution_continue( distrib ) ); + _distribution_continue( distrib ) && + _monitoring_continue( selected_pop ) + ); } private: @@ -427,7 +426,7 @@ private: // iteration for plotting. //------------------------------------------------------------- - // std::string _pop_results_destination; + std::string _pop_results_destination; // std::ofstream _ofs_params; // std::ofstream _ofs_params_var; From 91fa58ccafc17740ac973a70870e86176c253ab2 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 18 Aug 2010 18:23:01 +0200 Subject: [PATCH 31/74] - useless comments and files removed --- copying | 1 - 1 file changed, 1 deletion(-) delete mode 100644 copying diff --git a/copying b/copying deleted file mode 100644 index 90cbe47b..00000000 --- a/copying +++ /dev/null @@ -1 +0,0 @@ -Private license From a70a0837356be4e2629e92ec43881336a61c39cf Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 18 Aug 2010 18:24:16 +0200 Subject: [PATCH 32/74] - useless comments and files removed --- matrix.hpp | 560 ----------------------------------------------------- 1 file changed, 560 deletions(-) delete mode 100644 matrix.hpp diff --git a/matrix.hpp b/matrix.hpp deleted file mode 100644 index 89b77d85..00000000 --- a/matrix.hpp +++ /dev/null @@ -1,560 +0,0 @@ -/*************************************************************************** - * $Id: matrix.hpp,v 1.11 2006/05/13 10:05:53 nojhan Exp $ - * Copyright : Free Software Foundation - * Author : Johann Dréo - ****************************************************************************/ - -/* - * This program 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 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 Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser 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 MATRIX -#define MATRIX - -#include -#include - -#include "Exception_oMetah.hpp" - -using namespace std; - -namespace ometah { - -//! Test if a vector is comprised in bounds -template -bool isInBounds( T aVector, T mins, T maxs) -{ - unsigned int i; - for(i=0; i maxs[i] ){ - return false; - } - } - return true; -} - - -//! Force a vector to be in bounds -template -T forceBounds( T aVector, T mins, T maxs) -{ - T CastedVector=aVector; - - unsigned int i; - for(i=0; i maxs[i] ){ - CastedVector[i]=maxs[i]; - } - } - return CastedVector; -} - -//! Create a 2D matrix filled with values -/* - if we want a vector > : - T stand for double - V stand for vector > -*/ -template -U matrixFilled( unsigned int dimL, unsigned int dimC, T fillValue ) -{ - unsigned int i; - - // make the vector possible at this step - typename U::value_type vec(dimC, fillValue); - - U mat; - for(i=0; i -vector > matrixFilled( unsigned int dimL, unsigned int dimC, T fillValue ) -{ - unsigned int i; - - // make the vector possible at this step - vector< T > vec(dimC, fillValue); - - vector > mat; - for(i=0; i -T multiply( T matA, T matB) -{ - - T newMat; - - unsigned int Al=matA.size(); - unsigned int Ac=matA[0].size(); - unsigned int Bl=matB.size(); - unsigned int Bc=matB[0].size(); - - newMat=matrixFilled( Al,Bc,0.0); - - if(Ac!=Bl) { - throw Exception_Size_Match("Cannot multiply matrices, sizes does not match", EXCEPTION_INFOS ); - } - - for( unsigned int i=0; i -U multiply(U aVector, T aNb) -{ - U res; - - res.reserve( aVector.size() ); - - unsigned int i; - for(i=0; i -T cholesky( T A) -{ - - // FIXME : vérifier que A est symétrique définie positive - - T B; - unsigned int Al=A.size(); - unsigned int Ac=A[0].size(); - B = matrixFilled(Al, Ac, 0.0); - - unsigned int i,j,k; - - // first column - i=0; - - // diagonal - j=0; - B[0][0]=sqrt(A[0][0]); - - // end of the column - for(j=1;j -T transpose( T &mat) -{ - unsigned int iSize=mat.size(); - unsigned int jSize=mat[0].size(); - - if ( iSize == 0 || jSize == 0 ) { - ostringstream msg; - msg << "ErrorSize: matrix not defined " - << "(iSize:" << iSize << ", jSize:" << jSize << ")"; - throw Exception_Size( msg.str(), EXCEPTION_INFOS ); - } - - typename T::value_type aVector; - T newMat; - - unsigned int i, j; - - for (j=0; j -vector mean( vector > mat) -{ - vector moyDim; - moyDim.reserve(mat.size()); - - unsigned int i,a; - a=mat.size(); - - for(i=0;i -T mean( vector aVector, unsigned int begin=0, unsigned int during=0) -{ - if (during==0) { - during = aVector.size() - begin; // if no end : take all - } - - T aSum, aMean; - - aSum = sum(aVector, begin, during); // Sum - aMean = aSum / (during - begin); // Mean - - return aMean; -} - -//! Calculate a variance-covariance matrix from a list of vector -/*! - For a population of p points on n dimensions : - if onRow==true, the matrix should have p rows and n columns. - if onRow==false, the matrix should have n rows and p columns. -*/ -template -U varianceCovariance( U pop, bool onRow = true) -{ -/* - // vector of means - typename U::value_type vecMeanCentered; - if(onRow) { - vecMeanCentered = mean( transpose(pop) ); // p rows and n columns => means of p - } else { - vecMeanCentered = mean( pop ); // n rows and p columns => means of n - } - - // centered population - // same size as the initial matrix - U popMeanCentered = matrixFilled(pop.size(),pop[0].size(), 0.0); - - // centering - // rows - for(unsigned int i=0;i covariance of p - } else { - popVar = multiply( popMeanCentered, popMeanCenteredT ); // if n rows and p columns => covariance of n - } - - // multiplication by 1/n : - for(unsigned int i=0;i -T sum(vector aVector, unsigned int begin=0, unsigned int during=0) -{ - if ( begin > aVector.size() || during > aVector.size() ) { - ostringstream msg; - msg << "ErrorSize: parameters are out of vector bounds " - << "(begin:" << begin << ", during:" << during - << ", size:" << aVector.size() << ")"; - throw Exception_Size_Index( msg.str(), EXCEPTION_INFOS ); - } - - if (during==0) { - during = aVector.size() - begin; - } - - T aSum=0; - - for (unsigned int j=begin; j -T stdev(vector aVector, unsigned int begin=0, unsigned int during=0) -{ - if ( begin > aVector.size() || during > aVector.size() ) { - ostringstream msg; - msg << "ErrorSize: parameters are out of vector bounds " - << "(begin:" << begin << ", during:" << during - << ", size:" << aVector.size() << ")"; - throw Exception_Size_Index( msg.str(), EXCEPTION_INFOS ); - } - - if (during==0) { - during = aVector.size() - begin; - } - - vector deviation; - T aMean, aDev, aStd; - - aMean = mean(aVector, begin, during); // mean - - for (unsigned int j=begin; j -typename T::value_type min(T aVector, unsigned int begin=0, unsigned int during=0) -{ - if ( begin > aVector.size() || during > aVector.size() ) { - ostringstream msg; - msg << "ErrorSize: parameters are out of vector bounds " - << "(begin:" << begin << ", during:" << during - << ", size:" << aVector.size() << ")"; - throw Exception_Size_Index( msg.str(), EXCEPTION_INFOS ); - } - - if (during==0) { - during = aVector.size() - begin; - } - - typename T::value_type aMin = aVector[begin]; - - for (unsigned int i=begin+1; i -vector mins(vector > aMatrix) -{ - vector mins; - - for( unsigned int i=0; i < aMatrix.size(); i++ ) { - mins.push_back( min(aMatrix[i]) ); - } - - return mins; -} - -//! Find the maximums values of a matrix, for each row -template -vector maxs(vector > aMatrix) -{ - vector maxs; - - for( unsigned int i=0; i < aMatrix.size(); i++ ) { - maxs.push_back( max(aMatrix[i]) ); - } - - return maxs; -} - -//! Find the maximum value of a vector -template -typename T::value_type max(T aVector, unsigned int begin=0, unsigned int during=0) -{ - if ( begin > aVector.size() || during > aVector.size() ) { - ostringstream msg; - msg << "ErrorSize: parameters are out of vector bounds " - << "(begin:" << begin << ", during:" << during - << ", size:" << aVector.size() << ")"; - throw Exception_Size_Index( msg.str(), EXCEPTION_INFOS ); - } - - if (during==0) { - during = aVector.size() - begin; - } - - typename T::value_type aMax = aVector[begin]; - - for (unsigned int i=begin+1; i aMax ) { - aMax = aVector[i]; - } - } - - return aMax; -} - -//! Substraction of two vectors, terms by terms -template -T substraction(T from, T that) -{ - T res; - - res.reserve(from.size()); - - for(unsigned int i=0; i -T addition(T from, T that) -{ - T res; - - res.reserve( from.size() ); - - for(unsigned int i=0; i -T absolute(T aVector) -{ - for(unsigned int i=0; i -vector gravityCenter( vector > points, vector weights ) -{ - - // if we have only one weight, we use it for all items - if ( weights.size() == 1 ) { - for ( unsigned int i=1; i < points.size(); i++ ) { - weights.push_back( weights[0] ); - } - } - - // if sizes does not match : error - if ( points.size() != weights.size() ) { - ostringstream msg; - msg << "ErrorSize: " - << "points size (" << points.size() << ")" - << " does not match weights size (" << weights.size() << ")"; - throw Exception_Size_Match( msg.str(), EXCEPTION_INFOS ); - } - - T weightsSum = sum(weights); - - vector > pointsT = transpose( points ); - - vector gravity; - - for ( unsigned int i=0; i < pointsT.size(); i++ ) { // dimensions - T g = 0; - for ( unsigned int j=0; j < pointsT[i].size(); j++ ) { // points - g += ( pointsT[i][j] * weights[j] ) / weightsSum; - } - gravity.push_back( g ); - } - - return gravity; -} - -} // ometah - -#endif // MATRIX From a84417d3498a578893b4ddbd624aca6bff6afd92 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 18 Aug 2010 18:39:58 +0200 Subject: [PATCH 33/74] * cma-sa name has been replace by eda-sa in the project --- application/CMakeLists.txt | 2 +- application/{cma_sa => eda_sa}/CMakeLists.txt | 4 ++-- application/{cma_sa => eda_sa}/Rosenbrock.h | 0 application/{cma_sa => eda_sa}/Sphere.h | 0 .../cma_sa.param => eda_sa/eda_sa.param} | 0 application/{cma_sa => eda_sa}/main.cpp | 6 +++--- application/{cma_sa => eda_sa}/plot.py | 2 +- src/do | 2 +- src/{doCMASA.h => doEDASA.h} | 18 +++++++++--------- 9 files changed, 17 insertions(+), 17 deletions(-) rename application/{cma_sa => eda_sa}/CMakeLists.txt (95%) rename application/{cma_sa => eda_sa}/Rosenbrock.h (100%) rename application/{cma_sa => eda_sa}/Sphere.h (100%) rename application/{cma_sa/cma_sa.param => eda_sa/eda_sa.param} (100%) rename application/{cma_sa => eda_sa}/main.cpp (98%) rename application/{cma_sa => eda_sa}/plot.py (99%) rename src/{doCMASA.h => doEDASA.h} (97%) diff --git a/application/CMakeLists.txt b/application/CMakeLists.txt index 07bcc2d0..591fb303 100644 --- a/application/CMakeLists.txt +++ b/application/CMakeLists.txt @@ -2,6 +2,6 @@ ### 1) Where do we go now ?!? ###################################################################################### -ADD_SUBDIRECTORY(cma_sa) +ADD_SUBDIRECTORY(eda_sa) ###################################################################################### diff --git a/application/cma_sa/CMakeLists.txt b/application/eda_sa/CMakeLists.txt similarity index 95% rename from application/cma_sa/CMakeLists.txt rename to application/eda_sa/CMakeLists.txt index c67ab0dd..8cdc8c13 100644 --- a/application/cma_sa/CMakeLists.txt +++ b/application/eda_sa/CMakeLists.txt @@ -1,4 +1,4 @@ -PROJECT(cma_sa) +PROJECT(eda_sa) FIND_PACKAGE(Boost 1.33.0) @@ -8,7 +8,7 @@ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) SET(RESOURCES - cma_sa.param + eda_sa.param plot.py ) diff --git a/application/cma_sa/Rosenbrock.h b/application/eda_sa/Rosenbrock.h similarity index 100% rename from application/cma_sa/Rosenbrock.h rename to application/eda_sa/Rosenbrock.h diff --git a/application/cma_sa/Sphere.h b/application/eda_sa/Sphere.h similarity index 100% rename from application/cma_sa/Sphere.h rename to application/eda_sa/Sphere.h diff --git a/application/cma_sa/cma_sa.param b/application/eda_sa/eda_sa.param similarity index 100% rename from application/cma_sa/cma_sa.param rename to application/eda_sa/eda_sa.param diff --git a/application/cma_sa/main.cpp b/application/eda_sa/main.cpp similarity index 98% rename from application/cma_sa/main.cpp rename to application/eda_sa/main.cpp index 4fc41bbb..2653ddab 100644 --- a/application/cma_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -35,7 +35,7 @@ int main(int ac, char** av) eoState state; //----------------------------------------------------------------------------- - // Instantiate all need parameters for CMASA algorithm + // Instantiate all need parameters for EDASA algorithm //----------------------------------------------------------------------------- eoSelect< EOT >* selector = new eoDetSelect< EOT >(0.5); @@ -193,10 +193,10 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- - // CMASA algorithm configuration + // EDASA algorithm configuration //----------------------------------------------------------------------------- - doAlgo< Distrib >* algo = new doCMASA< Distrib > + doAlgo< Distrib >* algo = new doEDASA< Distrib > (*selector, *estimator, *selectone, *modifier, *sampler, monitoring_continue, *distribution_continue, eval, *sa_continue, *cooling_schedule, diff --git a/application/cma_sa/plot.py b/application/eda_sa/plot.py similarity index 99% rename from application/cma_sa/plot.py rename to application/eda_sa/plot.py index 4fc5924c..f5fa7c42 100644 --- a/application/cma_sa/plot.py +++ b/application/eda_sa/plot.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -"""plot.py -- Plot CMA-SA results file""" +"""plot.py -- Plot EDA-SA results file""" import os, time, math, tempfile import numpy diff --git a/src/do b/src/do index cd18c140..74df1ca1 100644 --- a/src/do +++ b/src/do @@ -9,7 +9,7 @@ #define _do_ #include "doAlgo.h" -#include "doCMASA.h" +#include "doEDASA.h" #include "doDistrib.h" #include "doUniform.h" diff --git a/src/doCMASA.h b/src/doEDASA.h similarity index 97% rename from src/doCMASA.h rename to src/doEDASA.h index c0c0cb86..35cec339 100644 --- a/src/doCMASA.h +++ b/src/doEDASA.h @@ -5,8 +5,8 @@ Caner Candan */ -#ifndef _doCMASA_h -#define _doCMASA_h +#ifndef _doEDASA_h +#define _doEDASA_h //----------------------------------------------------------------------------- // Temporary solution to store populations state at each iteration for plotting. @@ -47,7 +47,7 @@ using namespace boost::numeric::ublas; template < typename D > -class doCMASA : public doAlgo< D > +class doEDASA : public doAlgo< D > { public: //! Alias for the type EOT @@ -61,9 +61,9 @@ public: public: - //! doCMASA constructor + //! doEDASA constructor /*! - All the boxes used by a CMASA need to be given. + All the boxes used by a EDASA need to be given. \param selector The EOT selector \param estomator The EOT selector @@ -76,7 +76,7 @@ public: \param initial_temperature The initial temperature. \param replacor The EOT replacor */ - doCMASA (eoSelect< EOT > & selector, + doEDASA (eoSelect< EOT > & selector, doEstimator< D > & estimator, eoSelectOne< EOT > & selectone, doModifierMass< D > & modifier, @@ -143,9 +143,9 @@ public: } - //! function that launches the CMASA algorithm. + //! function that launches the EDASA algorithm. /*! - As a moTS or a moHC, the CMASA can be used for HYBRIDATION in an evolutionary algorithm. + As a moTS or a moHC, the EDASA can be used for HYBRIDATION in an evolutionary algorithm. \param pop A population to improve. \return TRUE. @@ -442,4 +442,4 @@ private: }; -#endif // !_doCMASA_h +#endif // !_doEDASA_h From 20c90d93f9baaf9a392c7d64d3a03183ea986e38 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 18 Aug 2010 19:13:38 +0200 Subject: [PATCH 34/74] added a FIXME --- application/eda_sa/main.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index 2653ddab..e689d936 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -57,8 +57,8 @@ int main(int ac, char** av) state.storeFunctor(modifier); eoEvalFunc< EOT >* plainEval = - //new BopoRosenbrock< EOT, typename EOT::AtomType, const EOT& >(); - new Sphere< EOT >(); + new Rosenbrock< EOT >(); + //new Sphere< EOT >(); state.storeFunctor(plainEval); unsigned long max_eval = parser.getORcreateParam((unsigned long)0, "maxEval", "Maximum number of evaluations (0 = none)", 'E', "Stopping criterion").value(); // E @@ -113,6 +113,8 @@ int main(int ac, char** av) state.storeFunctor(sampler); + // FIXME: should I set the default value of rho to pop size ?!? + unsigned int rho = parser.createParam((unsigned int)0, "rho", "Rho: metropolis sample size", 'p', section).value(); // p moGenSolContinue< EOT >* sa_continue = new moGenSolContinue< EOT >(rho); From 0c5545c421d0ab996b1b8610849f06c5c08634c5 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 23 Aug 2010 15:56:58 +0200 Subject: [PATCH 35/74] + plot populations by generation - removed dump from doEDASA --- application/eda_sa/main.cpp | 86 ++++++++++++---- src/do | 3 + src/doEDASA.h | 196 ++---------------------------------- src/doFileSnapshot.cpp | 119 ++++++++++++++++++++++ src/doFileSnapshot.h | 189 ++++++---------------------------- src/doPopStat.h | 75 ++++++++++++++ 6 files changed, 299 insertions(+), 369 deletions(-) create mode 100644 src/doFileSnapshot.cpp create mode 100644 src/doPopStat.h diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index e689d936..b362529c 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -24,18 +24,19 @@ int main(int ac, char** av) { eoParserLogger parser(ac, av); - // Letters used by the following declarations : + // Letters used by the following declarations: // a d i p t std::string section("Algorithm parameters"); - // FIXME: a verifier la valeur par defaut + // FIXME: default value to check double initial_temperature = parser.createParam((double)10e5, "temperature", "Initial temperature", 'i', section).value(); // i eoState state; + //----------------------------------------------------------------------------- - // Instantiate all need parameters for EDASA algorithm + // Instantiate all needed parameters for EDASA algorithm //----------------------------------------------------------------------------- eoSelect< EOT >* selector = new eoDetSelect< EOT >(0.5); @@ -81,10 +82,10 @@ int main(int ac, char** av) // (1) Population init and sampler //----------------------------------------------------------------------------- - // Generation of population from do_make_pop (creates parameter, manages persistance and so on...) - // ... and creates the parameter letters: L P r S + // Generation of population from do_make_pop (creates parameters, manages persistance and so on...) + // ... and creates the parameters: L P r S - // this first sampler creates a uniform distribution independently of our distribution (it doesnot use doUniform). + // this first sampler creates a uniform distribution independently from our distribution (it does not use doUniform). eoPop< EOT >& pop = do_make_pop(parser, state, *init); @@ -100,18 +101,37 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- + //----------------------------------------------------------------------------- + // Prepare bounder class to set bounds of sampling. + // This is used by doSampler. + //----------------------------------------------------------------------------- + + //doBounder< EOT >* bounder = new doBounderNo< EOT >(); doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), EOT(pop[0].size(), 5), *gen); state.storeFunctor(bounder); + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare sampler class with a specific distribution + //----------------------------------------------------------------------------- + doSampler< Distrib >* sampler = //new doSamplerUniform< EOT >(); //new doSamplerNormalMono< EOT >( *bounder ); new doSamplerNormalMulti< EOT >( *bounder ); state.storeFunctor(sampler); + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Metropolis sample parameters + //----------------------------------------------------------------------------- // FIXME: should I set the default value of rho to pop size ?!? @@ -120,42 +140,63 @@ int main(int ac, char** av) moGenSolContinue< EOT >* sa_continue = new moGenSolContinue< EOT >(rho); state.storeFunctor(sa_continue); + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // SA parameters + //----------------------------------------------------------------------------- + double threshold = parser.createParam((double)0.1, "threshold", "Threshold: temperature threshold stopping criteria", 't', section).value(); // t double alpha = parser.createParam((double)0.1, "alpha", "Alpha: temperature dicrease rate", 'a', section).value(); // a moCoolingSchedule* cooling_schedule = new moGeometricCoolingSchedule(threshold, alpha); state.storeFunctor(cooling_schedule); + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- // stopping criteria // ... and creates the parameter letters: C E g G s T + //----------------------------------------------------------------------------- eoContinue< EOT >& eo_continue = do_make_continue(parser, state, eval); - // output + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // general output + //----------------------------------------------------------------------------- eoCheckPoint< EOT >& monitoring_continue = do_make_checkpoint(parser, state, eval, eo_continue); - // eoPopStat< EOT >* popStat = new eoPopStat; - // state.storeFunctor(popStat); + //----------------------------------------------------------------------------- - // checkpoint.add(*popStat); - // eoGnuplot1DMonitor* gnuplot = new eoGnuplot1DMonitor("gnuplot.txt"); - // state.storeFunctor(gnuplot); + //----------------------------------------------------------------------------- + // population output + //----------------------------------------------------------------------------- - // gnuplot->add(eval); - // gnuplot->add(*popStat); + eoCheckPoint< EOT >* pop_continue = new eoCheckPoint< EOT >( eo_continue ); + state.storeFunctor(pop_continue); - //gnuplot->gnuplotCommand("set yrange [0:500]"); + doPopStat< EOT >* popStat = new doPopStat; + state.storeFunctor(popStat); + pop_continue->add(*popStat); - // checkpoint.add(*gnuplot); + doFileSnapshot* fileSnapshot = new doFileSnapshot("ResPop"); + state.storeFunctor(fileSnapshot); + fileSnapshot->add(*popStat); + pop_continue->add(*fileSnapshot); - // eoMonitor* fileSnapshot = new doFileSnapshot< std::vector< std::string > >("ResPop"); - // state.storeFunctor(fileSnapshot); + //----------------------------------------------------------------------------- - // fileSnapshot->add(*popStat); - // checkpoint.add(*fileSnapshot); + //----------------------------------------------------------------------------- + // distribution output + //----------------------------------------------------------------------------- doDummyContinue< Distrib >* dummy_continue = new doDummyContinue< Distrib >(); state.storeFunctor(dummy_continue); @@ -178,6 +219,9 @@ int main(int ac, char** av) file_monitor->add(*distrib_stat); distribution_continue->add( *file_monitor ); + //----------------------------------------------------------------------------- + + //----------------------------------------------------------------------------- // eoEPRemplacement causes the using of the current and previous // sample for sampling. @@ -200,7 +244,7 @@ int main(int ac, char** av) doAlgo< Distrib >* algo = new doEDASA< Distrib > (*selector, *estimator, *selectone, *modifier, *sampler, - monitoring_continue, *distribution_continue, + monitoring_continue, *pop_continue, *distribution_continue, eval, *sa_continue, *cooling_schedule, initial_temperature, *replacor); diff --git a/src/do b/src/do index 74df1ca1..e96262c9 100644 --- a/src/do +++ b/src/do @@ -48,4 +48,7 @@ #include "doStatNormalMono.h" #include "doStatNormalMulti.h" +#include "doFileSnapshot.h" +#include "doPopStat.h" + #endif // !_do_ diff --git a/src/doEDASA.h b/src/doEDASA.h index 35cec339..25fc5e5d 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -8,29 +8,6 @@ #ifndef _doEDASA_h #define _doEDASA_h -//----------------------------------------------------------------------------- -// Temporary solution to store populations state at each iteration for plotting. -//----------------------------------------------------------------------------- - -// system header inclusion -#include -// end system header inclusion - -// mkdir headers inclusion -#include -#include -// end mkdir headers inclusion - -#include -#include - -#include - -#include -#include - -//----------------------------------------------------------------------------- - #include #include @@ -44,8 +21,6 @@ #include "doStat.h" #include "doContinue.h" -using namespace boost::numeric::ublas; - template < typename D > class doEDASA : public doAlgo< D > { @@ -82,6 +57,7 @@ public: doModifierMass< D > & modifier, doSampler< D > & sampler, eoContinue< EOT > & monitoring_continue, + eoContinue< EOT > & pop_continue, doContinue< D > & distribution_continue, eoEvalFunc < EOT > & evaluation, moSolContinue < EOT > & sa_continue, @@ -95,53 +71,14 @@ public: _modifier(modifier), _sampler(sampler), _monitoring_continue(monitoring_continue), + _pop_continue(pop_continue), _distribution_continue(distribution_continue), _evaluation(evaluation), _sa_continue(sa_continue), _cooling_schedule(cooling_schedule), _initial_temperature(initial_temperature), - _replacor(replacor), - - _pop_results_destination("ResPop")//, - - // directory where populations state are going to be stored. - // _ofs_params("ResParams.txt"), - // _ofs_params_var("ResVars.txt"), - - // _bounds_results_destination("ResBounds") - { - - //------------------------------------------------------------- - // Temporary solution to store populations state at each - // iteration for plotting. - //------------------------------------------------------------- - - { - std::stringstream os; - os << "rm -rf " << _pop_results_destination; - ::system(os.str().c_str()); - } - - ::mkdir(_pop_results_destination.c_str(), 0755); // create a first time - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // Temporary solution to store bounds values for each distribution. - //------------------------------------------------------------- - - // { - // std::stringstream os; - // os << "rm -rf " << _bounds_results_destination; - // ::system(os.str().c_str()); - // } - - //::mkdir(_bounds_results_destination.c_str(), 0755); // create once directory - - //------------------------------------------------------------- - - } + _replacor(replacor) + {} //! function that launches the EDASA algorithm. /*! @@ -150,7 +87,6 @@ public: \param pop A population to improve. \return TRUE. */ - //bool operator ()(eoPop< EOT > & pop) void operator ()(eoPop< EOT > & pop) { assert(pop.size() > 0); @@ -162,16 +98,6 @@ public: eoPop< EOT > selected_pop; - //------------------------------------------------------------- - // Temporary solution used by plot to enumerate iterations in - // several files. - //------------------------------------------------------------- - - int number_of_iterations = 0; - - //------------------------------------------------------------- - - //------------------------------------------------------------- // Estimating a first time the distribution parameter thanks // to population. @@ -185,22 +111,6 @@ public: //------------------------------------------------------------- - // { - // D distrib = _estimator(pop); - - // double size = distrib.size(); - // assert(size > 0); - - // doHyperVolume< EOT > hv; - - // for (int i = 0; i < size; ++i) - // { - // //hv.update( distrib.varcovar()[i] ); - // } - - // // _ofs_params_var << hv << std::endl; - // } - do { if (pop != current_pop) @@ -283,102 +193,10 @@ public: } while ( _sa_continue( current_solution) ); - - //------------------------------------------------------------- - // Temporary solution to store populations state - // at each iteration for plotting. - //------------------------------------------------------------- - - { - std::ostringstream os; - os << _pop_results_destination << "/" << number_of_iterations; - std::ofstream ofs(os.str().c_str()); - ofs << current_pop; - } - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // Temporary solution used by plot to enumerate iterations in - // several files. - //------------------------------------------------------------- - - // { - // double size = distrib.size(); - - // assert(size > 0); - - // std::stringstream os; - // os << _bounds_results_destination << "/" << number_of_iterations; - // std::ofstream ofs(os.str().c_str()); - - // ofs << size << " "; - //ublas::vector< AtomType > mean = distrib.mean(); - //std::copy(mean.begin(), mean.end(), std::ostream_iterator< double >(ofs, " ")); - //std::copy(distrib.varcovar().begin(), distrib.varcovar().end(), std::ostream_iterator< double >(ofs, " ")); - // ofs << std::endl; - // } - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // Temporary saving to get a proof for distribution bounds - // dicreasement - //------------------------------------------------------------- - - // { - // double size = distrib.size(); - // assert(size > 0); - - // vector< double > vmin(size); - // vector< double > vmax(size); - - // std::copy(distrib.param(0).begin(), distrib.param(0).end(), vmin.begin()); - // std::copy(distrib.param(1).begin(), distrib.param(1).end(), vmax.begin()); - - // vector< double > vrange = vmax - vmin; - - // doHyperVolume hv; - - // for (int i = 0, size = vrange.size(); i < size; ++i) - // { - // hv.update( vrange(i) ); - // } - - // ofs_params << hv << std::endl; - // } - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // Temporary saving to get a proof for distribution bounds - // dicreasement - //------------------------------------------------------------- - - // { - // double size = distrib.size(); - // assert(size > 0); - - // doHyperVolume< EOT > hv; - - // for (int i = 0; i < size; ++i) - // { - // //hv.update( distrib.varcovar()[i] ); - // } - - // //_ofs_params_var << hv << std::endl; - // } - - //------------------------------------------------------------- - - ++number_of_iterations; - } while ( _cooling_schedule( temperature ) && _distribution_continue( distrib ) && + _pop_continue( current_pop ) && _monitoring_continue( selected_pop ) ); } @@ -403,6 +221,9 @@ private: //! A EOT monitoring continuator eoContinue < EOT > & _monitoring_continue; + //! A EOT population continuator + eoContinue < EOT > & _pop_continue; + //! A D continuator doContinue < D > & _distribution_continue; @@ -426,7 +247,6 @@ private: // iteration for plotting. //------------------------------------------------------------- - std::string _pop_results_destination; // std::ofstream _ofs_params; // std::ofstream _ofs_params_var; diff --git a/src/doFileSnapshot.cpp b/src/doFileSnapshot.cpp new file mode 100644 index 00000000..0bda8ea6 --- /dev/null +++ b/src/doFileSnapshot.cpp @@ -0,0 +1,119 @@ +//----------------------------------------------------------------------------- +// doFileSnapshot.cpp +// (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2001 +/* + 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 + Marc.Schoenauer@polytechnique.fr + mkeijzer@dhi.dk + Johann Dreo + Caner Candan + */ +//----------------------------------------------------------------------------- + +#include +#include +#include + +#include +#include +#include + +doFileSnapshot::doFileSnapshot(std::string dirname, + unsigned int frequency /*= 1*/, + std::string filename /*= "gen"*/, + std::string delim /*= " "*/, + unsigned int counter /*= 0*/, + bool rmFiles /*= true*/) + : _dirname(dirname), _frequency(frequency), + _filename(filename), _delim(delim), + _counter(counter), _boolChanged(true) +{ + std::string s = "test -d " + _dirname; + + int res = system(s.c_str()); + + // test for (unlikely) errors + + if ( (res == -1) || (res == 127) ) + { + throw std::runtime_error("Problem executing test of dir in eoFileSnapshot"); + } + + // now make sure there is a dir without any genXXX file in it + if (res) // no dir present + { + s = std::string("mkdir ") + _dirname; + } + else if (!res && rmFiles) + { + s = std::string("/bin/rm ") + _dirname+ "/" + _filename + "*"; + } + else + { + s = " "; + } + + int dummy; + dummy = system(s.c_str()); + // all done +} + + +void doFileSnapshot::setCurrentFileName() +{ + std::ostringstream oscount; + oscount << _counter; + _currentFileName = _dirname + "/" + _filename + oscount.str(); +} + +eoMonitor& doFileSnapshot::operator()(void) +{ + if (_counter % _frequency) + { + _boolChanged = false; // subclass with gnuplot will do nothing + _counter++; + return (*this); + } + _counter++; + _boolChanged = true; + setCurrentFileName(); + std::ofstream os(_currentFileName.c_str()); + + if (!os) + { + std::string str = "doFileSnapshot: Could not open " + _currentFileName; + throw std::runtime_error(str); + } + + return operator()(os); +} + +eoMonitor& doFileSnapshot::operator()(std::ostream& os) +{ + iterator it = vec.begin(); + + os << (*it)->getValue(); + + for ( ++it; it != vec.end(); ++it ) + { + os << _delim.c_str() << (*it)->getValue(); + } + + os << '\n'; + + return *this; +} diff --git a/src/doFileSnapshot.h b/src/doFileSnapshot.h index def9efc2..9329eed9 100644 --- a/src/doFileSnapshot.h +++ b/src/doFileSnapshot.h @@ -1,5 +1,5 @@ //----------------------------------------------------------------------------- -// eoFileSnapshot.h +// doFileSnapshot.h // (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2001 /* This library is free software; you can redistribute it and/or @@ -19,182 +19,51 @@ Contact: todos@geneura.ugr.es, http://geneura.ugr.es Marc.Schoenauer@polytechnique.fr mkeijzer@dhi.dk - Caner Candan caner@candan.fr - Johann Dréo nojhan@gmail.com + Johann Dreo + Caner Candan */ //----------------------------------------------------------------------------- #ifndef _doFileSnapshot_h #define _doFileSnapshot_h -#include // for mkdir -#include // for mkdir -#include // for unlink - -#include -#include #include +#include +#include -#include -#include -#include +#include "utils/eoMonitor.h" -#include - -/** -Prints snapshots of fitnesses to a (new) file every N generations - -Assumes that the parameters that are passed to the monitor -(method add in eoMonitor.h) are eoValueParam > of same size. - -A dir is created and one file per snapshot is created there - -so you can later generate a movie! - -TODO: The counter is handled internally, but this should be changed -so that you can pass e.g. an evalcounter (minor) - -I failed to templatize everything so that it can handle eoParam > -for any type T, simply calling their getValue method ... -*/ - -template < typename EOTParam > class doFileSnapshot : public eoMonitor { -public : - doFileSnapshot(std::string _dirname, unsigned _frequency = 1, - std::string _filename = "gen", - std::string _delim = " ", unsigned _counter = 0, - bool _rmFiles = true): - dirname(_dirname), frequency(_frequency), - filename(_filename), delim(_delim), counter(_counter), boolChanged(true) - { - // FIXME START - // TO REPLACE test command by somethink more gernerical +public: - std::string s = "test -d " + dirname; + doFileSnapshot(std::string dirname, + unsigned int frequency = 1, + std::string filename = "gen", + std::string delim = " ", + unsigned int counter = 0, + bool rmFiles = true); - int res = system(s.c_str()); - // test for (unlikely) errors - if ( (res==-1) || (res==127) ) - throw std::runtime_error("Problem executing test of dir in eoFileSnapshot"); + virtual bool hasChanged() {return _boolChanged;} + virtual std::string getDirName() { return _dirname; } + virtual unsigned int getCounter() { return _counter; } + virtual const std::string baseFileName() { return _filename;} + std::string getFileName() {return _currentFileName;} - // FIXME END + void setCurrentFileName(); - // now make sure there is a dir without any genXXX file in it - if (res) // no dir present - { - ::mkdir(dirname.c_str(), 0755); - } - else if (!res && _rmFiles) - { - std::string s = dirname+ "/" + filename + "*"; - ::unlink(s.c_str()); - } - } + virtual eoMonitor& operator()(void); - /** accessor: has something changed (for gnuplot subclass) - */ - virtual bool hasChanged() {return boolChanged;} - - /** accessor to the counter: needed by the gnuplot subclass - */ - unsigned getCounter() {return counter;} - - /** accessor to the current filename: needed by the gnuplot subclass - */ - std::string getFileName() {return currentFileName;} - - /** sets the current filename depending on the counter - */ - void setCurrentFileName() - { - std::ostringstream oscount; - oscount << counter; - currentFileName = dirname + "/" + filename + oscount.str(); - } - - /** The operator(void): opens the std::ostream and calls the write method - */ - eoMonitor& operator()(void) - { - if (counter % frequency) - { - boolChanged = false; // subclass with gnuplot will do nothing - counter++; - return (*this); - } - counter++; - boolChanged = true; - setCurrentFileName(); - std::ofstream os(currentFileName.c_str()); - - if (!os) - { - std::string str = "eoFileSnapshot: Could not open " + currentFileName; - throw std::runtime_error(str); - } - - return operator()(os); - } - - /** The operator(): write on an std::ostream - */ - eoMonitor& operator()(std::ostream& _os) - { - const eoValueParam< EOTParam > * ptParam = - static_cast< const eoValueParam< EOTParam >* >(vec[0]); - - EOTParam v(ptParam->value()); - if (vec.size() == 1) // only one std::vector: -> add number in front - { - eo::log << "I am here..." << std::endl; - - for (unsigned k=0; k vv(vec.size()); - vv[0]=v; - for (unsigned i=1; i* >(vec[1]); - vv[i] = ptParam->value(); - if (vv[i].size() != v.size()) - throw std::runtime_error("Dimension error in eoSnapshotMonitor"); - } - for (unsigned k=0; k + Caner Candan + */ +//----------------------------------------------------------------------------- + +/** WARNING: this file contains 2 classes: + +eoPopString and eoSortedPopString + +that transform the population into a std::string +that can be used to dump to the screen +*/ + +#ifndef _doPopStat_h +#define _doPopStat_h + +#include + + +/** Thanks to MS/VC++, eoParam mechanism is unable to handle std::vectors of stats. +This snippet is a workaround: +This class will "print" a whole population into a std::string - that you can later +send to any stream +This is the plain version - see eoPopString for the Sorted version + +Note: this Stat should probably be used only within eoStdOutMonitor, and not +inside an eoFileMonitor, as the eoState construct will work much better there. +*/ +template +class doPopStat : public eoStat +{ +public: + + using eoStat::value; + + /** default Ctor, void std::string by default, as it appears + on the description line once at beginning of evolution. and + is meaningless there. _howMany defaults to 0, that is, the whole + population*/ + doPopStat(std::string _desc ="") + : eoStat("", _desc) {} + + /** Fills the value() of the eoParam with the dump of the population. */ + void operator()(const eoPop& _pop) + { + std::ostringstream os; + os << _pop; + value() = os.str(); + } +}; + +#endif // !_doPopStat_h From 7cfd111468fc694f6f0314d3d10f45a18be07495 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 23 Aug 2010 16:14:02 +0200 Subject: [PATCH 36/74] a C header include missed --- src/doFileSnapshot.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/doFileSnapshot.cpp b/src/doFileSnapshot.cpp index 0bda8ea6..6d0578e8 100644 --- a/src/doFileSnapshot.cpp +++ b/src/doFileSnapshot.cpp @@ -24,6 +24,8 @@ */ //----------------------------------------------------------------------------- +#include + #include #include #include From 5cbb27aee387988aec8d87635cb2724de1943808 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 23 Aug 2010 18:03:44 +0200 Subject: [PATCH 37/74] + multiplot with gnuplot --- application/eda_sa/plot.py | 127 ++++++++++++++++++++++++++++++------- 1 file changed, 103 insertions(+), 24 deletions(-) diff --git a/application/eda_sa/plot.py b/application/eda_sa/plot.py index f5fa7c42..1d3298e2 100644 --- a/application/eda_sa/plot.py +++ b/application/eda_sa/plot.py @@ -16,6 +16,42 @@ except ImportError: import funcutils Gnuplot.funcutils = funcutils +import optparse, logging, sys + +LEVELS = {'debug': logging.DEBUG, + 'info': logging.INFO, + 'warning': logging.WARNING, + 'error': logging.ERROR, + 'critical': logging.CRITICAL} + +def logger(level_name, filename='plot.log'): + logging.basicConfig( + level=logging.DEBUG, + format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s', + filename=filename, filemode='a' + ) + + console = logging.StreamHandler() + console.setLevel(LEVELS.get(level_name, logging.NOTSET)) + console.setFormatter(logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s')) + logging.getLogger('').addHandler(console) + +def parser(parser=optparse.OptionParser()): + parser.add_option('-v', '--verbose', choices=LEVELS.keys(), default='warning', help='set a verbose level') + parser.add_option('-f', '--file', help='give an input project filename', default='') + parser.add_option('-o', '--output', help='give an output filename for logging', default='plot.log') + parser.add_option('-d', '--dimension', help='give a dimension size', default=2) + parser.add_option('-m', '--multiplot', action="store_true", help='plot all graphics in one window', dest="multiplot", default=True) + parser.add_option('-p', '--plot', action="store_false", help='plot graphics separetly, one by window', dest="multiplot") + + options, args = parser.parse_args() + + logger(options.verbose, options.output) + + return options + +options = parser() + def wait(str=None, prompt='Press return to show results...\n'): if str is not None: print str @@ -65,7 +101,10 @@ def plotXPointYFitness(path, fields='3:1', state=None, g=None): for filename in getSortedFiles(path): files.append(Gnuplot.File(path + '/' + filename, using=fields, with_='points', - title='distribution \'' + filename + '\'')) + #title='distribution \'' + filename + '\'' + title="" + ) + ) g.plot(*files) @@ -84,7 +123,10 @@ def plotXYPointZFitness(path, fields='4:3:1', state=None, g=None): for filename in getSortedFiles(path): files.append(Gnuplot.File(path + '/' + filename, using=fields, with_='points', - title='distribution \'' + filename + '\'')) + #title='distribution \'' + filename + '\'' + title="" + ) + ) g.splot(*files) @@ -102,7 +144,10 @@ def plotXYPoint(path, fields='3:4', state=None, g=None): for filename in getSortedFiles(path): files.append(Gnuplot.File(path + '/' + filename, using=fields, with_='points', - title='distribution \'' + filename + '\'')) + #title='distribution \'' + filename + '\'' + title="" + ) + ) g.plot(*files) @@ -121,7 +166,10 @@ def plotXYZPoint(path, fields='3:4:5', state=None, g=None): for filename in getSortedFiles(path): files.append(Gnuplot.File(path + '/' + filename, using=fields, with_='points', - title='distribution \'' + filename + '\'')) + #title='distribution \'' + filename + '\'' + title="" + ) + ) g.splot(*files) @@ -195,27 +243,60 @@ def plot2DRectFromFiles(path, state=None, g=None, plot=True): def main(n): gstate = [] - if n >= 1: - plotXPointYFitness('./ResPop', state=gstate) + if options.multiplot: + g = Gnuplot.Gnuplot() - if n >= 2: - plotXPointYFitness('./ResPop', '4:1', state=gstate) + g('set size 1.0, 1.0') + g('set origin 0.0, 0.0') + g('set multiplot') - if n >= 2: - plotXYPointZFitness('./ResPop', state=gstate) + g('set size 0.5, 0.5') + g('set origin 0.0, 0.5') - if n >= 3: - plotXYZPoint('./ResPop', state=gstate) + if n >= 1: + plotXPointYFitness('./ResPop', state=gstate, g=g) - if n >= 1: - plotParams('./ResParams.txt', state=gstate) + g('set size 0.5, 0.5') + g('set origin 0.0, 0.0') - if n >= 2: - plot2DRectFromFiles('./ResBounds', state=gstate) - plotXYPoint('./ResPop', state=gstate) + if n >= 2: + plotXPointYFitness('./ResPop', '4:1', state=gstate, g=g) - g = plot2DRectFromFiles('./ResBounds', state=gstate, plot=False) - plotXYPoint('./ResPop', g=g) + g('set size 0.5, 0.5') + g('set origin 0.5, 0.5') + + if n >= 2: + plotXYPointZFitness('./ResPop', state=gstate, g=g) + + g('set size 0.5, 0.5') + g('set origin 0.5, 0.0') + + if n >= 3: + plotXYZPoint('./ResPop', state=gstate, g=g) + + g('unset multiplot') + else: + if n >= 1: + plotXPointYFitness('./ResPop', state=gstate) + + if n >= 2: + plotXPointYFitness('./ResPop', '4:1', state=gstate) + + if n >= 2: + plotXYPointZFitness('./ResPop', state=gstate) + + if n >= 3: + plotXYZPoint('./ResPop', state=gstate) + + # if n >= 1: + # plotParams('./ResParams.txt', state=gstate) + + # if n >= 2: + # plot2DRectFromFiles('./ResBounds', state=gstate) + # plotXYPoint('./ResPop', state=gstate) + + # g = plot2DRectFromFiles('./ResBounds', state=gstate, plot=False) + # plotXYPoint('./ResPop', g=g) wait(prompt='Press return to end the plot.\n') @@ -223,10 +304,8 @@ def main(n): # when executed, just run main(): if __name__ == '__main__': - from sys import argv, exit + logging.debug('### plotting started ###') - if len(argv) < 2: - print 'Usage: plot [dimension]' - exit() + main(int(options.dimension)) - main(int(argv[1])) + logging.debug('### plotting ended ###') From 5b3f42d277fb1bce08cab7dd767530049630eb2d Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 24 Aug 2010 10:26:36 +0200 Subject: [PATCH 38/74] + lib utils --- src/CMakeLists.txt | 9 +++++++++ src/TODO | 1 - src/do | 14 +++++++------- src/doContinue.h | 5 ++--- src/doEDASA.h | 2 -- src/utils/CMakeLists.txt | 14 ++++++++++++++ src/{ => utils}/doCheckPoint.h | 0 src/{ => utils}/doFileSnapshot.cpp | 2 +- src/{ => utils}/doFileSnapshot.h | 0 src/{ => utils}/doHyperVolume.h | 0 src/{ => utils}/doPopStat.h | 0 src/{ => utils}/doStat.h | 0 src/{ => utils}/doStatNormalMono.h | 0 src/{ => utils}/doStatNormalMulti.h | 0 src/{ => utils}/doStatUniform.h | 0 15 files changed, 33 insertions(+), 14 deletions(-) create mode 100644 src/utils/CMakeLists.txt rename src/{ => utils}/doCheckPoint.h (100%) rename src/{ => utils}/doFileSnapshot.cpp (98%) rename src/{ => utils}/doFileSnapshot.h (100%) rename src/{ => utils}/doHyperVolume.h (100%) rename src/{ => utils}/doPopStat.h (100%) rename src/{ => utils}/doStat.h (100%) rename src/{ => utils}/doStatNormalMono.h (100%) rename src/{ => utils}/doStatNormalMulti.h (100%) rename src/{ => utils}/doStatUniform.h (100%) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 8b6d787a..f4cdbfae 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -10,3 +10,12 @@ FILE(GLOB SOURCES *.cpp) SET(SAMPLE_SRCS ${SOURCES} PARENT_SCOPE) ###################################################################################### + + +###################################################################################### +### 2) Where must cmake go now ? +###################################################################################### + +ADD_SUBDIRECTORY(utils) + +###################################################################################### diff --git a/src/TODO b/src/TODO index 13785cc8..bed1db02 100644 --- a/src/TODO +++ b/src/TODO @@ -1,2 +1 @@ -* deplacer les ecritures pour gnuplot dans des classes type eoContinue (eoMonitor) * integrer ACP diff --git a/src/do b/src/do index e96262c9..bcd43e19 100644 --- a/src/do +++ b/src/do @@ -41,14 +41,14 @@ #include "doBounderRng.h" #include "doContinue.h" -#include "doCheckPoint.h" +#include "utils/doCheckPoint.h" -#include "doStat.h" -#include "doStatUniform.h" -#include "doStatNormalMono.h" -#include "doStatNormalMulti.h" +#include "utils/doStat.h" +#include "utils/doStatUniform.h" +#include "utils/doStatNormalMono.h" +#include "utils/doStatNormalMulti.h" -#include "doFileSnapshot.h" -#include "doPopStat.h" +#include "utils/doFileSnapshot.h" +#include "utils/doPopStat.h" #endif // !_do_ diff --git a/src/doContinue.h b/src/doContinue.h index a93de093..64f1d483 100644 --- a/src/doContinue.h +++ b/src/doContinue.h @@ -9,10 +9,9 @@ #define _doContinue_h #include -#include #include -//! eoContinue< EOT > classe fitted to Distribution Object library +//! doContinue< EOT > classe fitted to Distribution Object library template < typename D > class doContinue : public eoUF< const D&, bool >, public eoPersistent @@ -36,7 +35,7 @@ class doDummyContinue : public doContinue< D > { bool operator()(const D&){ return true; } - virtual std::string className() const { return "doNoContinue"; } + virtual std::string className() const { return "doDummyContinue"; } }; #endif // !_doContinue_h diff --git a/src/doEDASA.h b/src/doEDASA.h index 25fc5e5d..ae2e39cd 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -17,8 +17,6 @@ #include "doEstimator.h" #include "doModifierMass.h" #include "doSampler.h" -#include "doHyperVolume.h" -#include "doStat.h" #include "doContinue.h" template < typename D > diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt new file mode 100644 index 00000000..48a65519 --- /dev/null +++ b/src/utils/CMakeLists.txt @@ -0,0 +1,14 @@ +###################################################################################### +### 1) Set all needed source files for the project +###################################################################################### + +FILE(GLOB SOURCES *.cpp) + +SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) +ADD_LIBRARY(doutils ${SOURCES}) +INSTALL(TARGETS doutils ARCHIVE DESTINATION lib COMPONENT libraries) + +FILE(GLOB HDRS *.h utils) +INSTALL(FILES ${HDRS} DESTINATION include/do/utils COMPONENT headers) + +###################################################################################### diff --git a/src/doCheckPoint.h b/src/utils/doCheckPoint.h similarity index 100% rename from src/doCheckPoint.h rename to src/utils/doCheckPoint.h diff --git a/src/doFileSnapshot.cpp b/src/utils/doFileSnapshot.cpp similarity index 98% rename from src/doFileSnapshot.cpp rename to src/utils/doFileSnapshot.cpp index 6d0578e8..6879d75e 100644 --- a/src/doFileSnapshot.cpp +++ b/src/utils/doFileSnapshot.cpp @@ -30,7 +30,7 @@ #include #include -#include +#include #include #include diff --git a/src/doFileSnapshot.h b/src/utils/doFileSnapshot.h similarity index 100% rename from src/doFileSnapshot.h rename to src/utils/doFileSnapshot.h diff --git a/src/doHyperVolume.h b/src/utils/doHyperVolume.h similarity index 100% rename from src/doHyperVolume.h rename to src/utils/doHyperVolume.h diff --git a/src/doPopStat.h b/src/utils/doPopStat.h similarity index 100% rename from src/doPopStat.h rename to src/utils/doPopStat.h diff --git a/src/doStat.h b/src/utils/doStat.h similarity index 100% rename from src/doStat.h rename to src/utils/doStat.h diff --git a/src/doStatNormalMono.h b/src/utils/doStatNormalMono.h similarity index 100% rename from src/doStatNormalMono.h rename to src/utils/doStatNormalMono.h diff --git a/src/doStatNormalMulti.h b/src/utils/doStatNormalMulti.h similarity index 100% rename from src/doStatNormalMulti.h rename to src/utils/doStatNormalMulti.h diff --git a/src/doStatUniform.h b/src/utils/doStatUniform.h similarity index 100% rename from src/doStatUniform.h rename to src/utils/doStatUniform.h From 752b1722bb5725558b4b0f91b84467a1f0a47408 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 24 Aug 2010 11:19:31 +0200 Subject: [PATCH 39/74] * pkg-config updated + cmake file --- application/eda_sa/CMakeLists.txt | 2 +- do.pc | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/application/eda_sa/CMakeLists.txt b/application/eda_sa/CMakeLists.txt index 8cdc8c13..e8ec6f13 100644 --- a/application/eda_sa/CMakeLists.txt +++ b/application/eda_sa/CMakeLists.txt @@ -25,4 +25,4 @@ FILE(GLOB SOURCES *.cpp) SET(EXECUTABLE_OUTPUT_PATH ${DO_BINARY_DIR}) ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES}) -TARGET_LINK_LIBRARIES(${PROJECT_NAME} do ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) +TARGET_LINK_LIBRARIES(${PROJECT_NAME} do doutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) diff --git a/do.pc b/do.pc index 44155200..b207747d 100644 --- a/do.pc +++ b/do.pc @@ -8,5 +8,5 @@ includedir=${prefix}/include/do Name: Distribution Object Description: Distribution Object Version: 1.0 -Libs: -L${libdir} -ldo +Libs: -L${libdir} -ldo -ldoutils Cflags: -I${includedir} From b21f90c75ec262a10d04bcd9a49f9ac17daca2c1 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 24 Aug 2010 11:22:06 +0200 Subject: [PATCH 40/74] * fixed remove command issue --- src/utils/doFileSnapshot.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/doFileSnapshot.cpp b/src/utils/doFileSnapshot.cpp index 6879d75e..3ad012f7 100644 --- a/src/utils/doFileSnapshot.cpp +++ b/src/utils/doFileSnapshot.cpp @@ -62,7 +62,7 @@ doFileSnapshot::doFileSnapshot(std::string dirname, } else if (!res && rmFiles) { - s = std::string("/bin/rm ") + _dirname+ "/" + _filename + "*"; + s = std::string("/bin/rm -f ") + _dirname+ "/" + _filename + "*"; } else { From 74b23dd76b2fdf25f7a4d11a157127c0c185ccb4 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 24 Aug 2010 11:23:55 +0200 Subject: [PATCH 41/74] * LICENSE --- COPYING | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/COPYING b/COPYING index 90cbe47b..8862bf50 100644 --- a/COPYING +++ b/COPYING @@ -1 +1 @@ -Private license +(c) Thales group, 2010 From 799a8f01f324d5fb5988b16f591aa21bc3d41aec Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 24 Aug 2010 18:40:49 +0200 Subject: [PATCH 42/74] + script to plot on ggobi --- application/eda_sa/CMakeLists.txt | 2 +- application/eda_sa/plot_on_ggobi.py | 68 +++++++++++++++++++++++++++++ do.pc | 2 +- src/utils/doFileSnapshot.cpp | 2 +- 4 files changed, 71 insertions(+), 3 deletions(-) create mode 100755 application/eda_sa/plot_on_ggobi.py diff --git a/application/eda_sa/CMakeLists.txt b/application/eda_sa/CMakeLists.txt index 8cdc8c13..e8ec6f13 100644 --- a/application/eda_sa/CMakeLists.txt +++ b/application/eda_sa/CMakeLists.txt @@ -25,4 +25,4 @@ FILE(GLOB SOURCES *.cpp) SET(EXECUTABLE_OUTPUT_PATH ${DO_BINARY_DIR}) ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES}) -TARGET_LINK_LIBRARIES(${PROJECT_NAME} do ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) +TARGET_LINK_LIBRARIES(${PROJECT_NAME} do doutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) diff --git a/application/eda_sa/plot_on_ggobi.py b/application/eda_sa/plot_on_ggobi.py new file mode 100755 index 00000000..2e934183 --- /dev/null +++ b/application/eda_sa/plot_on_ggobi.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python + +from pprint import * +import sys, os + +if __name__ == '__main__': + + # parameter phase + + if len(sys.argv) < 2: + print 'Usage: %s [FILE]' % sys.argv[0] + sys.exit() + + filename = sys.argv[1] + + lines = open(filename).readlines() + + # formatting phase + + try: + results = [ x.split() for x in lines[1:-1] ] + except IOError, e: + print 'Error: %s' % e + sys.exit() + + # dimension estimating phase + + popsize = int(lines[0].split()[0]) + dimsize = int(results[0][1]) + + # printing phase + + print 'popsize: %d' % popsize + print 'dimsize: %d' % dimsize + + print + pprint( results ) + + # cvs converting phase + + i = 1 + for x in results: + x.insert(0, '"%d"' % i) + i += 1 + + header = ['""', '"fitness"', '"dimsize"'] + + for i in range(0, dimsize): + header.append( '"dim%d"' % i ) + + results.insert(0, header) + + # cvs printing phase + + file_results = '\n'.join( [ ','.join( x ) for x in results ] ) + + print + print file_results + + try: + open('%s.csv' % filename, 'w').write(file_results + '\n') + except IOError, e: + print 'Error: %s' % e + sys.exit() + + # ggobi plotting phase + + os.system('ggobi %s.csv' % filename) diff --git a/do.pc b/do.pc index 44155200..b207747d 100644 --- a/do.pc +++ b/do.pc @@ -8,5 +8,5 @@ includedir=${prefix}/include/do Name: Distribution Object Description: Distribution Object Version: 1.0 -Libs: -L${libdir} -ldo +Libs: -L${libdir} -ldo -ldoutils Cflags: -I${includedir} diff --git a/src/utils/doFileSnapshot.cpp b/src/utils/doFileSnapshot.cpp index 6879d75e..3ad012f7 100644 --- a/src/utils/doFileSnapshot.cpp +++ b/src/utils/doFileSnapshot.cpp @@ -62,7 +62,7 @@ doFileSnapshot::doFileSnapshot(std::string dirname, } else if (!res && rmFiles) { - s = std::string("/bin/rm ") + _dirname+ "/" + _filename + "*"; + s = std::string("/bin/rm -f ") + _dirname+ "/" + _filename + "*"; } else { From b017a0eb4602b1449090135ae05bc8a6371cbdc0 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 25 Aug 2010 19:15:32 +0200 Subject: [PATCH 43/74] * removed rho parameter and replaced it by popsize --- application/eda_sa/CMakeLists.txt | 1 + application/eda_sa/main.cpp | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/application/eda_sa/CMakeLists.txt b/application/eda_sa/CMakeLists.txt index e8ec6f13..25c07772 100644 --- a/application/eda_sa/CMakeLists.txt +++ b/application/eda_sa/CMakeLists.txt @@ -10,6 +10,7 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) SET(RESOURCES eda_sa.param plot.py + plot_on_ggobi.py ) FOREACH(file ${RESOURCES}) diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index b362529c..6c9d2738 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -135,9 +135,11 @@ int main(int ac, char** av) // FIXME: should I set the default value of rho to pop size ?!? - unsigned int rho = parser.createParam((unsigned int)0, "rho", "Rho: metropolis sample size", 'p', section).value(); // p + // unsigned int rho = parser.createParam((unsigned int)0, "rho", "Rho: metropolis sample size", 'p', section).value(); // p - moGenSolContinue< EOT >* sa_continue = new moGenSolContinue< EOT >(rho); + unsigned int popSize = parser.getORcreateParam((unsigned int)20, "popSize", "Population Size", 'P', "Evolution Engine").value(); + + moGenSolContinue< EOT >* sa_continue = new moGenSolContinue< EOT >( popSize ); state.storeFunctor(sa_continue); //----------------------------------------------------------------------------- From e71e86d6c103fd3d4efa05a4270151585116708f Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Thu, 26 Aug 2010 19:31:30 +0200 Subject: [PATCH 44/74] ... --- application/eda_sa/main.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index 6c9d2738..cdc615b0 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -133,8 +133,6 @@ int main(int ac, char** av) // Metropolis sample parameters //----------------------------------------------------------------------------- - // FIXME: should I set the default value of rho to pop size ?!? - // unsigned int rho = parser.createParam((unsigned int)0, "rho", "Rho: metropolis sample size", 'p', section).value(); // p unsigned int popSize = parser.getORcreateParam((unsigned int)20, "popSize", "Population Size", 'P', "Evolution Engine").value(); From 08754eeaee2caad86294e7a8c4b4bcfd0dde8b93 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 30 Aug 2010 16:20:55 +0200 Subject: [PATCH 45/74] fixed a bug with using of replacor, it didnt reduce the fitness --- src/doEDASA.h | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/src/doEDASA.h b/src/doEDASA.h index ae2e39cd..b8c94706 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -54,7 +54,7 @@ public: eoSelectOne< EOT > & selectone, doModifierMass< D > & modifier, doSampler< D > & sampler, - eoContinue< EOT > & monitoring_continue, + // eoContinue< EOT > & monitoring_continue, eoContinue< EOT > & pop_continue, doContinue< D > & distribution_continue, eoEvalFunc < EOT > & evaluation, @@ -68,7 +68,7 @@ public: _selectone(selectone), _modifier(modifier), _sampler(sampler), - _monitoring_continue(monitoring_continue), + // _monitoring_continue(monitoring_continue), _pop_continue(pop_continue), _distribution_continue(distribution_continue), _evaluation(evaluation), @@ -91,7 +91,7 @@ public: double temperature = _initial_temperature; - eoPop< EOT > current_pop = pop; + eoPop< EOT > current_pop; eoPop< EOT > selected_pop; @@ -111,19 +111,12 @@ public: do { - if (pop != current_pop) - { - _replacor(pop, current_pop); - } - - current_pop.clear(); - selected_pop.clear(); - - //------------------------------------------------------------- // (3) Selection of the best points in the population //------------------------------------------------------------- + selected_pop.clear(); + _selector(pop, selected_pop); assert( selected_pop.size() > 0 ); @@ -172,6 +165,8 @@ public: // Building of the sampler in current_pop //------------------------------------------------------------- + current_pop.clear(); + do { EOT candidate_solution = _sampler(distrib); @@ -191,12 +186,18 @@ public: } while ( _sa_continue( current_solution) ); + //selected_pop.sort(); + + _replacor(pop, current_pop); + + if ( ! _cooling_schedule( temperature ) ){ eo::log << eo::debug << "_cooling_schedule" << std::endl; break; } + + if ( ! _distribution_continue( distrib ) ){ eo::log << eo::debug << "_distribution_continue" << std::endl; break; } + + if ( ! _pop_continue( pop ) ){ eo::log << eo::debug << "_pop_continue" << std::endl; break; } + } - while ( _cooling_schedule( temperature ) && - _distribution_continue( distrib ) && - _pop_continue( current_pop ) && - _monitoring_continue( selected_pop ) - ); + while ( 1 ); } private: @@ -217,7 +218,7 @@ private: doSampler< D > & _sampler; //! A EOT monitoring continuator - eoContinue < EOT > & _monitoring_continue; + // eoContinue < EOT > & _monitoring_continue; //! A EOT population continuator eoContinue < EOT > & _pop_continue; From 1086dc4d492010a43633f60beb460b92634bf326 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 31 Aug 2010 17:16:48 +0200 Subject: [PATCH 46/74] * main.cpp: removed useless comments * src/do: added some lines to make detectable language file * doEDASA.h: added some comments --- application/eda_sa/main.cpp | 71 +++++++++++++++---------------------- src/do | 4 +++ src/doEDASA.h | 25 ++++++------- 3 files changed, 43 insertions(+), 57 deletions(-) diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index cdc615b0..023976ca 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -4,6 +4,8 @@ #include #include +#include + #include #include #include @@ -14,12 +16,11 @@ #include "Rosenbrock.h" #include "Sphere.h" -typedef eoReal EOT; -//typedef doUniform< EOT > Distrib; -//typedef doNormalMono< EOT > Distrib; +typedef eoReal EOT; typedef doNormalMulti< EOT > Distrib; + int main(int ac, char** av) { eoParserLogger parser(ac, av); @@ -39,34 +40,27 @@ int main(int ac, char** av) // Instantiate all needed parameters for EDASA algorithm //----------------------------------------------------------------------------- - eoSelect< EOT >* selector = new eoDetSelect< EOT >(0.5); + double selection_rate = parser.createParam((double)0.5, "selection_rate", "Selection Rate", 'R', section).value(); // R + + eoSelect< EOT >* selector = new eoDetSelect< EOT >( selection_rate ); state.storeFunctor(selector); - doEstimator< Distrib >* estimator = - //new doEstimatorUniform< EOT >(); - //new doEstimatorNormalMono< EOT >(); - new doEstimatorNormalMulti< EOT >(); + doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); state.storeFunctor(estimator); eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >( 2 ); state.storeFunctor(selectone); - doModifierMass< Distrib >* modifier = - //new doUniformCenter< EOT >(); - //new doNormalMonoCenter< EOT >(); - new doNormalMultiCenter< EOT >(); + doModifierMass< Distrib >* modifier = new doNormalMultiCenter< EOT >(); state.storeFunctor(modifier); - eoEvalFunc< EOT >* plainEval = - new Rosenbrock< EOT >(); - //new Sphere< EOT >(); + eoEvalFunc< EOT >* plainEval = new Rosenbrock< EOT >(); state.storeFunctor(plainEval); unsigned long max_eval = parser.getORcreateParam((unsigned long)0, "maxEval", "Maximum number of evaluations (0 = none)", 'E', "Stopping criterion").value(); // E - eoEvalFuncCounter< EOT > eval(*plainEval, max_eval); + eoEvalFuncCounterBounder< EOT > eval(*plainEval, max_eval); eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5); - //eoRndGenerator< double >* gen = new eoNormalGenerator< double >(0, 1); state.storeFunctor(gen); @@ -106,8 +100,6 @@ int main(int ac, char** av) // This is used by doSampler. //----------------------------------------------------------------------------- - - //doBounder< EOT >* bounder = new doBounderNo< EOT >(); doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), EOT(pop[0].size(), 5), *gen); @@ -120,10 +112,7 @@ int main(int ac, char** av) // Prepare sampler class with a specific distribution //----------------------------------------------------------------------------- - doSampler< Distrib >* sampler = - //new doSamplerUniform< EOT >(); - //new doSamplerNormalMono< EOT >( *bounder ); - new doSamplerNormalMulti< EOT >( *bounder ); + doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); state.storeFunctor(sampler); //----------------------------------------------------------------------------- @@ -133,8 +122,6 @@ int main(int ac, char** av) // Metropolis sample parameters //----------------------------------------------------------------------------- - // unsigned int rho = parser.createParam((unsigned int)0, "rho", "Rho: metropolis sample size", 'p', section).value(); // p - unsigned int popSize = parser.getORcreateParam((unsigned int)20, "popSize", "Population Size", 'P', "Evolution Engine").value(); moGenSolContinue< EOT >* sa_continue = new moGenSolContinue< EOT >( popSize ); @@ -170,7 +157,16 @@ int main(int ac, char** av) // general output //----------------------------------------------------------------------------- - eoCheckPoint< EOT >& monitoring_continue = do_make_checkpoint(parser, state, eval, eo_continue); + eoCheckPoint< EOT >& pop_continue = do_make_checkpoint(parser, state, eval, eo_continue); + + doPopStat< EOT >* popStat = new doPopStat; + state.storeFunctor(popStat); + pop_continue.add(*popStat); + + doFileSnapshot* fileSnapshot = new doFileSnapshot("ResPop"); + state.storeFunctor(fileSnapshot); + fileSnapshot->add(*popStat); + pop_continue.add(*fileSnapshot); //----------------------------------------------------------------------------- @@ -179,17 +175,6 @@ int main(int ac, char** av) // population output //----------------------------------------------------------------------------- - eoCheckPoint< EOT >* pop_continue = new eoCheckPoint< EOT >( eo_continue ); - state.storeFunctor(pop_continue); - - doPopStat< EOT >* popStat = new doPopStat; - state.storeFunctor(popStat); - pop_continue->add(*popStat); - - doFileSnapshot* fileSnapshot = new doFileSnapshot("ResPop"); - state.storeFunctor(fileSnapshot); - fileSnapshot->add(*popStat); - pop_continue->add(*fileSnapshot); //----------------------------------------------------------------------------- @@ -244,7 +229,7 @@ int main(int ac, char** av) doAlgo< Distrib >* algo = new doEDASA< Distrib > (*selector, *estimator, *selectone, *modifier, *sampler, - monitoring_continue, *pop_continue, *distribution_continue, + pop_continue, *distribution_continue, eval, *sa_continue, *cooling_schedule, initial_temperature, *replacor); @@ -273,13 +258,13 @@ int main(int ac, char** av) { do_run(*algo, pop); } - catch (eoReachedThresholdException& e) - { - eo::log << eo::warnings << e.what() << std::endl; - } + catch (eoEvalFuncCounterBounderException& e) + { + eo::log << eo::warnings << "warning: " << e.what() << std::endl; + } catch (std::exception& e) { - eo::log << eo::errors << "exception: " << e.what() << std::endl; + eo::log << eo::errors << "error: " << e.what() << std::endl; exit(EXIT_FAILURE); } diff --git a/src/do b/src/do index bcd43e19..1f91d392 100644 --- a/src/do +++ b/src/do @@ -52,3 +52,7 @@ #include "utils/doPopStat.h" #endif // !_do_ + +// Local Variables: +// mode: C++ +// End: diff --git a/src/doEDASA.h b/src/doEDASA.h index b8c94706..db49375c 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -38,23 +38,24 @@ public: /*! All the boxes used by a EDASA need to be given. - \param selector The EOT selector - \param estomator The EOT selector + \param selector Population Selector + \param estimator Distribution Estimator \param selectone SelectOne - \param modifier The D modifier - \param sampler The D sampler - \param evaluation The evaluation function. - \param continue The stopping criterion. - \param cooling_schedule The cooling schedule, describes how the temperature is modified. + \param modifier Distribution Modifier + \param sampler Distribution Sampler + \param pop_continue Population Continuator + \param distribution_continue Distribution Continuator + \param evaluation Evaluation function. + \param sa_continue Stopping criterion. + \param cooling_schedule Cooling schedule, describes how the temperature is modified. \param initial_temperature The initial temperature. - \param replacor The EOT replacor + \param replacor Population replacor */ doEDASA (eoSelect< EOT > & selector, doEstimator< D > & estimator, eoSelectOne< EOT > & selectone, doModifierMass< D > & modifier, doSampler< D > & sampler, - // eoContinue< EOT > & monitoring_continue, eoContinue< EOT > & pop_continue, doContinue< D > & distribution_continue, eoEvalFunc < EOT > & evaluation, @@ -68,7 +69,6 @@ public: _selectone(selectone), _modifier(modifier), _sampler(sampler), - // _monitoring_continue(monitoring_continue), _pop_continue(pop_continue), _distribution_continue(distribution_continue), _evaluation(evaluation), @@ -186,7 +186,7 @@ public: } while ( _sa_continue( current_solution) ); - //selected_pop.sort(); + pop.sort(); _replacor(pop, current_pop); @@ -217,9 +217,6 @@ private: //! A D sampler doSampler< D > & _sampler; - //! A EOT monitoring continuator - // eoContinue < EOT > & _monitoring_continue; - //! A EOT population continuator eoContinue < EOT > & _pop_continue; From 13b9b623975824ce384102fe9412f425201790a1 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 31 Aug 2010 19:29:05 +0200 Subject: [PATCH 47/74] added temporary population sorting --- src/doEDASA.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/doEDASA.h b/src/doEDASA.h index db49375c..05c8cc1c 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -184,12 +184,12 @@ public: current_solution = candidate_solution; } } - while ( _sa_continue( current_solution) ); + while ( _sa_continue( current_solution) ); + + _replacor(pop, current_pop); // copy current_pop in pop pop.sort(); - _replacor(pop, current_pop); - if ( ! _cooling_schedule( temperature ) ){ eo::log << eo::debug << "_cooling_schedule" << std::endl; break; } if ( ! _distribution_continue( distrib ) ){ eo::log << eo::debug << "_distribution_continue" << std::endl; break; } From 97143d65a398de62fb1c0d4dfc1a28545010fb16 Mon Sep 17 00:00:00 2001 From: Johann Dreo Date: Fri, 3 Sep 2010 18:32:27 +0200 Subject: [PATCH 48/74] switch to new MO 1.3 classes and interface --- src/doEDASA.h | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/doEDASA.h b/src/doEDASA.h index 05c8cc1c..c0dce883 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -59,8 +59,8 @@ public: eoContinue< EOT > & pop_continue, doContinue< D > & distribution_continue, eoEvalFunc < EOT > & evaluation, - moSolContinue < EOT > & sa_continue, - moCoolingSchedule & cooling_schedule, + moContinuator< moDummyNeighbor > & sa_continue, + moCoolingSchedule & cooling_schedule, double initial_temperature, eoReplacement< EOT > & replacor ) @@ -227,10 +227,10 @@ private: eoEvalFunc < EOT > & _evaluation; //! Stopping criterion before temperature update - moSolContinue < EOT > & _sa_continue; + moContinuator< moDummyNeighbor > & _sa_continue; //! The cooling schedule - moCoolingSchedule & _cooling_schedule; + moCoolingSchedule & _cooling_schedule; //! Initial temperature double _initial_temperature; From 5dc8a1a8fe55b92b468d5bdc189fd02426095f79 Mon Sep 17 00:00:00 2001 From: Johann Dreo Date: Sat, 4 Sep 2010 23:07:37 +0200 Subject: [PATCH 49/74] some MO types replacement --- application/eda_sa/main.cpp | 8 ++++---- src/doEDASA.h | 7 +++++-- src/doSampler.h | 7 +++++++ 3 files changed, 16 insertions(+), 6 deletions(-) diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index 023976ca..b873c1d6 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -124,7 +124,7 @@ int main(int ac, char** av) unsigned int popSize = parser.getORcreateParam((unsigned int)20, "popSize", "Population Size", 'P', "Evolution Engine").value(); - moGenSolContinue< EOT >* sa_continue = new moGenSolContinue< EOT >( popSize ); + moContinuator< moDummyNeighbor >* sa_continue = new moIterContinuator< moDummyNeighbor >( popSize ); state.storeFunctor(sa_continue); //----------------------------------------------------------------------------- @@ -134,10 +134,10 @@ int main(int ac, char** av) // SA parameters //----------------------------------------------------------------------------- - double threshold = parser.createParam((double)0.1, "threshold", "Threshold: temperature threshold stopping criteria", 't', section).value(); // t - double alpha = parser.createParam((double)0.1, "alpha", "Alpha: temperature dicrease rate", 'a', section).value(); // a + double threshold_temperature = parser.createParam((double)0.1, "threshold", "Minimal temperature at which stop", 't', section).value(); // t + double alpha = parser.createParam((double)0.1, "alpha", "Temperature decrease rate", 'a', section).value(); // a - moCoolingSchedule* cooling_schedule = new moGeometricCoolingSchedule(threshold, alpha); + moCoolingSchedule* cooling_schedule = new moSimpleCoolingSchedule(initial_temperature, alpha, 0, threshold_temperature); state.storeFunctor(cooling_schedule); //----------------------------------------------------------------------------- diff --git a/src/doEDASA.h b/src/doEDASA.h index c0dce883..93586249 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -75,7 +75,9 @@ public: _sa_continue(sa_continue), _cooling_schedule(cooling_schedule), _initial_temperature(initial_temperature), - _replacor(replacor) + _replacor(replacor), + _dummy_neighbor() + {} //! function that launches the EDASA algorithm. @@ -124,7 +126,7 @@ public: //------------------------------------------------------------- - _sa_continue.init(); + _sa_continue.init( _dummy_neighbor ); //------------------------------------------------------------- @@ -256,6 +258,7 @@ private: //------------------------------------------------------------- + moDummyNeighbor _dummy_neighbor; }; #endif // !_doEDASA_h diff --git a/src/doSampler.h b/src/doSampler.h index 63641247..dac38e5f 100644 --- a/src/doSampler.h +++ b/src/doSampler.h @@ -11,6 +11,7 @@ #include #include "doBounder.h" +#include "doBounderNo.h" template < typename D > class doSampler : public eoUF< D&, typename D::EOType > @@ -22,6 +23,10 @@ public: : _bounder(bounder) {} + doSampler() + : _bounder( _dummy_bounder ) + {} + // virtual EOType operator()( D& ) = 0 (provided by eoUF< A1, R >) virtual EOType sample( D& ) = 0; @@ -60,6 +65,8 @@ public: private: //! Bounder functor doBounder< EOType > & _bounder; + + doBounderNo _dummy_bounder; }; #endif // !_doSampler_h From c8d9acd0a5f7d28ff93960685b87d4837425b46a Mon Sep 17 00:00:00 2001 From: Johann Dreo Date: Mon, 6 Sep 2010 10:43:07 +0200 Subject: [PATCH 50/74] constructors for passing the bounder to super class --- src/doSamplerUniform.h | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/src/doSamplerUniform.h b/src/doSamplerUniform.h index e407360d..1d62b903 100644 --- a/src/doSamplerUniform.h +++ b/src/doSamplerUniform.h @@ -18,10 +18,23 @@ * This class uses the Uniform distribution parameters (bounds) to return * a random position used for population sampling. */ -template < typename EOT > +template < typename EOT, class D=doUniform > class doSamplerUniform : public doSampler< doUniform< EOT > > { public: + + typedef D Distrib; + + doSamplerUniform(doBounder< EOT > & bounder) + : doSampler< doUniform >(bounder) + {} + + /* + doSamplerUniform() + : doSampler< doUniform >() + {} + */ + EOT sample( doUniform< EOT >& distrib ) { unsigned int size = distrib.size(); From acadd9928157f7c6da6c0e0bb010d2fdd092d20b Mon Sep 17 00:00:00 2001 From: Johann Dreo Date: Mon, 6 Sep 2010 10:43:34 +0200 Subject: [PATCH 51/74] no more dummy bounder --- src/doSampler.h | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/doSampler.h b/src/doSampler.h index dac38e5f..0d69223c 100644 --- a/src/doSampler.h +++ b/src/doSampler.h @@ -20,12 +20,14 @@ public: typedef typename D::EOType EOType; doSampler(doBounder< EOType > & bounder) - : _bounder(bounder) + : /*_dummy_bounder(),*/ _bounder(bounder) {} + /* doSampler() - : _bounder( _dummy_bounder ) + : _dummy_bounder(), _bounder( _dummy_bounder ) {} + */ // virtual EOType operator()( D& ) = 0 (provided by eoUF< A1, R >) @@ -63,10 +65,11 @@ public: } private: + //doBounderNo _dummy_bounder; + //! Bounder functor doBounder< EOType > & _bounder; - doBounderNo _dummy_bounder; }; #endif // !_doSampler_h From 56680e865dac21a81086d3e854dcd4607dff88cc Mon Sep 17 00:00:00 2001 From: Caner CANDAN Date: Tue, 7 Sep 2010 15:36:16 +0200 Subject: [PATCH 52/74] * fixed bad using of method moNeighbor< EOT >::init( EOT& ) --- src/doEDASA.h | 28 +++------------------------- 1 file changed, 3 insertions(+), 25 deletions(-) diff --git a/src/doEDASA.h b/src/doEDASA.h index 93586249..c8e9ad9a 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -75,8 +75,7 @@ public: _sa_continue(sa_continue), _cooling_schedule(cooling_schedule), _initial_temperature(initial_temperature), - _replacor(replacor), - _dummy_neighbor() + _replacor(replacor) {} @@ -126,9 +125,6 @@ public: //------------------------------------------------------------- - _sa_continue.init( _dummy_neighbor ); - - //------------------------------------------------------------- // (4) Estimation of the distribution parameters //------------------------------------------------------------- @@ -167,6 +163,8 @@ public: // Building of the sampler in current_pop //------------------------------------------------------------- + _sa_continue.init( current_solution ); + current_pop.clear(); do @@ -239,26 +237,6 @@ private: //! A EOT replacor eoReplacement < EOT > & _replacor; - - //------------------------------------------------------------- - // Temporary solution to store populations state at each - // iteration for plotting. - //------------------------------------------------------------- - - // std::ofstream _ofs_params; - // std::ofstream _ofs_params_var; - - //------------------------------------------------------------- - - //------------------------------------------------------------- - // Temporary solution to store bounds values for each distribution. - //------------------------------------------------------------- - - // std::string _bounds_results_destination; - - //------------------------------------------------------------- - - moDummyNeighbor _dummy_neighbor; }; #endif // !_doEDASA_h From 2e43f4743ae43ddf096001647c2aeb3f3d1aed10 Mon Sep 17 00:00:00 2001 From: Johann Dreo Date: Wed, 8 Sep 2010 12:14:15 +0200 Subject: [PATCH 53/74] bounder on uniform distribution that can handle different bounds on several dimensions --- src/doBounderUniform.h | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 src/doBounderUniform.h diff --git a/src/doBounderUniform.h b/src/doBounderUniform.h new file mode 100644 index 00000000..9fac7dac --- /dev/null +++ b/src/doBounderUniform.h @@ -0,0 +1,35 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo +*/ + +#ifndef _doBounderUniform_h +#define _doBounderUniform_h + +#include "doBounder.h" + +template < typename EOT > +class doBounderUniform : public doBounder< EOT > +{ +public: + doBounderUniform( EOT min, EOT max ) + : doBounder< EOT >( min, max ) + {} + + void operator()( EOT& sol ) + { + unsigned int size = sol.size(); + assert(size > 0); + + for (unsigned int d = 0; d < size; ++d) { + + if ( sol[d] < this->min()[d] || sol[d] > this->max()[d]) { + // use EO's global "rng" + sol[d] = rng.uniform( this->min()[d], this->max()[d] ); + } + } // for d in size + } +}; + +#endif // !_doBounderUniform_h From 70cfb72205225baf1d7e41bc0a83c22cf4df2cfb Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Thu, 9 Sep 2010 07:56:15 +0200 Subject: [PATCH 54/74] * added some features in plot.py plotting script --- application/eda_sa/plot.py | 33 ++++++++++++++++++++++++--------- 1 file changed, 24 insertions(+), 9 deletions(-) mode change 100644 => 100755 application/eda_sa/plot.py diff --git a/application/eda_sa/plot.py b/application/eda_sa/plot.py old mode 100644 new mode 100755 index 1d3298e2..81a3cabf --- a/application/eda_sa/plot.py +++ b/application/eda_sa/plot.py @@ -38,11 +38,12 @@ def logger(level_name, filename='plot.log'): def parser(parser=optparse.OptionParser()): parser.add_option('-v', '--verbose', choices=LEVELS.keys(), default='warning', help='set a verbose level') - parser.add_option('-f', '--file', help='give an input project filename', default='') + parser.add_option('-f', '--files', help='give some input sample files separated by comma (cf. gen1,gen2,...)', default='') parser.add_option('-o', '--output', help='give an output filename for logging', default='plot.log') parser.add_option('-d', '--dimension', help='give a dimension size', default=2) parser.add_option('-m', '--multiplot', action="store_true", help='plot all graphics in one window', dest="multiplot", default=True) parser.add_option('-p', '--plot', action="store_false", help='plot graphics separetly, one by window', dest="multiplot") + parser.add_option('-w', '--window', help='give the number of the window you want to display, 0 means you want to display all ones', default=0) options, args = parser.parse_args() @@ -84,8 +85,14 @@ def draw3DRect(min=(0,0,0), max=(1,1,1), state=None, g=None): def getSortedFiles(path): assert path != None - filelist = os.listdir(path) - filelist.sort() + if options.files == '': + + filelist = os.listdir(path) + filelist.sort() + + else: + + filelist = options.files.split(',') return filelist @@ -240,9 +247,12 @@ def plot2DRectFromFiles(path, state=None, g=None, plot=True): return g -def main(n): +def main(): gstate = [] + n = int(options.dimension) + w = int(options.window) + if options.multiplot: g = Gnuplot.Gnuplot() @@ -275,19 +285,24 @@ def main(n): plotXYZPoint('./ResPop', state=gstate, g=g) g('unset multiplot') + else: - if n >= 1: + + if n >= 1 and w in [0, 1]: plotXPointYFitness('./ResPop', state=gstate) - if n >= 2: + if n >= 2 and w in [0, 2]: plotXPointYFitness('./ResPop', '4:1', state=gstate) - if n >= 2: + if n >= 2 and w in [0, 3]: plotXYPointZFitness('./ResPop', state=gstate) - if n >= 3: + if n >= 3 and w in [0, 4]: plotXYZPoint('./ResPop', state=gstate) + if n >= 2 and w in [0, 5]: + plotXYPoint('./ResPop', state=gstate) + # if n >= 1: # plotParams('./ResParams.txt', state=gstate) @@ -306,6 +321,6 @@ def main(n): if __name__ == '__main__': logging.debug('### plotting started ###') - main(int(options.dimension)) + main() logging.debug('### plotting ended ###') From 573bc959116c7027f84629774fc1da135f7728a7 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Thu, 9 Sep 2010 07:58:05 +0200 Subject: [PATCH 55/74] renamed scripts filenames --- application/eda_sa/{plot_on_ggobi.py => ggobi.py} | 0 application/eda_sa/{plot.py => gplot.py} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename application/eda_sa/{plot_on_ggobi.py => ggobi.py} (100%) rename application/eda_sa/{plot.py => gplot.py} (100%) diff --git a/application/eda_sa/plot_on_ggobi.py b/application/eda_sa/ggobi.py similarity index 100% rename from application/eda_sa/plot_on_ggobi.py rename to application/eda_sa/ggobi.py diff --git a/application/eda_sa/plot.py b/application/eda_sa/gplot.py similarity index 100% rename from application/eda_sa/plot.py rename to application/eda_sa/gplot.py From 839392f0dcf07b0c238ac012dcdd63727473ca39 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Thu, 9 Sep 2010 07:59:50 +0200 Subject: [PATCH 56/74] buxfixed on CMakeLists.txt regarding copying failures --- application/eda_sa/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/application/eda_sa/CMakeLists.txt b/application/eda_sa/CMakeLists.txt index 25c07772..63901a33 100644 --- a/application/eda_sa/CMakeLists.txt +++ b/application/eda_sa/CMakeLists.txt @@ -9,8 +9,8 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) SET(RESOURCES eda_sa.param - plot.py - plot_on_ggobi.py + gplot.py + ggobi.py ) FOREACH(file ${RESOURCES}) From f542d3f894ecede36369af494577033294ceacc3 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Thu, 9 Sep 2010 08:03:01 +0200 Subject: [PATCH 57/74] * README --- README | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README b/README index 64629f58..f58d9d3c 100644 --- a/README +++ b/README @@ -1,4 +1,4 @@ -This package contains the source code for BOPO problems. +This package contains the source code for DO. # Step 1 - Configuration ------------------------ @@ -10,7 +10,7 @@ On Windows write your path with double antislash (ex: C:\\Users\\...) # Step 2 - Build process ------------------------ ParadisEO is assumed to be compiled. To download ParadisEO, please visit http://paradiseo.gforge.inria.fr/. -Go to the BOPO/build/ directory and lunch cmake: +Go to the DO/build/ directory and lunch cmake: (Unix) > cmake .. (Windows) > cmake .. -G"Visual Studio 9 2008" @@ -19,7 +19,7 @@ Note for windows users: if you don't use VisualStudio 9, enter the name of your # Step 3 - Compilation ---------------------- -In the bopo/build/ directory: +In the do/build/ directory: (Unix) > make (Windows) Open the VisualStudio solution and compile it, compile also the target install. You can refer to this tutorial if you don't know how to compile a solution: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial @@ -29,15 +29,15 @@ You can refer to this tutorial if you don't know how to compile a solution: http --------------------- A toy example is given to test the components. You can run these tests as following. To define problem-related components for your own problem, please refer to the tutorials available on the website : http://paradiseo.gforge.inria.fr/. -In the bopo/build/ directory: +In the do/build/ directory: (Unix) > ctest Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial -In the directory "application", there are several directory such as p_eoco which instantiate NSGAII on BOPO problems. +In the directory "application", there are several directory such as eda_sa which instantiate EDA-SA solver. -(Unix) After compilation you can run the script "bopo/run.sh" and see results in "NSGAII.out". Parameters can be modified in the script. +(Unix) After compilation you can run the binary "build/eda_sa" and see results. Parameters can be modified from command line. -(Windows) Add argument "NSGAII.param" and execute the corresponding algorithms. +(Windows) Add argument "eda_sa.param" and execute the corresponding algorithms. Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial @@ -46,7 +46,7 @@ Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/i The API-documentation is available in doc/html/index.html -# Things to keep in mind when using BOPO +# Things to keep in mind when using DO ---------------------------------------- * By default, the EO random generator's seed is initialized by the number of seconds since the epoch (with time(0)). It is available in the status file dumped at each execution. Please, keep in mind that if you start two run at the same second without modifying the seed, you will get exactly the same results. From 8f735f0b165477ca43fa04fab15daa623a9a65eb Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Thu, 9 Sep 2010 11:24:35 +0200 Subject: [PATCH 58/74] * some updates on gplot.py to have a better display + screenshots from gnuplot --- application/eda_sa/gplot.py | 16 ++++++++++++---- screenshots/gplot-eda_sa-P-1000-d-10-a-0.9.png | Bin 0 -> 78493 bytes screenshots/gplot-eda_sa-P-10000-d-2-a-0.1.png | Bin 0 -> 50871 bytes 3 files changed, 12 insertions(+), 4 deletions(-) create mode 100644 screenshots/gplot-eda_sa-P-1000-d-10-a-0.9.png create mode 100644 screenshots/gplot-eda_sa-P-10000-d-2-a-0.1.png diff --git a/application/eda_sa/gplot.py b/application/eda_sa/gplot.py index 81a3cabf..159c1caf 100755 --- a/application/eda_sa/gplot.py +++ b/application/eda_sa/gplot.py @@ -43,7 +43,7 @@ def parser(parser=optparse.OptionParser()): parser.add_option('-d', '--dimension', help='give a dimension size', default=2) parser.add_option('-m', '--multiplot', action="store_true", help='plot all graphics in one window', dest="multiplot", default=True) parser.add_option('-p', '--plot', action="store_false", help='plot graphics separetly, one by window', dest="multiplot") - parser.add_option('-w', '--window', help='give the number of the window you want to display, 0 means you want to display all ones', default=0) + parser.add_option('-w', '--windowid', help='give the window id you want to display, 0 means we display all ones', default=0) options, args = parser.parse_args() @@ -251,11 +251,17 @@ def main(): gstate = [] n = int(options.dimension) - w = int(options.window) + w = int(options.windowid) if options.multiplot: g = Gnuplot.Gnuplot() + g('set parametric') + g('set nokey') + g('set noxtic') + g('set noytic') + g('set noztic') + g('set size 1.0, 1.0') g('set origin 0.0, 0.0') g('set multiplot') @@ -281,10 +287,12 @@ def main(): g('set size 0.5, 0.5') g('set origin 0.5, 0.0') - if n >= 3: + if n >= 2: + plotXYPoint('./ResPop', state=gstate, g=g) + elif n >= 3: plotXYZPoint('./ResPop', state=gstate, g=g) - g('unset multiplot') + g('set nomultiplot') else: diff --git a/screenshots/gplot-eda_sa-P-1000-d-10-a-0.9.png b/screenshots/gplot-eda_sa-P-1000-d-10-a-0.9.png new file mode 100644 index 0000000000000000000000000000000000000000..9f1f6c8855392117d3a6d17796ad3341be759a06 GIT binary patch literal 78493 zcmafbWmFwY6YUTZoM6E%gy0SVf(LhZ3+@`+A$V|icXxMp*Wm6R+~4Hh`@LUpt@q=s zbC~JruI}1hwRcS~e#uA)Bf{ap0RVs~Dk2~U0B^j(4*>H9ypnjB6bXJo+VY7iz`(#P zZAhm^JJowG~q1Qpzqs)vwWV3Y0c|Hd(HCiijMED8*|A-_9s4} zlYfBoI5*I7m76~EtO(w<=%Ea#FRq&#&G0Dz0F#L$7xMQ` z%n@M-1MvCxMys@vkG6lh)7_~!i5udPAb9V?P^f^-m&;YM;$gB}=d@x~i+=`b?9>JT zu8Z>(OgK(8UKRNXxgQ?9ojb$#WsI!-mk8Ye(EkH(@AmQ8qrHuYHBlvcu&0VN&Y&18 ze$P2h=hG((QPE$&U}2{sQXowJF?#0fHEIbduntp3uiU0^e0eXG!g+9c4*>}kf_$DJ z3{VdzNGK(b8h+;Tji|VxellaM1TaD>>17GzG>C%wPq-XuIaqIXtMepB4Q(5TW~%f5 z+Rp3^3pk}!(2qcTla;+lWZIJ;MH|12G@P!kcRZP^)ZB`*pzlxRbUD9mf8Tz2sU;Og z*1p^I0LO1Tg@4Xg{^<4=RQCJjG;_^8~HHc%X7KP0|?VvF6DyG=k 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z#1E1rN{FuDng?(7Gp(C(k$s2LqMxI`XxttGF8uE?M-7zEHvmP&;pgT8NO^NxoUgZO zEAh>-;pgvSV`Stc`3O?su|@zqcoE1^!I>ip0*C3asWURG*8DAk<77#Q( zlkziwtsUH4KFV2uI3@O=yWxxsl72mZ|G$8E3Qm41WbwzdPsI|?_kl?uZhTko!1TJae&hX+AwpzOe^JvfMk%Wa|HO}oYy`ptjlOPRQV zA=Xng&Y}L7&xe=t@M{r%kSgW>&u{P$>%)@q-viUk`2H%eQ_Fb%h0H(x--qSk<7I#6 zfxsGg$=;~WT3eFO&tnipgd^}m`2+CI0O)i_Y25!l<&vGr0xF4E%w6?Z@;r8-yW)P+ zrzbk?6ZRD|>iEx(5ILSAiHRF)B=Fp~`s}l!JpW{L8ZkeYi}mwSp8vkCmM*xti<_5I z)c-lwmoun;rp?nf0VIpxcBkJ8Lh(MJ)>#VYdE6v+3UBz}5GuSRt)C= From 26ac5cae052cc2204c92c2f8832cd27f5a5efc98 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 14 Sep 2010 13:19:43 +0200 Subject: [PATCH 67/74] bugfixed from ublas::vector assignement ctor for old version of boost --- test/t-doEstimatorNormalMulti.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/t-doEstimatorNormalMulti.cpp b/test/t-doEstimatorNormalMulti.cpp index 4dbc658c..71b07e2a 100644 --- a/test/t-doEstimatorNormalMulti.cpp +++ b/test/t-doEstimatorNormalMulti.cpp @@ -82,7 +82,10 @@ int main(int ac, char** av) // (2) distribution initial parameters //----------------------------------------------------------------------------- - ublas::vector< AtomType > mean( s_size, mean_value ); + ublas::vector< AtomType > mean( s_size ); + + for (unsigned int i = 0; i < s_size; ++i) { mean( i ) = mean_value; } + ublas::symmetric_matrix< AtomType, ublas::lower > varcovar( s_size, s_size ); varcovar( 0, 0 ) = covar1_value; From b70a60bc59135ff71003e492d8be53d3302a9246 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 21 Sep 2010 15:08:38 +0200 Subject: [PATCH 68/74] + t-mean-distance: program to generate distance value between the theorical and visual means --- test/t-mean-distance.cpp | 176 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 176 insertions(+) create mode 100644 test/t-mean-distance.cpp diff --git a/test/t-mean-distance.cpp b/test/t-mean-distance.cpp new file mode 100644 index 00000000..3e852a4a --- /dev/null +++ b/test/t-mean-distance.cpp @@ -0,0 +1,176 @@ +#include +#include +#include + +#include +#include + +#include +#include + +#include + +#include "Rosenbrock.h" +#include "Sphere.h" + +typedef eoReal< eoMinimizingFitness > EOT; +typedef doNormalMulti< EOT > Distrib; +typedef EOT::AtomType AtomType; + +int main(int ac, char** av) +{ + //----------------------------------------------------- + // (0) parser + eo routines + //----------------------------------------------------- + + eoParserLogger parser(ac, av); + + std::string section("Algorithm parameters"); + + unsigned int p_min = parser.createParam((unsigned int)10, "population-min", "Population min", 'p', section).value(); // p + unsigned int p_max = parser.createParam((unsigned int)10000, "population-max", "Population max", 'P', section).value(); // P + unsigned int p_step = parser.createParam((unsigned int)10, "population-step", "Population step", 't', section).value(); // t + unsigned int s_size = parser.createParam((unsigned int)2, "dimension-size", "Dimension size", 'd', section).value(); // d + + AtomType mean_value = parser.createParam((AtomType)0, "mean", "Mean value", 'm', section).value(); // m + AtomType covar1_value = parser.createParam((AtomType)1.0, "covar1", "Covar value 1", '1', section).value(); // 1 + AtomType covar2_value = parser.createParam((AtomType)0.5, "covar2", "Covar value 2", '2', section).value(); // 2 + AtomType covar3_value = parser.createParam((AtomType)1.0, "covar3", "Covar value 3", '3', section).value(); // 3 + + if (parser.userNeedsHelp()) + { + parser.printHelp(std::cout); + exit(1); + } + + make_verbose(parser); + make_help(parser); + + //----------------------------------------------------- + + + assert(s_size >= 2); + + eo::log << eo::debug << "p_size s_size mean(0) mean(1) new-mean(0) new-mean(1) distance" << std::endl; + + eo::log << eo::logging; + + for ( unsigned int p_size = p_min; p_size <= p_max; p_size *= p_step ) + { + + assert(p_size >= p_min); + + eoState state; + + + //----------------------------------------------------- + // (1) Population init and sampler + //----------------------------------------------------- + + eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5); + state.storeFunctor(gen); + + eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( s_size, *gen ); + state.storeFunctor(init); + + // create an empty pop and let the state handle the memory + // fill population thanks to eoInit instance + eoPop< EOT >& pop = state.takeOwnership( eoPop< EOT >( p_size, *init ) ); + + //----------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (2) distribution initial parameters + //----------------------------------------------------------------------------- + + ublas::vector< AtomType > mean( s_size, mean_value ); + ublas::symmetric_matrix< AtomType, ublas::lower > varcovar( s_size, s_size ); + + varcovar( 0, 0 ) = covar1_value; + varcovar( 0, 1 ) = covar2_value; + varcovar( 1, 1 ) = covar3_value; + + Distrib distrib( mean, varcovar ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare bounder class to set bounds of sampling. + // This is used by doSampler. + //----------------------------------------------------------------------------- + + doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + EOT(pop[0].size(), 5), + *gen); + state.storeFunctor(bounder); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare sampler class with a specific distribution + //----------------------------------------------------------------------------- + + doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); + state.storeFunctor(sampler); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (4) sampling phase + //----------------------------------------------------------------------------- + + pop.clear(); + + for (unsigned int i = 0; i < p_size; ++i) + { + EOT candidate_solution = (*sampler)( distrib ); + pop.push_back( candidate_solution ); + } + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (6) estimation phase + //----------------------------------------------------------------------------- + + doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); + state.storeFunctor(estimator); + + distrib = (*estimator)( pop ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (8) euclidianne distance estimation + //----------------------------------------------------------------------------- + + ublas::vector< AtomType > new_mean = distrib.mean(); + ublas::symmetric_matrix< AtomType, ublas::lower > new_varcovar = distrib.varcovar(); + + AtomType distance = 0; + + for ( unsigned int d = 0; d < s_size; ++d ) + { + distance += pow( mean[ d ] - new_mean[ d ], 2 ); + } + + distance = sqrt( distance ); + + eo::log << p_size << " " << s_size << " " + << mean(0) << " " << mean(1) << " " + << new_mean(0) << " " << new_mean(1) << " " + << distance << std::endl + ; + + //----------------------------------------------------------------------------- + + } + + return 0; +} From ba6770df43079143b13e4536c1a07d8522ffe7e0 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 21 Sep 2010 15:12:19 +0200 Subject: [PATCH 69/74] + boxplot.py: script to generate graphic with boxplot to illustrate distances between theorical and visual means for each population value --- test/CMakeLists.txt | 1 + test/boxplot.py | 19 +++ test/t-mean-distance.cpp | 241 +++++++++++++++++++++------------------ 3 files changed, 153 insertions(+), 108 deletions(-) create mode 100755 test/boxplot.py diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index cf1c0b4f..80651e53 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -34,6 +34,7 @@ INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/application/eda_sa) SET(SOURCES t-doEstimatorNormalMulti + t-mean-distance ) FOREACH(current ${SOURCES}) diff --git a/test/boxplot.py b/test/boxplot.py new file mode 100755 index 00000000..3e10e406 --- /dev/null +++ b/test/boxplot.py @@ -0,0 +1,19 @@ +#!/usr/bin/env python + +from pylab import * + +FILE_LOCATIONS = 'means_distances_results/files_description.txt' + +data = [] + +locations = [ line.split()[0] for line in open( FILE_LOCATIONS ) ] + +for cur_file in locations: + data.append( [ float(line.split()[7]) for line in open( cur_file ).readlines() ] ) + +print locations +#print data + +boxplot( data ) + +show() diff --git a/test/t-mean-distance.cpp b/test/t-mean-distance.cpp index 3e852a4a..46173883 100644 --- a/test/t-mean-distance.cpp +++ b/test/t-mean-distance.cpp @@ -1,3 +1,6 @@ +#include +#include + #include #include #include @@ -27,9 +30,10 @@ int main(int ac, char** av) std::string section("Algorithm parameters"); + unsigned int r_max = parser.createParam((unsigned int)100, "run-number", "Number of run", 'r', section).value(); // r unsigned int p_min = parser.createParam((unsigned int)10, "population-min", "Population min", 'p', section).value(); // p - unsigned int p_max = parser.createParam((unsigned int)10000, "population-max", "Population max", 'P', section).value(); // P - unsigned int p_step = parser.createParam((unsigned int)10, "population-step", "Population step", 't', section).value(); // t + unsigned int p_max = parser.createParam((unsigned int)1000, "population-max", "Population max", 'P', section).value(); // P + unsigned int p_step = parser.createParam((unsigned int)50, "population-step", "Population step", 't', section).value(); // t unsigned int s_size = parser.createParam((unsigned int)2, "dimension-size", "Dimension size", 'd', section).value(); // d AtomType mean_value = parser.createParam((AtomType)0, "mean", "Mean value", 'm', section).value(); // m @@ -37,6 +41,9 @@ int main(int ac, char** av) AtomType covar2_value = parser.createParam((AtomType)0.5, "covar2", "Covar value 2", '2', section).value(); // 2 AtomType covar3_value = parser.createParam((AtomType)1.0, "covar3", "Covar value 3", '3', section).value(); // 3 + std::string results_directory = parser.createParam((std::string)"means_distances_results", "results-directory", "Results directory", 'R', section).value(); // R + std::string files_description = parser.createParam((std::string)"files_description.txt", "files-description", "Files description", 'F', section).value(); // F + if (parser.userNeedsHelp()) { parser.printHelp(std::cout); @@ -48,128 +55,146 @@ int main(int ac, char** av) //----------------------------------------------------- - + assert(r_max >= 1); assert(s_size >= 2); - eo::log << eo::debug << "p_size s_size mean(0) mean(1) new-mean(0) new-mean(1) distance" << std::endl; + eo::log << eo::quiet; - eo::log << eo::logging; + ::mkdir( results_directory.c_str(), 0755 ); - for ( unsigned int p_size = p_min; p_size <= p_max; p_size *= p_step ) + for ( unsigned int p_size = p_min; p_size <= p_max; p_size += p_step ) { - assert(p_size >= p_min); - eoState state; + std::ostringstream desc_file; + desc_file << results_directory << "/" << files_description; + std::ostringstream cur_file; + cur_file << results_directory << "/pop_" << p_size << ".txt"; - //----------------------------------------------------- - // (1) Population init and sampler - //----------------------------------------------------- + eo::log << eo::file( desc_file.str() ) << cur_file.str().c_str() << std::endl; - eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5); - state.storeFunctor(gen); + eo::log << eo::file( cur_file.str() ); - eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( s_size, *gen ); - state.storeFunctor(init); + eo::log << eo::logging << "run_number p_size s_size mean(0) mean(1) new-mean(0) new-mean(1) distance" << std::endl; - // create an empty pop and let the state handle the memory - // fill population thanks to eoInit instance - eoPop< EOT >& pop = state.takeOwnership( eoPop< EOT >( p_size, *init ) ); + eo::log << eo::quiet; - //----------------------------------------------------- - - - //----------------------------------------------------------------------------- - // (2) distribution initial parameters - //----------------------------------------------------------------------------- - - ublas::vector< AtomType > mean( s_size, mean_value ); - ublas::symmetric_matrix< AtomType, ublas::lower > varcovar( s_size, s_size ); - - varcovar( 0, 0 ) = covar1_value; - varcovar( 0, 1 ) = covar2_value; - varcovar( 1, 1 ) = covar3_value; - - Distrib distrib( mean, varcovar ); - - //----------------------------------------------------------------------------- - - - //----------------------------------------------------------------------------- - // Prepare bounder class to set bounds of sampling. - // This is used by doSampler. - //----------------------------------------------------------------------------- - - doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), - EOT(pop[0].size(), 5), - *gen); - state.storeFunctor(bounder); - - //----------------------------------------------------------------------------- - - - //----------------------------------------------------------------------------- - // Prepare sampler class with a specific distribution - //----------------------------------------------------------------------------- - - doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); - state.storeFunctor(sampler); - - //----------------------------------------------------------------------------- - - - //----------------------------------------------------------------------------- - // (4) sampling phase - //----------------------------------------------------------------------------- - - pop.clear(); - - for (unsigned int i = 0; i < p_size; ++i) + for ( unsigned int r = 1; r <= r_max; ++r) { - EOT candidate_solution = (*sampler)( distrib ); - pop.push_back( candidate_solution ); + + eoState state; + + + //----------------------------------------------------- + // (1) Population init and sampler + //----------------------------------------------------- + + eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5); + state.storeFunctor(gen); + + eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( s_size, *gen ); + state.storeFunctor(init); + + // create an empty pop and let the state handle the memory + // fill population thanks to eoInit instance + eoPop< EOT >& pop = state.takeOwnership( eoPop< EOT >( p_size, *init ) ); + + //----------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (2) distribution initial parameters + //----------------------------------------------------------------------------- + + ublas::vector< AtomType > mean( s_size, mean_value ); + ublas::symmetric_matrix< AtomType, ublas::lower > varcovar( s_size, s_size ); + + varcovar( 0, 0 ) = covar1_value; + varcovar( 0, 1 ) = covar2_value; + varcovar( 1, 1 ) = covar3_value; + + Distrib distrib( mean, varcovar ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare bounder class to set bounds of sampling. + // This is used by doSampler. + //----------------------------------------------------------------------------- + + doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + EOT(pop[0].size(), 5), + *gen); + state.storeFunctor(bounder); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare sampler class with a specific distribution + //----------------------------------------------------------------------------- + + doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); + state.storeFunctor(sampler); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (4) sampling phase + //----------------------------------------------------------------------------- + + pop.clear(); + + for (unsigned int i = 0; i < p_size; ++i) + { + EOT candidate_solution = (*sampler)( distrib ); + pop.push_back( candidate_solution ); + } + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (6) estimation phase + //----------------------------------------------------------------------------- + + doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); + state.storeFunctor(estimator); + + distrib = (*estimator)( pop ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (8) euclidianne distance estimation + //----------------------------------------------------------------------------- + + ublas::vector< AtomType > new_mean = distrib.mean(); + ublas::symmetric_matrix< AtomType, ublas::lower > new_varcovar = distrib.varcovar(); + + AtomType distance = 0; + + for ( unsigned int d = 0; d < s_size; ++d ) + { + distance += pow( mean[ d ] - new_mean[ d ], 2 ); + } + + distance = sqrt( distance ); + + eo::log << r << " " << p_size << " " << s_size << " " + << mean(0) << " " << mean(1) << " " + << new_mean(0) << " " << new_mean(1) << " " + << distance << std::endl + ; + + //----------------------------------------------------------------------------- + } - //----------------------------------------------------------------------------- - - - //----------------------------------------------------------------------------- - // (6) estimation phase - //----------------------------------------------------------------------------- - - doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); - state.storeFunctor(estimator); - - distrib = (*estimator)( pop ); - - //----------------------------------------------------------------------------- - - - //----------------------------------------------------------------------------- - // (8) euclidianne distance estimation - //----------------------------------------------------------------------------- - - ublas::vector< AtomType > new_mean = distrib.mean(); - ublas::symmetric_matrix< AtomType, ublas::lower > new_varcovar = distrib.varcovar(); - - AtomType distance = 0; - - for ( unsigned int d = 0; d < s_size; ++d ) - { - distance += pow( mean[ d ] - new_mean[ d ], 2 ); - } - - distance = sqrt( distance ); - - eo::log << p_size << " " << s_size << " " - << mean(0) << " " << mean(1) << " " - << new_mean(0) << " " << new_mean(1) << " " - << distance << std::endl - ; - - //----------------------------------------------------------------------------- - } return 0; From 65191e221259530d45b22fe8939b841a520da146 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 22 Sep 2010 14:38:15 +0200 Subject: [PATCH 70/74] + eda algo: same algo than eda-sa without sa, + plotting scripts and problem functions moved to application/common --- CMakeLists.txt | 1 + application/CMakeLists.txt | 6 + application/common/CMakeLists.txt | 14 + application/{eda_sa => common}/Rosenbrock.h | 0 application/{eda_sa => common}/Sphere.h | 0 application/{eda_sa => common}/ggobi.py | 0 application/{eda_sa => common}/gplot.py | 0 application/eda/CMakeLists.txt | 27 ++ application/eda/eda.param | 7 + application/eda/main.cpp | 267 ++++++++++++++++++++ application/eda_sa/CMakeLists.txt | 4 +- application/eda_sa/main.cpp | 4 +- src/do | 1 + src/doEDA.h | 252 ++++++++++++++++++ src/doEDASA.h | 24 +- test/CMakeLists.txt | 2 +- 16 files changed, 595 insertions(+), 14 deletions(-) create mode 100644 application/common/CMakeLists.txt rename application/{eda_sa => common}/Rosenbrock.h (100%) rename application/{eda_sa => common}/Sphere.h (100%) rename application/{eda_sa => common}/ggobi.py (100%) rename application/{eda_sa => common}/gplot.py (100%) create mode 100644 application/eda/CMakeLists.txt create mode 100644 application/eda/eda.param create mode 100644 application/eda/main.cpp create mode 100644 src/doEDA.h diff --git a/CMakeLists.txt b/CMakeLists.txt index da961550..31da2b9c 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -83,6 +83,7 @@ ADD_SUBDIRECTORY(doc) ###################################################################################### + ###################################################################################### ### 7) Create executable, link libraries and prepare target ###################################################################################### diff --git a/application/CMakeLists.txt b/application/CMakeLists.txt index 591fb303..dabb9ea0 100644 --- a/application/CMakeLists.txt +++ b/application/CMakeLists.txt @@ -2,6 +2,12 @@ ### 1) Where do we go now ?!? ###################################################################################### +INCLUDE_DIRECTORIES( + ${CMAKE_CURRENT_SOURCE_DIR}/common + ) + +ADD_SUBDIRECTORY(common) ADD_SUBDIRECTORY(eda_sa) +ADD_SUBDIRECTORY(eda) ###################################################################################### diff --git a/application/common/CMakeLists.txt b/application/common/CMakeLists.txt new file mode 100644 index 00000000..41a16ecf --- /dev/null +++ b/application/common/CMakeLists.txt @@ -0,0 +1,14 @@ +PROJECT(common) + +SET(RESOURCES + gplot.py + ggobi.py + ) + +FOREACH(file ${RESOURCES}) + EXECUTE_PROCESS( + COMMAND ${CMAKE_COMMAND} -E copy_if_different + ${CMAKE_CURRENT_SOURCE_DIR}/${file} + ${DO_BINARY_DIR}/${file} + ) +ENDFOREACH(file) diff --git a/application/eda_sa/Rosenbrock.h b/application/common/Rosenbrock.h similarity index 100% rename from application/eda_sa/Rosenbrock.h rename to application/common/Rosenbrock.h diff --git a/application/eda_sa/Sphere.h b/application/common/Sphere.h similarity index 100% rename from application/eda_sa/Sphere.h rename to application/common/Sphere.h diff --git a/application/eda_sa/ggobi.py b/application/common/ggobi.py similarity index 100% rename from application/eda_sa/ggobi.py rename to application/common/ggobi.py diff --git a/application/eda_sa/gplot.py b/application/common/gplot.py similarity index 100% rename from application/eda_sa/gplot.py rename to application/common/gplot.py diff --git a/application/eda/CMakeLists.txt b/application/eda/CMakeLists.txt new file mode 100644 index 00000000..41d61ce0 --- /dev/null +++ b/application/eda/CMakeLists.txt @@ -0,0 +1,27 @@ +PROJECT(eda) + +FIND_PACKAGE(Boost 1.33.0) + +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) +LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) + +SET(RESOURCES + ${PROJECT_NAME}.param + ) + +FOREACH(file ${RESOURCES}) + EXECUTE_PROCESS( + COMMAND ${CMAKE_COMMAND} -E copy_if_different + ${CMAKE_CURRENT_SOURCE_DIR}/${file} + ${DO_BINARY_DIR}/${file} + ) +ENDFOREACH(file) + +FILE(GLOB SOURCES *.cpp) + +SET(EXECUTABLE_OUTPUT_PATH ${DO_BINARY_DIR}) + +ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES}) +TARGET_LINK_LIBRARIES(${PROJECT_NAME} do doutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) diff --git a/application/eda/eda.param b/application/eda/eda.param new file mode 100644 index 00000000..9aceb230 --- /dev/null +++ b/application/eda/eda.param @@ -0,0 +1,7 @@ +--rho=0 # -p : +#include + +#include +#include + +#include + +#include +#include +#include +#include + +#include + +#include "Rosenbrock.h" +#include "Sphere.h" + + +typedef eoReal EOT; +typedef doNormalMulti< EOT > Distrib; + + +int main(int ac, char** av) +{ + eoParserLogger parser(ac, av); + + // Letters used by the following declarations: + // a d i p t + + std::string section("Algorithm parameters"); + + // FIXME: default value to check + //double initial_temperature = parser.createParam((double)10e5, "temperature", "Initial temperature", 'i', section).value(); // i + + eoState state; + + + //----------------------------------------------------------------------------- + // Instantiate all needed parameters for EDA algorithm + //----------------------------------------------------------------------------- + + double selection_rate = parser.createParam((double)0.5, "selection_rate", "Selection Rate", 'R', section).value(); // R + + eoSelect< EOT >* selector = new eoDetSelect< EOT >( selection_rate ); + state.storeFunctor(selector); + + doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); + state.storeFunctor(estimator); + + eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >( 2 ); + state.storeFunctor(selectone); + + doModifierMass< Distrib >* modifier = new doNormalMultiCenter< EOT >(); + state.storeFunctor(modifier); + + eoEvalFunc< EOT >* plainEval = new Rosenbrock< EOT >(); + state.storeFunctor(plainEval); + + unsigned long max_eval = parser.getORcreateParam((unsigned long)0, "maxEval", "Maximum number of evaluations (0 = none)", 'E', "Stopping criterion").value(); // E + eoEvalFuncCounterBounder< EOT > eval(*plainEval, max_eval); + + eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5); + state.storeFunctor(gen); + + + unsigned int dimension_size = parser.createParam((unsigned int)10, "dimension-size", "Dimension size", 'd', section).value(); // d + + eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( dimension_size, *gen ); + state.storeFunctor(init); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (1) Population init and sampler + //----------------------------------------------------------------------------- + + // Generation of population from do_make_pop (creates parameters, manages persistance and so on...) + // ... and creates the parameters: L P r S + + // this first sampler creates a uniform distribution independently from our distribution (it does not use doUniform). + + eoPop< EOT >& pop = do_make_pop(parser, state, *init); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (2) First evaluation before starting the research algorithm + //----------------------------------------------------------------------------- + + apply(eval, pop); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare bounder class to set bounds of sampling. + // This is used by doSampler. + //----------------------------------------------------------------------------- + + doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + EOT(pop[0].size(), 5), + *gen); + state.storeFunctor(bounder); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare sampler class with a specific distribution + //----------------------------------------------------------------------------- + + doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); + state.storeFunctor(sampler); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Metropolis sample parameters + //----------------------------------------------------------------------------- + + //unsigned int popSize = parser.getORcreateParam((unsigned int)20, "popSize", "Population Size", 'P', "Evolution Engine").value(); + + //moContinuator< moDummyNeighbor >* sa_continue = new moIterContinuator< moDummyNeighbor >( popSize ); + //state.storeFunctor(sa_continue); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // SA parameters + //----------------------------------------------------------------------------- + + //double threshold_temperature = parser.createParam((double)0.1, "threshold", "Minimal temperature at which stop", 't', section).value(); // t + //double alpha = parser.createParam((double)0.1, "alpha", "Temperature decrease rate", 'a', section).value(); // a + + //moCoolingSchedule* cooling_schedule = new moSimpleCoolingSchedule(initial_temperature, alpha, 0, threshold_temperature); + //state.storeFunctor(cooling_schedule); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // stopping criteria + // ... and creates the parameter letters: C E g G s T + //----------------------------------------------------------------------------- + + eoContinue< EOT >& eo_continue = do_make_continue(parser, state, eval); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // population output + //----------------------------------------------------------------------------- + + eoCheckPoint< EOT >& pop_continue = do_make_checkpoint(parser, state, eval, eo_continue); + + doPopStat< EOT >* popStat = new doPopStat; + state.storeFunctor(popStat); + pop_continue.add(*popStat); + + doFileSnapshot* fileSnapshot = new doFileSnapshot("EDA_ResPop"); + state.storeFunctor(fileSnapshot); + fileSnapshot->add(*popStat); + pop_continue.add(*fileSnapshot); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // distribution output + //----------------------------------------------------------------------------- + + doDummyContinue< Distrib >* dummy_continue = new doDummyContinue< Distrib >(); + state.storeFunctor(dummy_continue); + + doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue ); + state.storeFunctor(distribution_continue); + + doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); + state.storeFunctor(distrib_stat); + + distribution_continue->add( *distrib_stat ); + + // eoMonitor* stdout_monitor = new eoStdoutMonitor(); + // state.storeFunctor(stdout_monitor); + // stdout_monitor->add(*distrib_stat); + // distribution_continue->add( *stdout_monitor ); + + eoFileMonitor* file_monitor = new eoFileMonitor("eda_distribution_bounds.txt"); + state.storeFunctor(file_monitor); + file_monitor->add(*distrib_stat); + distribution_continue->add( *file_monitor ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // eoEPRemplacement causes the using of the current and previous + // sample for sampling. + //----------------------------------------------------------------------------- + + eoReplacement< EOT >* replacor = new eoEPReplacement< EOT >(pop.size()); + + // Below, use eoGenerationalReplacement to sample only on the current sample + + //eoReplacement< EOT >* replacor = new eoGenerationalReplacement< EOT >(); // FIXME: to define the size + + state.storeFunctor(replacor); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // EDA algorithm configuration + //----------------------------------------------------------------------------- + + doAlgo< Distrib >* algo = new doEDA< Distrib > + (*selector, *estimator, *selectone, *modifier, *sampler, + pop_continue, *distribution_continue, + eval, + //*sa_continue, *cooling_schedule, initial_temperature, + *replacor); + + //----------------------------------------------------------------------------- + + + // state.storeFunctor(algo); + + if (parser.userNeedsHelp()) + { + parser.printHelp(std::cout); + exit(1); + } + + // Help + Verbose routines + + make_verbose(parser); + make_help(parser); + + + //----------------------------------------------------------------------------- + // Beginning of the algorithm call + //----------------------------------------------------------------------------- + + try + { + do_run(*algo, pop); + } + catch (eoEvalFuncCounterBounderException& e) + { + eo::log << eo::warnings << "warning: " << e.what() << std::endl; + } + catch (std::exception& e) + { + eo::log << eo::errors << "error: " << e.what() << std::endl; + exit(EXIT_FAILURE); + } + + //----------------------------------------------------------------------------- + + return 0; +} diff --git a/application/eda_sa/CMakeLists.txt b/application/eda_sa/CMakeLists.txt index 63901a33..f92e105f 100644 --- a/application/eda_sa/CMakeLists.txt +++ b/application/eda_sa/CMakeLists.txt @@ -8,9 +8,7 @@ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) SET(RESOURCES - eda_sa.param - gplot.py - ggobi.py + ${PROJECT_NAME}.param ) FOREACH(file ${RESOURCES}) diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index 00cbea6f..6e4729de 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -163,7 +163,7 @@ int main(int ac, char** av) state.storeFunctor(popStat); pop_continue.add(*popStat); - doFileSnapshot* fileSnapshot = new doFileSnapshot("ResPop"); + doFileSnapshot* fileSnapshot = new doFileSnapshot("EDASA_ResPop"); state.storeFunctor(fileSnapshot); fileSnapshot->add(*popStat); pop_continue.add(*fileSnapshot); @@ -191,7 +191,7 @@ int main(int ac, char** av) // stdout_monitor->add(*distrib_stat); // distribution_continue->add( *stdout_monitor ); - eoFileMonitor* file_monitor = new eoFileMonitor("distribution_bounds.txt"); + eoFileMonitor* file_monitor = new eoFileMonitor("eda_sa_distribution_bounds.txt"); state.storeFunctor(file_monitor); file_monitor->add(*distrib_stat); distribution_continue->add( *file_monitor ); diff --git a/src/do b/src/do index 1f91d392..ff2b3e67 100644 --- a/src/do +++ b/src/do @@ -10,6 +10,7 @@ #include "doAlgo.h" #include "doEDASA.h" +#include "doEDA.h" #include "doDistrib.h" #include "doUniform.h" diff --git a/src/doEDA.h b/src/doEDA.h new file mode 100644 index 00000000..6873e5da --- /dev/null +++ b/src/doEDA.h @@ -0,0 +1,252 @@ +// (c) Thales group, 2010 +/* + Authors: + Johann Dreo + Caner Candan +*/ + +#ifndef _doEDA_h +#define _doEDA_h + +#include +#include + +#include + +#include "doAlgo.h" +#include "doEstimator.h" +#include "doModifierMass.h" +#include "doSampler.h" +#include "doContinue.h" + +template < typename D > +class doEDA : public doAlgo< D > +{ +public: + //! Alias for the type EOT + typedef typename D::EOType EOT; + + //! Alias for the atom type + typedef typename EOT::AtomType AtomType; + + //! Alias for the fitness + typedef typename EOT::Fitness Fitness; + +public: + + //! doEDA constructor + /*! + All the boxes used by a EDASA need to be given. + + \param selector Population Selector + \param estimator Distribution Estimator + \param selectone SelectOne + \param modifier Distribution Modifier + \param sampler Distribution Sampler + \param pop_continue Population Continuator + \param distribution_continue Distribution Continuator + \param evaluation Evaluation function. + \param sa_continue Stopping criterion. + \param cooling_schedule Cooling schedule, describes how the temperature is modified. + \param initial_temperature The initial temperature. + \param replacor Population replacor + */ + doEDA (eoSelect< EOT > & selector, + doEstimator< D > & estimator, + eoSelectOne< EOT > & selectone, + doModifierMass< D > & modifier, + doSampler< D > & sampler, + eoContinue< EOT > & pop_continue, + doContinue< D > & distribution_continue, + eoEvalFunc < EOT > & evaluation, + //moContinuator< moDummyNeighbor > & sa_continue, + //moCoolingSchedule & cooling_schedule, + //double initial_temperature, + eoReplacement< EOT > & replacor + ) + : _selector(selector), + _estimator(estimator), + _selectone(selectone), + _modifier(modifier), + _sampler(sampler), + _pop_continue(pop_continue), + _distribution_continue(distribution_continue), + _evaluation(evaluation), + //_sa_continue(sa_continue), + //_cooling_schedule(cooling_schedule), + //_initial_temperature(initial_temperature), + _replacor(replacor) + + {} + + //! function that launches the EDASA algorithm. + /*! + As a moTS or a moHC, the EDASA can be used for HYBRIDATION in an evolutionary algorithm. + + \param pop A population to improve. + \return TRUE. + */ + void operator ()(eoPop< EOT > & pop) + { + assert(pop.size() > 0); + + //double temperature = _initial_temperature; + + eoPop< EOT > current_pop; + + eoPop< EOT > selected_pop; + + + //------------------------------------------------------------- + // Estimating a first time the distribution parameter thanks + // to population. + //------------------------------------------------------------- + + D distrib = _estimator(pop); + + double size = distrib.size(); + assert(size > 0); + + //------------------------------------------------------------- + + + do + { + //------------------------------------------------------------- + // (3) Selection of the best points in the population + //------------------------------------------------------------- + + selected_pop.clear(); + + _selector(pop, selected_pop); + + assert( selected_pop.size() > 0 ); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // (4) Estimation of the distribution parameters + //------------------------------------------------------------- + + distrib = _estimator(selected_pop); + + //------------------------------------------------------------- + + + // TODO: utiliser selected_pop ou pop ??? + + assert(selected_pop.size() > 0); + + + //------------------------------------------------------------- + // Init of a variable contening a point with the bestest fitnesses + //------------------------------------------------------------- + + EOT current_solution = _selectone(selected_pop); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Fit the current solution with the distribution parameters (bounds) + //------------------------------------------------------------- + + // FIXME: si besoin de modifier la dispersion de la distribution + // _modifier_dispersion(distribution, selected_pop); + _modifier(distrib, current_solution); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Evaluating a first time the current solution + //------------------------------------------------------------- + + _evaluation( current_solution ); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Building of the sampler in current_pop + //------------------------------------------------------------- + + //_sa_continue.init( current_solution ); + + current_pop.clear(); + + for ( unsigned int i = 0; i < pop.size(); ++i ) + //do + { + EOT candidate_solution = _sampler(distrib); + _evaluation( candidate_solution ); + + // TODO: verifier le critere d'acceptation + if ( candidate_solution.fitness() < current_solution.fitness() + // || rng.uniform() < exp( ::fabs(candidate_solution.fitness() - current_solution.fitness()) / temperature ) + ) + { + current_pop.push_back(candidate_solution); + current_solution = candidate_solution; + } + } + //while ( _sa_continue( current_solution) ); + + //------------------------------------------------------------- + + + _replacor(pop, current_pop); // copy current_pop in pop + + pop.sort(); + + //if ( ! _cooling_schedule( temperature ) ){ eo::log << eo::debug << "_cooling_schedule" << std::endl; break; } + + if ( ! _distribution_continue( distrib ) ){ eo::log << eo::debug << "_distribution_continue" << std::endl; break; } + + if ( ! _pop_continue( pop ) ){ eo::log << eo::debug << "_pop_continue" << std::endl; break; } + + } + while ( 1 ); + } + +private: + + //! A EOT selector + eoSelect < EOT > & _selector; + + //! A EOT estimator. It is going to estimate distribution parameters. + doEstimator< D > & _estimator; + + //! SelectOne + eoSelectOne< EOT > & _selectone; + + //! A D modifier + doModifierMass< D > & _modifier; + + //! A D sampler + doSampler< D > & _sampler; + + //! A EOT population continuator + eoContinue < EOT > & _pop_continue; + + //! A D continuator + doContinue < D > & _distribution_continue; + + //! A full evaluation function. + eoEvalFunc < EOT > & _evaluation; + + //! Stopping criterion before temperature update + //moContinuator< moDummyNeighbor > & _sa_continue; + + //! The cooling schedule + //moCoolingSchedule & _cooling_schedule; + + //! Initial temperature + //double _initial_temperature; + + //! A EOT replacor + eoReplacement < EOT > & _replacor; +}; + +#endif // !_doEDA_h diff --git a/src/doEDASA.h b/src/doEDASA.h index c8e9ad9a..c6fb4927 100644 --- a/src/doEDASA.h +++ b/src/doEDASA.h @@ -159,6 +159,15 @@ public: //------------------------------------------------------------- + //------------------------------------------------------------- + // Evaluating a first time the current solution + //------------------------------------------------------------- + + _evaluation( current_solution ); + + //------------------------------------------------------------- + + //------------------------------------------------------------- // Building of the sampler in current_pop //------------------------------------------------------------- @@ -170,21 +179,20 @@ public: do { EOT candidate_solution = _sampler(distrib); - - EOT& e1 = candidate_solution; - _evaluation( e1 ); - EOT& e2 = current_solution; - _evaluation( e2 ); + _evaluation( candidate_solution ); // TODO: verifier le critere d'acceptation - if ( e1.fitness() < e2.fitness() || - rng.uniform() < exp( ::fabs(e1.fitness() - e2.fitness()) / temperature ) ) + if ( candidate_solution.fitness() < current_solution.fitness() || + rng.uniform() < exp( ::fabs(candidate_solution.fitness() - current_solution.fitness()) / temperature ) ) { current_pop.push_back(candidate_solution); current_solution = candidate_solution; } } - while ( _sa_continue( current_solution) ); + while ( _sa_continue( current_solution ) ); + + //------------------------------------------------------------- + _replacor(pop, current_pop); // copy current_pop in pop diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 80651e53..dbb44481 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -30,7 +30,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) -INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/application/eda_sa) +INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/application/common) SET(SOURCES t-doEstimatorNormalMulti From b1798ad35154ad5939baff669f3ca8286e703d18 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Wed, 22 Sep 2010 19:25:37 +0200 Subject: [PATCH 71/74] * eda n eda_sa: bug fixed, while we were using -h the result folder was removed --- application/common/CMakeLists.txt | 1 + application/common/boxplot_eda_n_edasa.py | 36 +++++++++ application/eda/main.cpp | 95 ++++++++++++++--------- application/eda_sa/main.cpp | 93 +++++++++++++--------- src/utils/doFileSnapshot.cpp | 19 ++++- src/utils/doFileSnapshot.h | 7 +- 6 files changed, 175 insertions(+), 76 deletions(-) create mode 100755 application/common/boxplot_eda_n_edasa.py diff --git a/application/common/CMakeLists.txt b/application/common/CMakeLists.txt index 41a16ecf..d16353f5 100644 --- a/application/common/CMakeLists.txt +++ b/application/common/CMakeLists.txt @@ -3,6 +3,7 @@ PROJECT(common) SET(RESOURCES gplot.py ggobi.py + boxplot_eda_n_edasa.py ) FOREACH(file ${RESOURCES}) diff --git a/application/common/boxplot_eda_n_edasa.py b/application/common/boxplot_eda_n_edasa.py new file mode 100755 index 00000000..a4086a67 --- /dev/null +++ b/application/common/boxplot_eda_n_edasa.py @@ -0,0 +1,36 @@ +#!/usr/bin/env python + +from pylab import * +#from pprint import pprint + +FILE_LOCATIONS = 'EDA_ResPop/list_of_files.txt' + +data = [] + +locations = [ line.split()[0] for line in open( FILE_LOCATIONS ) ] +#pprint( locations ) + +for cur_file in locations: + fitnesses = [ float(line.split()[0]) for line in open( cur_file ).readlines()[1:-1] ] + data.append( fitnesses[1:] ) + +#pprint( data ) + +boxplot( data ) + +# FILE_LOCATIONS = 'EDASA_ResPop/list_of_files.txt' + +# data = [] + +# locations = [ line.split()[0] for line in open( FILE_LOCATIONS ) ] +# #pprint( locations ) + +# for cur_file in locations: +# fitnesses = [ float(line.split()[0]) for line in open( cur_file ).readlines()[1:-1] ] +# data.append( fitnesses[1:] ) + +# #pprint( data ) + +# boxplot( data ) + +show() diff --git a/application/eda/main.cpp b/application/eda/main.cpp index dd5b8137..3e8e0fae 100644 --- a/application/eda/main.cpp +++ b/application/eda/main.cpp @@ -159,15 +159,6 @@ int main(int ac, char** av) eoCheckPoint< EOT >& pop_continue = do_make_checkpoint(parser, state, eval, eo_continue); - doPopStat< EOT >* popStat = new doPopStat; - state.storeFunctor(popStat); - pop_continue.add(*popStat); - - doFileSnapshot* fileSnapshot = new doFileSnapshot("EDA_ResPop"); - state.storeFunctor(fileSnapshot); - fileSnapshot->add(*popStat); - pop_continue.add(*fileSnapshot); - //----------------------------------------------------------------------------- @@ -181,21 +172,6 @@ int main(int ac, char** av) doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue ); state.storeFunctor(distribution_continue); - doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); - state.storeFunctor(distrib_stat); - - distribution_continue->add( *distrib_stat ); - - // eoMonitor* stdout_monitor = new eoStdoutMonitor(); - // state.storeFunctor(stdout_monitor); - // stdout_monitor->add(*distrib_stat); - // distribution_continue->add( *stdout_monitor ); - - eoFileMonitor* file_monitor = new eoFileMonitor("eda_distribution_bounds.txt"); - state.storeFunctor(file_monitor); - file_monitor->add(*distrib_stat); - distribution_continue->add( *file_monitor ); - //----------------------------------------------------------------------------- @@ -216,21 +192,9 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- - // EDA algorithm configuration + // Some stuff to display helper when we are using -h option //----------------------------------------------------------------------------- - doAlgo< Distrib >* algo = new doEDA< Distrib > - (*selector, *estimator, *selectone, *modifier, *sampler, - pop_continue, *distribution_continue, - eval, - //*sa_continue, *cooling_schedule, initial_temperature, - *replacor); - - //----------------------------------------------------------------------------- - - - // state.storeFunctor(algo); - if (parser.userNeedsHelp()) { parser.printHelp(std::cout); @@ -242,6 +206,63 @@ int main(int ac, char** av) make_verbose(parser); make_help(parser); + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // population output (after helper) + // + // FIXME: theses objects are instanciate there in order to avoid a folder + // removing as doFileSnapshot does within ctor. + //----------------------------------------------------------------------------- + + doPopStat< EOT >* popStat = new doPopStat; + state.storeFunctor(popStat); + pop_continue.add(*popStat); + + doFileSnapshot* fileSnapshot = new doFileSnapshot("EDA_ResPop"); + state.storeFunctor(fileSnapshot); + fileSnapshot->add(*popStat); + pop_continue.add(*fileSnapshot); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // distribution output (after helper) + //----------------------------------------------------------------------------- + + doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); + state.storeFunctor(distrib_stat); + + distribution_continue->add( *distrib_stat ); + + // eoMonitor* stdout_monitor = new eoStdoutMonitor(); + // state.storeFunctor(stdout_monitor); + // stdout_monitor->add(*distrib_stat); + // distribution_continue->add( *stdout_monitor ); + + eoFileMonitor* file_monitor = new eoFileMonitor("eda_distribution_bounds.txt"); + state.storeFunctor(file_monitor); + file_monitor->add(*distrib_stat); + distribution_continue->add( *file_monitor ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // EDA algorithm configuration + //----------------------------------------------------------------------------- + + doAlgo< Distrib >* algo = new doEDA< Distrib > + (*selector, *estimator, *selectone, *modifier, *sampler, + pop_continue, *distribution_continue, + eval, + //*sa_continue, *cooling_schedule, initial_temperature, + *replacor); + + //----------------------------------------------------------------------------- + //----------------------------------------------------------------------------- // Beginning of the algorithm call diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index 6e4729de..2d72ad83 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -159,15 +159,6 @@ int main(int ac, char** av) eoCheckPoint< EOT >& pop_continue = do_make_checkpoint(parser, state, eval, eo_continue); - doPopStat< EOT >* popStat = new doPopStat; - state.storeFunctor(popStat); - pop_continue.add(*popStat); - - doFileSnapshot* fileSnapshot = new doFileSnapshot("EDASA_ResPop"); - state.storeFunctor(fileSnapshot); - fileSnapshot->add(*popStat); - pop_continue.add(*fileSnapshot); - //----------------------------------------------------------------------------- @@ -181,21 +172,6 @@ int main(int ac, char** av) doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue ); state.storeFunctor(distribution_continue); - doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); - state.storeFunctor(distrib_stat); - - distribution_continue->add( *distrib_stat ); - - // eoMonitor* stdout_monitor = new eoStdoutMonitor(); - // state.storeFunctor(stdout_monitor); - // stdout_monitor->add(*distrib_stat); - // distribution_continue->add( *stdout_monitor ); - - eoFileMonitor* file_monitor = new eoFileMonitor("eda_sa_distribution_bounds.txt"); - state.storeFunctor(file_monitor); - file_monitor->add(*distrib_stat); - distribution_continue->add( *file_monitor ); - //----------------------------------------------------------------------------- @@ -216,20 +192,9 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- - // EDASA algorithm configuration + // Some stuff to display helper when we are using -h option //----------------------------------------------------------------------------- - doAlgo< Distrib >* algo = new doEDASA< Distrib > - (*selector, *estimator, *selectone, *modifier, *sampler, - pop_continue, *distribution_continue, - eval, *sa_continue, *cooling_schedule, - initial_temperature, *replacor); - - //----------------------------------------------------------------------------- - - - // state.storeFunctor(algo); - if (parser.userNeedsHelp()) { parser.printHelp(std::cout); @@ -241,6 +206,62 @@ int main(int ac, char** av) make_verbose(parser); make_help(parser); + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // population output (after helper) + // + // FIXME: theses objects are instanciate there in order to avoid a folder + // removing as doFileSnapshot does within ctor. + //----------------------------------------------------------------------------- + + doPopStat< EOT >* popStat = new doPopStat; + state.storeFunctor(popStat); + pop_continue.add(*popStat); + + doFileSnapshot* fileSnapshot = new doFileSnapshot("EDASA_ResPop"); + state.storeFunctor(fileSnapshot); + fileSnapshot->add(*popStat); + pop_continue.add(*fileSnapshot); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // distribution output (after helper) + //----------------------------------------------------------------------------- + + doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); + state.storeFunctor(distrib_stat); + + distribution_continue->add( *distrib_stat ); + + // eoMonitor* stdout_monitor = new eoStdoutMonitor(); + // state.storeFunctor(stdout_monitor); + // stdout_monitor->add(*distrib_stat); + // distribution_continue->add( *stdout_monitor ); + + eoFileMonitor* file_monitor = new eoFileMonitor("eda_sa_distribution_bounds.txt"); + state.storeFunctor(file_monitor); + file_monitor->add(*distrib_stat); + distribution_continue->add( *file_monitor ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // EDASA algorithm configuration + //----------------------------------------------------------------------------- + + doAlgo< Distrib >* algo = new doEDASA< Distrib > + (*selector, *estimator, *selectone, *modifier, *sampler, + pop_continue, *distribution_continue, + eval, *sa_continue, *cooling_schedule, + initial_temperature, *replacor); + + //----------------------------------------------------------------------------- + //----------------------------------------------------------------------------- // Beginning of the algorithm call diff --git a/src/utils/doFileSnapshot.cpp b/src/utils/doFileSnapshot.cpp index 3ad012f7..268cfe82 100644 --- a/src/utils/doFileSnapshot.cpp +++ b/src/utils/doFileSnapshot.cpp @@ -39,10 +39,12 @@ doFileSnapshot::doFileSnapshot(std::string dirname, std::string filename /*= "gen"*/, std::string delim /*= " "*/, unsigned int counter /*= 0*/, - bool rmFiles /*= true*/) + bool rmFiles /*= true*/, + bool saveFilenames /*= true*/) : _dirname(dirname), _frequency(frequency), _filename(filename), _delim(delim), - _counter(counter), _boolChanged(true) + _counter(counter), _saveFilenames(saveFilenames), + _descOfFiles( NULL ), _boolChanged(true) { std::string s = "test -d " + _dirname; @@ -72,8 +74,15 @@ doFileSnapshot::doFileSnapshot(std::string dirname, int dummy; dummy = system(s.c_str()); // all done + + _descOfFiles = new std::ofstream( std::string(dirname + "/list_of_files.txt").c_str() ); + } +doFileSnapshot::~doFileSnapshot() +{ + delete _descOfFiles; +} void doFileSnapshot::setCurrentFileName() { @@ -93,6 +102,7 @@ eoMonitor& doFileSnapshot::operator()(void) _counter++; _boolChanged = true; setCurrentFileName(); + std::ofstream os(_currentFileName.c_str()); if (!os) @@ -101,6 +111,11 @@ eoMonitor& doFileSnapshot::operator()(void) throw std::runtime_error(str); } + if ( _saveFilenames ) + { + *_descOfFiles << _currentFileName.c_str() << std::endl; + } + return operator()(os); } diff --git a/src/utils/doFileSnapshot.h b/src/utils/doFileSnapshot.h index 9329eed9..ea0ffeb6 100644 --- a/src/utils/doFileSnapshot.h +++ b/src/utils/doFileSnapshot.h @@ -42,7 +42,10 @@ public: std::string filename = "gen", std::string delim = " ", unsigned int counter = 0, - bool rmFiles = true); + bool rmFiles = true, + bool saveFilenames = true); + + virtual ~doFileSnapshot(); virtual bool hasChanged() {return _boolChanged;} virtual std::string getDirName() { return _dirname; } @@ -63,6 +66,8 @@ private : std::string _delim; std::string _currentFileName; unsigned int _counter; + bool _saveFilenames; + std::ofstream* _descOfFiles; bool _boolChanged; }; From ebb20c44c5058969754f8ded0e375eb6a81c8ff9 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 28 Sep 2010 10:38:38 +0200 Subject: [PATCH 72/74] there was an issue on doBounderNo class tied to the default values of the ctor of mother class doBounder: fixed --- application/CMakeLists.txt | 1 + src/doBounder.h | 2 +- src/doBounderNo.h | 3 +-- test/CMakeLists.txt | 1 + test/t-bounderno.cpp | 18 ++++++++++++++++++ 5 files changed, 22 insertions(+), 3 deletions(-) create mode 100644 test/t-bounderno.cpp diff --git a/application/CMakeLists.txt b/application/CMakeLists.txt index dabb9ea0..24b57198 100644 --- a/application/CMakeLists.txt +++ b/application/CMakeLists.txt @@ -9,5 +9,6 @@ INCLUDE_DIRECTORIES( ADD_SUBDIRECTORY(common) ADD_SUBDIRECTORY(eda_sa) ADD_SUBDIRECTORY(eda) +ADD_SUBDIRECTORY(sa) ###################################################################################### diff --git a/src/doBounder.h b/src/doBounder.h index 3ce4a554..44240246 100644 --- a/src/doBounder.h +++ b/src/doBounder.h @@ -14,7 +14,7 @@ template < typename EOT > class doBounder : public eoUF< EOT&, void > { public: - doBounder( EOT min = -5, EOT max = 5 ) + doBounder( EOT min = EOT(1, 0), EOT max = EOT(1, 0) ) : _min(min), _max(max) { assert(_min.size() > 0); diff --git a/src/doBounderNo.h b/src/doBounderNo.h index 94d873a8..0ca883bc 100644 --- a/src/doBounderNo.h +++ b/src/doBounderNo.h @@ -14,8 +14,7 @@ template < typename EOT > class doBounderNo : public doBounder< EOT > { public: - void operator()( EOT& x ) - {} + void operator()( EOT& ) {} }; #endif // !_doBounderNo_h diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index dbb44481..4e8bffc7 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -35,6 +35,7 @@ INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/application/common) SET(SOURCES t-doEstimatorNormalMulti t-mean-distance + t-bounderno ) FOREACH(current ${SOURCES}) diff --git a/test/t-bounderno.cpp b/test/t-bounderno.cpp new file mode 100644 index 00000000..1a157163 --- /dev/null +++ b/test/t-bounderno.cpp @@ -0,0 +1,18 @@ +#include +#include +#include + +#include +#include + +#include "Rosenbrock.h" +#include "Sphere.h" + +typedef eoReal< eoMinimizingFitness > EOT; + +int main(void) +{ + doBounderNo< EOT > bounder; + + return 0; +} From f2e1e40c30b9ac466019e2e84d6383a04cddb063 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Tue, 12 Oct 2010 10:09:56 +0200 Subject: [PATCH 73/74] I have fixed some bugs and added some tests for doDistrib classes --- src/TODO | 1 - src/doDistrib.h | 4 +++- src/doSamplerUniform.h | 7 +++---- test/CMakeLists.txt | 2 ++ test/t-bounderno.cpp | 5 ----- test/t-continue.cpp | 17 +++++++++++++++++ test/t-uniform.cpp | 16 ++++++++++++++++ 7 files changed, 41 insertions(+), 11 deletions(-) create mode 100644 test/t-continue.cpp create mode 100644 test/t-uniform.cpp diff --git a/src/TODO b/src/TODO index bed1db02..e69de29b 100644 --- a/src/TODO +++ b/src/TODO @@ -1 +0,0 @@ -* integrer ACP diff --git a/src/doDistrib.h b/src/doDistrib.h index 15b051f8..f150e8e0 100644 --- a/src/doDistrib.h +++ b/src/doDistrib.h @@ -8,8 +8,10 @@ #ifndef _doDistrib_h #define _doDistrib_h +#include + template < typename EOT > -class doDistrib +class doDistrib : public eoFunctorBase { public: //! Alias for the type diff --git a/src/doSamplerUniform.h b/src/doSamplerUniform.h index 1d62b903..6f79c138 100644 --- a/src/doSamplerUniform.h +++ b/src/doSamplerUniform.h @@ -18,15 +18,14 @@ * This class uses the Uniform distribution parameters (bounds) to return * a random position used for population sampling. */ -template < typename EOT, class D=doUniform > +template < typename EOT, class D=doUniform > // FIXME: D template name is there really used ?!? class doSamplerUniform : public doSampler< doUniform< EOT > > { public: - typedef D Distrib; - + doSamplerUniform(doBounder< EOT > & bounder) - : doSampler< doUniform >(bounder) + : doSampler< doUniform >(bounder) // FIXME: Why D is not used here ? {} /* diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 4e8bffc7..74ad84ac 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -36,6 +36,8 @@ SET(SOURCES t-doEstimatorNormalMulti t-mean-distance t-bounderno + t-uniform + t-continue ) FOREACH(current ${SOURCES}) diff --git a/test/t-bounderno.cpp b/test/t-bounderno.cpp index 1a157163..0898520b 100644 --- a/test/t-bounderno.cpp +++ b/test/t-bounderno.cpp @@ -1,12 +1,7 @@ #include #include -#include - -#include -#include #include "Rosenbrock.h" -#include "Sphere.h" typedef eoReal< eoMinimizingFitness > EOT; diff --git a/test/t-continue.cpp b/test/t-continue.cpp new file mode 100644 index 00000000..5cae79ff --- /dev/null +++ b/test/t-continue.cpp @@ -0,0 +1,17 @@ +#include +#include + +#include "Rosenbrock.h" + +typedef eoReal< eoMinimizingFitness > EOT; +typedef doUniform< EOT > Distrib; + +int main(void) +{ + eoState state; + + doContinue< Distrib >* continuator = new doDummyContinue< Distrib >(); + state.storeFunctor(continuator); + + return 0; +} diff --git a/test/t-uniform.cpp b/test/t-uniform.cpp new file mode 100644 index 00000000..d7aedfea --- /dev/null +++ b/test/t-uniform.cpp @@ -0,0 +1,16 @@ +#include +#include + +#include "Rosenbrock.h" + +typedef eoReal< eoMinimizingFitness > EOT; + +int main(void) +{ + eoState state; + + doUniform< EOT >* distrib = new doUniform< EOT >( EOT(3, -1), EOT(3, 1) ); + state.storeFunctor(distrib); + + return 0; +} From d618ab07dfb2e98f8c798a3569b8dd976584b496 Mon Sep 17 00:00:00 2001 From: Johann Dreo Date: Thu, 27 Jan 2011 11:23:23 +0100 Subject: [PATCH 74/74] rename everything from 'do' to 'edo' --- AUTHORS | 36 ++ CMakeLists.txt | 10 +- COPYING | 503 +++++++++++++++++- README | 8 +- application/CMakeLists.txt | 2 +- application/eda/CMakeLists.txt | 6 +- application/eda/main.cpp | 51 +- application/eda_sa/CMakeLists.txt | 6 +- application/eda_sa/main.cpp | 26 +- build_gcc_linux_debug | 2 +- build_gcc_linux_release | 2 +- do.pc | 12 - doc/CMakeLists.txt | 2 +- edo.pc | 12 + src/CMakeLists.txt | 4 +- src/do | 59 -- src/do.cpp | 8 - src/doAlgo.h | 23 - src/doBounder.h | 34 -- src/doBounderBound.h | 42 -- src/doBounderNo.h | 20 - src/doBounderRng.h | 42 -- src/doBounderUniform.h | 35 -- src/doContinue.h | 41 -- src/doDistrib.h | 23 - src/doEstimator.h | 23 - src/doEstimatorNormalMono.h | 77 --- src/doEstimatorUniform.h | 51 -- src/doModifier.h | 20 - src/doModifierDispersion.h | 23 - src/doModifierMass.h | 24 - src/doNormalMono.h | 38 -- src/doNormalMonoCenter.h | 26 - src/doNormalMultiCenter.h | 28 - src/doSampler.h | 75 --- src/doSamplerNormalMono.h | 71 --- src/doSamplerUniform.h | 76 --- src/doUniform.h | 23 - src/doUniformCenter.h | 35 -- src/doVectorBounds.h | 36 -- src/edo | 79 +++ src/edo.cpp | 28 + src/edoAlgo.h | 44 ++ src/edoBounder.h | 54 ++ src/edoBounderBound.h | 62 +++ src/edoBounderNo.h | 40 ++ src/edoBounderRng.h | 63 +++ src/edoBounderUniform.h | 55 ++ src/edoContinue.h | 61 +++ src/edoDistrib.h | 43 ++ src/{doEDA.h => edoEDA.h} | 66 ++- src/{doEDASA.h => edoEDASA.h} | 66 ++- src/edoEstimator.h | 43 ++ src/edoEstimatorNormalMono.h | 97 ++++ ...ormalMulti.h => edoEstimatorNormalMulti.h} | 45 +- src/edoEstimatorUniform.h | 71 +++ src/edoModifier.h | 41 ++ src/edoModifierDispersion.h | 43 ++ src/edoModifierMass.h | 45 ++ src/edoNormalMono.h | 58 ++ src/edoNormalMonoCenter.h | 47 ++ src/{doNormalMulti.h => edoNormalMulti.h} | 12 +- src/edoNormalMultiCenter.h | 48 ++ src/edoSampler.h | 95 ++++ src/edoSamplerNormalMono.h | 91 ++++ ...rNormalMulti.h => edoSamplerNormalMulti.h} | 59 +- src/edoSamplerUniform.h | 96 ++++ src/edoUniform.h | 43 ++ src/edoUniformCenter.h | 55 ++ src/edoVectorBounds.h | 56 ++ src/utils/CMakeLists.txt | 6 +- src/utils/doFileSnapshot.h | 74 --- src/utils/doHyperVolume.h | 32 -- src/utils/doPopStat.h | 75 --- src/utils/doStat.h | 54 -- src/utils/doStatNormalMono.h | 35 -- src/utils/doStatNormalMulti.h | 48 -- src/utils/doStatUniform.h | 35 -- src/utils/{doCheckPoint.h => edoCheckPoint.h} | 52 +- ...doFileSnapshot.cpp => edoFileSnapshot.cpp} | 61 ++- src/utils/edoFileSnapshot.h | 79 +++ src/utils/edoHyperVolume.h | 52 ++ src/utils/edoPopStat.h | 70 +++ src/utils/edoStat.h | 74 +++ src/utils/edoStatNormalMono.h | 55 ++ src/utils/edoStatNormalMulti.h | 68 +++ src/utils/edoStatUniform.h | 55 ++ test/CMakeLists.txt | 6 +- test/t-bounderno.cpp | 31 +- test/t-continue.cpp | 33 +- ...ulti.cpp => t-edoEstimatorNormalMulti.cpp} | 53 +- test/t-mean-distance.cpp | 42 +- test/t-uniform.cpp | 31 +- test/test_cov_parameters.py | 2 +- 94 files changed, 2933 insertions(+), 1531 deletions(-) create mode 100644 AUTHORS delete mode 100644 do.pc create mode 100644 edo.pc delete mode 100644 src/do delete mode 100644 src/do.cpp delete mode 100644 src/doAlgo.h delete mode 100644 src/doBounder.h delete mode 100644 src/doBounderBound.h delete mode 100644 src/doBounderNo.h delete mode 100644 src/doBounderRng.h delete mode 100644 src/doBounderUniform.h delete mode 100644 src/doContinue.h delete mode 100644 src/doDistrib.h delete mode 100644 src/doEstimator.h delete mode 100644 src/doEstimatorNormalMono.h delete mode 100644 src/doEstimatorUniform.h delete mode 100644 src/doModifier.h delete mode 100644 src/doModifierDispersion.h delete mode 100644 src/doModifierMass.h delete mode 100644 src/doNormalMono.h delete mode 100644 src/doNormalMonoCenter.h delete mode 100644 src/doNormalMultiCenter.h delete mode 100644 src/doSampler.h delete mode 100644 src/doSamplerNormalMono.h delete mode 100644 src/doSamplerUniform.h delete mode 100644 src/doUniform.h delete mode 100644 src/doUniformCenter.h delete mode 100644 src/doVectorBounds.h create mode 100644 src/edo create mode 100644 src/edo.cpp create mode 100644 src/edoAlgo.h create mode 100644 src/edoBounder.h create mode 100644 src/edoBounderBound.h create mode 100644 src/edoBounderNo.h create mode 100644 src/edoBounderRng.h create mode 100644 src/edoBounderUniform.h create mode 100644 src/edoContinue.h create mode 100644 src/edoDistrib.h rename src/{doEDA.h => edoEDA.h} (79%) rename src/{doEDASA.h => edoEDASA.h} (79%) create mode 100644 src/edoEstimator.h create mode 100644 src/edoEstimatorNormalMono.h rename src/{doEstimatorNormalMulti.h => edoEstimatorNormalMulti.h} (68%) create mode 100644 src/edoEstimatorUniform.h create mode 100644 src/edoModifier.h create mode 100644 src/edoModifierDispersion.h create mode 100644 src/edoModifierMass.h create mode 100644 src/edoNormalMono.h create mode 100644 src/edoNormalMonoCenter.h rename src/{doNormalMulti.h => edoNormalMulti.h} (86%) create mode 100644 src/edoNormalMultiCenter.h create mode 100644 src/edoSampler.h create mode 100644 src/edoSamplerNormalMono.h rename src/{doSamplerNormalMulti.h => edoSamplerNormalMulti.h} (67%) create mode 100644 src/edoSamplerUniform.h create mode 100644 src/edoUniform.h create mode 100644 src/edoUniformCenter.h create mode 100644 src/edoVectorBounds.h delete mode 100644 src/utils/doFileSnapshot.h delete mode 100644 src/utils/doHyperVolume.h delete mode 100644 src/utils/doPopStat.h delete mode 100644 src/utils/doStat.h delete mode 100644 src/utils/doStatNormalMono.h delete mode 100644 src/utils/doStatNormalMulti.h delete mode 100644 src/utils/doStatUniform.h rename src/utils/{doCheckPoint.h => edoCheckPoint.h} (57%) rename src/utils/{doFileSnapshot.cpp => edoFileSnapshot.cpp} (57%) create mode 100644 src/utils/edoFileSnapshot.h create mode 100644 src/utils/edoHyperVolume.h create mode 100644 src/utils/edoPopStat.h create mode 100644 src/utils/edoStat.h create mode 100644 src/utils/edoStatNormalMono.h create mode 100644 src/utils/edoStatNormalMulti.h create mode 100644 src/utils/edoStatUniform.h rename test/{t-doEstimatorNormalMulti.cpp => t-edoEstimatorNormalMulti.cpp} (78%) diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 00000000..550b46c0 --- /dev/null +++ b/AUTHORS @@ -0,0 +1,36 @@ + +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: + +N:Johann Dréo +P:nojhan +E:johann.dreo@thalesgroup.com +D:2010-07-01 +C:original design and code + +N:Caner Candan +P: +E:caner.candan@thalesgroup.com +D:2010-07-01 +C:original design and code + +As of 2011-01-25, Thales SA disclaims all copyright interest in the Evolving Distribution Objects (EDO) framework. diff --git a/CMakeLists.txt b/CMakeLists.txt index 31da2b9c..868c456b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -5,7 +5,7 @@ # Checks cmake version compatibility CMAKE_MINIMUM_REQUIRED(VERSION 2.6) -PROJECT(DO) +PROJECT(EDO) SET(PROJECT_VERSION_MAJOR 1) SET(PROJECT_VERSION_MINOR 0) @@ -31,7 +31,7 @@ INCLUDE_DIRECTORIES( ${EO_INCLUDE_DIRS} ${MO_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS} - /Dev/ometah-0.3/common + # /Dev/ometah-0.3/common ) ###################################################################################### @@ -92,8 +92,8 @@ SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) LINK_DIRECTORIES(${LIBRARY_OUTPUT_PATH}) -ADD_LIBRARY(do STATIC ${SAMPLE_SRCS}) -INSTALL(TARGETS do ARCHIVE DESTINATION lib COMPONENT libraries) +ADD_LIBRARY(edo STATIC ${SAMPLE_SRCS}) +INSTALL(TARGETS edo ARCHIVE DESTINATION lib COMPONENT libraries) ###################################################################################### @@ -102,7 +102,7 @@ INSTALL(TARGETS do ARCHIVE DESTINATION lib COMPONENT libraries) ### 8) Install pkg-config config file for EO ###################################################################################### -INSTALL(FILES do.pc DESTINATION lib/pkgconfig COMPONENT headers) +INSTALL(FILES edo.pc DESTINATION lib/pkgconfig COMPONENT headers) ###################################################################################### diff --git a/COPYING b/COPYING index 8862bf50..4362b491 100644 --- a/COPYING +++ b/COPYING @@ -1 +1,502 @@ -(c) Thales group, 2010 + GNU LESSER GENERAL PUBLIC LICENSE + Version 2.1, February 1999 + + Copyright (C) 1991, 1999 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +[This is the first released version of the Lesser GPL. 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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 + +Also add information on how to contact you by electronic and paper mail. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the library, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random Hacker. + + , 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! diff --git a/README b/README index f58d9d3c..5b814b15 100644 --- a/README +++ b/README @@ -1,4 +1,4 @@ -This package contains the source code for DO. +This package contains the source code for EDO. # Step 1 - Configuration ------------------------ @@ -19,7 +19,7 @@ Note for windows users: if you don't use VisualStudio 9, enter the name of your # Step 3 - Compilation ---------------------- -In the do/build/ directory: +In the edo/build/ directory: (Unix) > make (Windows) Open the VisualStudio solution and compile it, compile also the target install. You can refer to this tutorial if you don't know how to compile a solution: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial @@ -29,7 +29,7 @@ You can refer to this tutorial if you don't know how to compile a solution: http --------------------- A toy example is given to test the components. You can run these tests as following. To define problem-related components for your own problem, please refer to the tutorials available on the website : http://paradiseo.gforge.inria.fr/. -In the do/build/ directory: +In the edo/build/ directory: (Unix) > ctest Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial @@ -46,7 +46,7 @@ Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/i The API-documentation is available in doc/html/index.html -# Things to keep in mind when using DO +# Things to keep in mind when using EDO ---------------------------------------- * By default, the EO random generator's seed is initialized by the number of seconds since the epoch (with time(0)). It is available in the status file dumped at each execution. Please, keep in mind that if you start two run at the same second without modifying the seed, you will get exactly the same results. diff --git a/application/CMakeLists.txt b/application/CMakeLists.txt index 24b57198..eea3dcb9 100644 --- a/application/CMakeLists.txt +++ b/application/CMakeLists.txt @@ -9,6 +9,6 @@ INCLUDE_DIRECTORIES( ADD_SUBDIRECTORY(common) ADD_SUBDIRECTORY(eda_sa) ADD_SUBDIRECTORY(eda) -ADD_SUBDIRECTORY(sa) +#ADD_SUBDIRECTORY(sa) ###################################################################################### diff --git a/application/eda/CMakeLists.txt b/application/eda/CMakeLists.txt index 41d61ce0..2f1a52a5 100644 --- a/application/eda/CMakeLists.txt +++ b/application/eda/CMakeLists.txt @@ -15,13 +15,13 @@ FOREACH(file ${RESOURCES}) EXECUTE_PROCESS( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/${file} - ${DO_BINARY_DIR}/${file} + ${EDO_BINARY_DIR}/${file} ) ENDFOREACH(file) FILE(GLOB SOURCES *.cpp) -SET(EXECUTABLE_OUTPUT_PATH ${DO_BINARY_DIR}) +SET(EXECUTABLE_OUTPUT_PATH ${EDO_BINARY_DIR}) ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES}) -TARGET_LINK_LIBRARIES(${PROJECT_NAME} do doutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) +TARGET_LINK_LIBRARIES(${PROJECT_NAME} edo edoutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) diff --git a/application/eda/main.cpp b/application/eda/main.cpp index 3e8e0fae..8fc663fd 100644 --- a/application/eda/main.cpp +++ b/application/eda/main.cpp @@ -1,3 +1,30 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + #include #include @@ -11,14 +38,14 @@ #include #include -#include +#include #include "Rosenbrock.h" #include "Sphere.h" typedef eoReal EOT; -typedef doNormalMulti< EOT > Distrib; +typedef edoNormalMulti< EOT > Distrib; int main(int ac, char** av) @@ -45,13 +72,13 @@ int main(int ac, char** av) eoSelect< EOT >* selector = new eoDetSelect< EOT >( selection_rate ); state.storeFunctor(selector); - doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); + edoEstimator< Distrib >* estimator = new edoEstimatorNormalMulti< EOT >(); state.storeFunctor(estimator); eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >( 2 ); state.storeFunctor(selectone); - doModifierMass< Distrib >* modifier = new doNormalMultiCenter< EOT >(); + edoModifierMass< Distrib >* modifier = new edoNormalMultiCenter< EOT >(); state.storeFunctor(modifier); eoEvalFunc< EOT >* plainEval = new Rosenbrock< EOT >(); @@ -100,7 +127,7 @@ int main(int ac, char** av) // This is used by doSampler. //----------------------------------------------------------------------------- - doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + edoBounder< EOT >* bounder = new edoBounderRng< EOT >(EOT(pop[0].size(), -5), EOT(pop[0].size(), 5), *gen); state.storeFunctor(bounder); @@ -112,7 +139,7 @@ int main(int ac, char** av) // Prepare sampler class with a specific distribution //----------------------------------------------------------------------------- - doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); + edoSampler< Distrib >* sampler = new edoSamplerNormalMulti< EOT >( *bounder ); state.storeFunctor(sampler); //----------------------------------------------------------------------------- @@ -166,10 +193,10 @@ int main(int ac, char** av) // distribution output //----------------------------------------------------------------------------- - doDummyContinue< Distrib >* dummy_continue = new doDummyContinue< Distrib >(); + edoDummyContinue< Distrib >* dummy_continue = new edoDummyContinue< Distrib >(); state.storeFunctor(dummy_continue); - doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue ); + edoCheckPoint< Distrib >* distribution_continue = new edoCheckPoint< Distrib >( *dummy_continue ); state.storeFunctor(distribution_continue); //----------------------------------------------------------------------------- @@ -216,11 +243,11 @@ int main(int ac, char** av) // removing as doFileSnapshot does within ctor. //----------------------------------------------------------------------------- - doPopStat< EOT >* popStat = new doPopStat; + edoPopStat< EOT >* popStat = new edoPopStat; state.storeFunctor(popStat); pop_continue.add(*popStat); - doFileSnapshot* fileSnapshot = new doFileSnapshot("EDA_ResPop"); + edoFileSnapshot* fileSnapshot = new edoFileSnapshot("EDA_ResPop"); state.storeFunctor(fileSnapshot); fileSnapshot->add(*popStat); pop_continue.add(*fileSnapshot); @@ -232,7 +259,7 @@ int main(int ac, char** av) // distribution output (after helper) //----------------------------------------------------------------------------- - doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); + edoDistribStat< Distrib >* distrib_stat = new edoStatNormalMulti< EOT >(); state.storeFunctor(distrib_stat); distribution_continue->add( *distrib_stat ); @@ -254,7 +281,7 @@ int main(int ac, char** av) // EDA algorithm configuration //----------------------------------------------------------------------------- - doAlgo< Distrib >* algo = new doEDA< Distrib > + edoAlgo< Distrib >* algo = new edoEDA< Distrib > (*selector, *estimator, *selectone, *modifier, *sampler, pop_continue, *distribution_continue, eval, diff --git a/application/eda_sa/CMakeLists.txt b/application/eda_sa/CMakeLists.txt index f92e105f..39a9a546 100644 --- a/application/eda_sa/CMakeLists.txt +++ b/application/eda_sa/CMakeLists.txt @@ -15,13 +15,13 @@ FOREACH(file ${RESOURCES}) EXECUTE_PROCESS( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/${file} - ${DO_BINARY_DIR}/${file} + ${EDO_BINARY_DIR}/${file} ) ENDFOREACH(file) FILE(GLOB SOURCES *.cpp) -SET(EXECUTABLE_OUTPUT_PATH ${DO_BINARY_DIR}) +SET(EXECUTABLE_OUTPUT_PATH ${EDO_BINARY_DIR}) ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES}) -TARGET_LINK_LIBRARIES(${PROJECT_NAME} do doutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) +TARGET_LINK_LIBRARIES(${PROJECT_NAME} edo edoutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index 2d72ad83..8ee173e3 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -11,14 +11,14 @@ #include #include -#include +#include #include "Rosenbrock.h" #include "Sphere.h" typedef eoReal EOT; -typedef doNormalMulti< EOT > Distrib; +typedef edoNormalMulti< EOT > Distrib; int main(int ac, char** av) @@ -45,13 +45,13 @@ int main(int ac, char** av) eoSelect< EOT >* selector = new eoDetSelect< EOT >( selection_rate ); state.storeFunctor(selector); - doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); + edoEstimator< Distrib >* estimator = new edoEstimatorNormalMulti< EOT >(); state.storeFunctor(estimator); eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >( 2 ); state.storeFunctor(selectone); - doModifierMass< Distrib >* modifier = new doNormalMultiCenter< EOT >(); + edoModifierMass< Distrib >* modifier = new edoNormalMultiCenter< EOT >(); state.storeFunctor(modifier); eoEvalFunc< EOT >* plainEval = new Rosenbrock< EOT >(); @@ -100,7 +100,7 @@ int main(int ac, char** av) // This is used by doSampler. //----------------------------------------------------------------------------- - doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + edoBounder< EOT >* bounder = new edoBounderRng< EOT >(EOT(pop[0].size(), -5), EOT(pop[0].size(), 5), *gen); state.storeFunctor(bounder); @@ -112,7 +112,7 @@ int main(int ac, char** av) // Prepare sampler class with a specific distribution //----------------------------------------------------------------------------- - doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); + edoSampler< Distrib >* sampler = new edoSamplerNormalMulti< EOT >( *bounder ); state.storeFunctor(sampler); //----------------------------------------------------------------------------- @@ -166,10 +166,10 @@ int main(int ac, char** av) // distribution output //----------------------------------------------------------------------------- - doDummyContinue< Distrib >* dummy_continue = new doDummyContinue< Distrib >(); + edoDummyContinue< Distrib >* dummy_continue = new edoDummyContinue< Distrib >(); state.storeFunctor(dummy_continue); - doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue ); + edoCheckPoint< Distrib >* distribution_continue = new edoCheckPoint< Distrib >( *dummy_continue ); state.storeFunctor(distribution_continue); //----------------------------------------------------------------------------- @@ -213,14 +213,14 @@ int main(int ac, char** av) // population output (after helper) // // FIXME: theses objects are instanciate there in order to avoid a folder - // removing as doFileSnapshot does within ctor. + // removing as edoFileSnapshot does within ctor. //----------------------------------------------------------------------------- - doPopStat< EOT >* popStat = new doPopStat; + edoPopStat< EOT >* popStat = new edoPopStat; state.storeFunctor(popStat); pop_continue.add(*popStat); - doFileSnapshot* fileSnapshot = new doFileSnapshot("EDASA_ResPop"); + edoFileSnapshot* fileSnapshot = new edoFileSnapshot("EDASA_ResPop"); state.storeFunctor(fileSnapshot); fileSnapshot->add(*popStat); pop_continue.add(*fileSnapshot); @@ -232,7 +232,7 @@ int main(int ac, char** av) // distribution output (after helper) //----------------------------------------------------------------------------- - doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); + edoDistribStat< Distrib >* distrib_stat = new edoStatNormalMulti< EOT >(); state.storeFunctor(distrib_stat); distribution_continue->add( *distrib_stat ); @@ -254,7 +254,7 @@ int main(int ac, char** av) // EDASA algorithm configuration //----------------------------------------------------------------------------- - doAlgo< Distrib >* algo = new doEDASA< Distrib > + edoAlgo< Distrib >* algo = new edoEDASA< Distrib > (*selector, *estimator, *selectone, *modifier, *sampler, pop_continue, *distribution_continue, eval, *sa_continue, *cooling_schedule, diff --git a/build_gcc_linux_debug b/build_gcc_linux_debug index da385fdb..144a5298 100755 --- a/build_gcc_linux_debug +++ b/build_gcc_linux_debug @@ -1,6 +1,6 @@ #!/usr/bin/env sh -mkdir debug +mkdir -p debug cd debug cmake -DCMAKE_BUILD_TYPE=Debug .. make diff --git a/build_gcc_linux_release b/build_gcc_linux_release index 78a66c55..fb220d04 100755 --- a/build_gcc_linux_release +++ b/build_gcc_linux_release @@ -1,6 +1,6 @@ #!/usr/bin/env sh -mkdir release +mkdir -p release cd release cmake .. make diff --git a/do.pc b/do.pc deleted file mode 100644 index b207747d..00000000 --- a/do.pc +++ /dev/null @@ -1,12 +0,0 @@ -# Package Information for pkg-config - -prefix=/usr -exec_prefix=${prefix} -libdir=${exec_prefix}/lib -includedir=${prefix}/include/do - -Name: Distribution Object -Description: Distribution Object -Version: 1.0 -Libs: -L${libdir} -ldo -ldoutils -Cflags: -I${includedir} diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index 056f3f2f..6c7b1593 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -22,7 +22,7 @@ IF (DOXYGEN_FOUND) INSTALL( DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - DESTINATION share/do COMPONENT libraries + DESTINATION share/edo COMPONENT libraries PATTERN "CMakeFiles" EXCLUDE PATTERN "cmake_install.cmake" EXCLUDE PATTERN "Makefile" EXCLUDE diff --git a/edo.pc b/edo.pc new file mode 100644 index 00000000..a7043438 --- /dev/null +++ b/edo.pc @@ -0,0 +1,12 @@ +# Package Information for pkg-config + +prefix=/usr +exec_prefix=${prefix} +libdir=${exec_prefix}/lib +includedir=${prefix}/include/edo + +Name: Evolving Distribution Objects +Description: Evolving Distribution Objects +Version: 1.0 +Libs: -L${libdir} -ledo -ledoutils +Cflags: -I${includedir} diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index f4cdbfae..6b2176f5 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -2,8 +2,8 @@ ### 1) Set all needed source files for the project ###################################################################################### -FILE(GLOB HDRS *.h do) -INSTALL(FILES ${HDRS} DESTINATION include/do COMPONENT headers) +FILE(GLOB HDRS *.h edo) +INSTALL(FILES ${HDRS} DESTINATION include/edo COMPONENT headers) FILE(GLOB SOURCES *.cpp) diff --git a/src/do b/src/do deleted file mode 100644 index ff2b3e67..00000000 --- a/src/do +++ /dev/null @@ -1,59 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _do_ -#define _do_ - -#include "doAlgo.h" -#include "doEDASA.h" -#include "doEDA.h" - -#include "doDistrib.h" -#include "doUniform.h" -#include "doNormalMono.h" -#include "doNormalMulti.h" - -#include "doEstimator.h" -#include "doEstimatorUniform.h" -#include "doEstimatorNormalMono.h" -#include "doEstimatorNormalMulti.h" - -#include "doModifier.h" -#include "doModifierDispersion.h" -#include "doModifierMass.h" -#include "doUniformCenter.h" -#include "doNormalMonoCenter.h" -#include "doNormalMultiCenter.h" - -#include "doSampler.h" -#include "doSamplerUniform.h" -#include "doSamplerNormalMono.h" -#include "doSamplerNormalMulti.h" - -#include "doVectorBounds.h" - -#include "doBounder.h" -#include "doBounderNo.h" -#include "doBounderBound.h" -#include "doBounderRng.h" - -#include "doContinue.h" -#include "utils/doCheckPoint.h" - -#include "utils/doStat.h" -#include "utils/doStatUniform.h" -#include "utils/doStatNormalMono.h" -#include "utils/doStatNormalMulti.h" - -#include "utils/doFileSnapshot.h" -#include "utils/doPopStat.h" - -#endif // !_do_ - -// Local Variables: -// mode: C++ -// End: diff --git a/src/do.cpp b/src/do.cpp deleted file mode 100644 index 082374a4..00000000 --- a/src/do.cpp +++ /dev/null @@ -1,8 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#include "do" diff --git a/src/doAlgo.h b/src/doAlgo.h deleted file mode 100644 index 0f260d93..00000000 --- a/src/doAlgo.h +++ /dev/null @@ -1,23 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doAlgo_h -#define _doAlgo_h - -#include - -template < typename D > -class doAlgo : public eoAlgo< typename D::EOType > -{ - //! Alias for the type - typedef typename D::EOType EOT; - -public: - virtual ~doAlgo(){} -}; - -#endif // !_doAlgo_h diff --git a/src/doBounder.h b/src/doBounder.h deleted file mode 100644 index 44240246..00000000 --- a/src/doBounder.h +++ /dev/null @@ -1,34 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doBounder_h -#define _doBounder_h - -#include - -template < typename EOT > -class doBounder : public eoUF< EOT&, void > -{ -public: - doBounder( EOT min = EOT(1, 0), EOT max = EOT(1, 0) ) - : _min(min), _max(max) - { - assert(_min.size() > 0); - assert(_min.size() == _max.size()); - } - - // virtual void operator()( EOT& ) = 0 (provided by eoUF< A1, R >) - - EOT& min(){return _min;} - EOT& max(){return _max;} - -private: - EOT _min; - EOT _max; -}; - -#endif // !_doBounder_h diff --git a/src/doBounderBound.h b/src/doBounderBound.h deleted file mode 100644 index cff765b8..00000000 --- a/src/doBounderBound.h +++ /dev/null @@ -1,42 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doBounderBound_h -#define _doBounderBound_h - -#include "doBounder.h" - -template < typename EOT > -class doBounderBound : public doBounder< EOT > -{ -public: - doBounderBound( EOT min, EOT max ) - : doBounder< EOT >( min, max ) - {} - - void operator()( EOT& x ) - { - unsigned int size = x.size(); - assert(size > 0); - - for (unsigned int d = 0; d < size; ++d) // browse all dimensions - { - if (x[d] < this->min()[d]) - { - x[d] = this->min()[d]; - continue; - } - - if (x[d] > this->max()[d]) - { - x[d] = this->max()[d]; - } - } - } -}; - -#endif // !_doBounderBound_h diff --git a/src/doBounderNo.h b/src/doBounderNo.h deleted file mode 100644 index 0ca883bc..00000000 --- a/src/doBounderNo.h +++ /dev/null @@ -1,20 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doBounderNo_h -#define _doBounderNo_h - -#include "doBounder.h" - -template < typename EOT > -class doBounderNo : public doBounder< EOT > -{ -public: - void operator()( EOT& ) {} -}; - -#endif // !_doBounderNo_h diff --git a/src/doBounderRng.h b/src/doBounderRng.h deleted file mode 100644 index 52b95bca..00000000 --- a/src/doBounderRng.h +++ /dev/null @@ -1,42 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doBounderRng_h -#define _doBounderRng_h - -#include "doBounder.h" - -template < typename EOT > -class doBounderRng : public doBounder< EOT > -{ -public: - doBounderRng( EOT min, EOT max, eoRndGenerator< double > & rng ) - : doBounder< EOT >( min, max ), _rng(rng) - {} - - void operator()( EOT& x ) - { - unsigned int size = x.size(); - assert(size > 0); - - for (unsigned int d = 0; d < size; ++d) // browse all dimensions - { - - // FIXME: attention: les bornes RNG ont les memes bornes quelque soit les dimensions idealement on voudrait avoir des bornes differentes pour chaque dimensions. - - if (x[d] < this->min()[d] || x[d] > this->max()[d]) - { - x[d] = _rng(); - } - } - } - -private: - eoRndGenerator< double> & _rng; -}; - -#endif // !_doBounderRng_h diff --git a/src/doBounderUniform.h b/src/doBounderUniform.h deleted file mode 100644 index 9fac7dac..00000000 --- a/src/doBounderUniform.h +++ /dev/null @@ -1,35 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo -*/ - -#ifndef _doBounderUniform_h -#define _doBounderUniform_h - -#include "doBounder.h" - -template < typename EOT > -class doBounderUniform : public doBounder< EOT > -{ -public: - doBounderUniform( EOT min, EOT max ) - : doBounder< EOT >( min, max ) - {} - - void operator()( EOT& sol ) - { - unsigned int size = sol.size(); - assert(size > 0); - - for (unsigned int d = 0; d < size; ++d) { - - if ( sol[d] < this->min()[d] || sol[d] > this->max()[d]) { - // use EO's global "rng" - sol[d] = rng.uniform( this->min()[d], this->max()[d] ); - } - } // for d in size - } -}; - -#endif // !_doBounderUniform_h diff --git a/src/doContinue.h b/src/doContinue.h deleted file mode 100644 index 64f1d483..00000000 --- a/src/doContinue.h +++ /dev/null @@ -1,41 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doContinue_h -#define _doContinue_h - -#include -#include - -//! doContinue< EOT > classe fitted to Distribution Object library - -template < typename D > -class doContinue : public eoUF< const D&, bool >, public eoPersistent -{ -public: - virtual std::string className(void) const { return "doContinue"; } - - void readFrom(std::istream&) - { - /* It should be implemented by subclasses ! */ - } - - void printOn(std::ostream&) const - { - /* It should be implemented by subclasses ! */ - } -}; - -template < typename D > -class doDummyContinue : public doContinue< D > -{ - bool operator()(const D&){ return true; } - - virtual std::string className() const { return "doDummyContinue"; } -}; - -#endif // !_doContinue_h diff --git a/src/doDistrib.h b/src/doDistrib.h deleted file mode 100644 index f150e8e0..00000000 --- a/src/doDistrib.h +++ /dev/null @@ -1,23 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doDistrib_h -#define _doDistrib_h - -#include - -template < typename EOT > -class doDistrib : public eoFunctorBase -{ -public: - //! Alias for the type - typedef EOT EOType; - - virtual ~doDistrib(){} -}; - -#endif // !_doDistrib_h diff --git a/src/doEstimator.h b/src/doEstimator.h deleted file mode 100644 index 956bed78..00000000 --- a/src/doEstimator.h +++ /dev/null @@ -1,23 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doEstimator_h -#define _doEstimator_h - -#include -#include - -template < typename D > -class doEstimator : public eoUF< eoPop< typename D::EOType >&, D > -{ -public: - typedef typename D::EOType EOType; - - // virtual D operator() ( eoPop< EOT >& )=0 (provided by eoUF< A1, R >) -}; - -#endif // !_doEstimator_h diff --git a/src/doEstimatorNormalMono.h b/src/doEstimatorNormalMono.h deleted file mode 100644 index fb9c1f2f..00000000 --- a/src/doEstimatorNormalMono.h +++ /dev/null @@ -1,77 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doEstimatorNormalMono_h -#define _doEstimatorNormalMono_h - -#include "doEstimator.h" -#include "doNormalMono.h" - -template < typename EOT > -class doEstimatorNormalMono : public doEstimator< doNormalMono< EOT > > -{ -public: - typedef typename EOT::AtomType AtomType; - - class Variance - { - public: - Variance() : _sumvar(0){} - - void update(AtomType v) - { - _n++; - - AtomType d = v - _mean; - - _mean += 1 / _n * d; - _sumvar += (_n - 1) / _n * d * d; - } - - AtomType get_mean() const {return _mean;} - AtomType get_var() const {return _sumvar / (_n - 1);} - AtomType get_std() const {return sqrt( get_var() );} - - private: - AtomType _n; - AtomType _mean; - AtomType _sumvar; - }; - -public: - doNormalMono< EOT > operator()(eoPop& pop) - { - unsigned int popsize = pop.size(); - assert(popsize > 0); - - unsigned int dimsize = pop[0].size(); - assert(dimsize > 0); - - std::vector< Variance > var( dimsize ); - - for (unsigned int i = 0; i < popsize; ++i) - { - for (unsigned int d = 0; d < dimsize; ++d) - { - var[d].update( pop[i][d] ); - } - } - - EOT mean( dimsize ); - EOT variance( dimsize ); - - for (unsigned int d = 0; d < dimsize; ++d) - { - mean[d] = var[d].get_mean(); - variance[d] = var[d].get_var(); - } - - return doNormalMono< EOT >( mean, variance ); - } -}; - -#endif // !_doEstimatorNormalMono_h diff --git a/src/doEstimatorUniform.h b/src/doEstimatorUniform.h deleted file mode 100644 index ca361ce0..00000000 --- a/src/doEstimatorUniform.h +++ /dev/null @@ -1,51 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doEstimatorUniform_h -#define _doEstimatorUniform_h - -#include "doEstimator.h" -#include "doUniform.h" - -// TODO: calcule de la moyenne + covariance dans une classe derivee - -template < typename EOT > -class doEstimatorUniform : public doEstimator< doUniform< EOT > > -{ -public: - doUniform< EOT > operator()(eoPop& pop) - { - unsigned int size = pop.size(); - - assert(size > 0); - - EOT min = pop[0]; - EOT max = pop[0]; - - for (unsigned int i = 1; i < size; ++i) - { - unsigned int size = pop[i].size(); - - assert(size > 0); - - // possibilité d'utiliser std::min_element et std::max_element mais exige 2 pass au lieu d'1. - - for (unsigned int d = 0; d < size; ++d) - { - if (pop[i][d] < min[d]) - min[d] = pop[i][d]; - - if (pop[i][d] > max[d]) - max[d] = pop[i][d]; - } - } - - return doUniform< EOT >(min, max); - } -}; - -#endif // !_doEstimatorUniform_h diff --git a/src/doModifier.h b/src/doModifier.h deleted file mode 100644 index b36106c9..00000000 --- a/src/doModifier.h +++ /dev/null @@ -1,20 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doModifier_h -#define _doModifier_h - -template < typename D > -class doModifier -{ -public: - virtual ~doModifier(){} - - typedef typename D::EOType EOType; -}; - -#endif // !_doModifier_h diff --git a/src/doModifierDispersion.h b/src/doModifierDispersion.h deleted file mode 100644 index 4d5e42c4..00000000 --- a/src/doModifierDispersion.h +++ /dev/null @@ -1,23 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doModifierDispersion_h -#define _doModifierDispersion_h - -#include -#include - -#include "doModifier.h" - -template < typename D > -class doModifierDispersion : public doModifier< D >, public eoBF< D&, eoPop< typename D::EOType >&, void > -{ -public: - // virtual void operator() ( D&, eoPop< D::EOType >& )=0 (provided by eoBF< A1, A2, R >) -}; - -#endif // !_doModifierDispersion_h diff --git a/src/doModifierMass.h b/src/doModifierMass.h deleted file mode 100644 index 4f5df5c0..00000000 --- a/src/doModifierMass.h +++ /dev/null @@ -1,24 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doModifierMass_h -#define _doModifierMass_h - -#include - -#include "doModifier.h" - -template < typename D > -class doModifierMass : public doModifier< D >, public eoBF< D&, typename D::EOType&, void > -{ -public: - //typedef typename D::EOType::AtomType AtomType; // does not work !!! - - // virtual void operator() ( D&, D::EOType& )=0 (provided by eoBF< A1, A2, R >) -}; - -#endif // !_doModifierMass_h diff --git a/src/doNormalMono.h b/src/doNormalMono.h deleted file mode 100644 index fa8f8e6f..00000000 --- a/src/doNormalMono.h +++ /dev/null @@ -1,38 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doNormalMono_h -#define _doNormalMono_h - -#include "doDistrib.h" - -template < typename EOT > -class doNormalMono : public doDistrib< EOT > -{ -public: - doNormalMono( const EOT& mean, const EOT& variance ) - : _mean(mean), _variance(variance) - { - assert(_mean.size() > 0); - assert(_mean.size() == _variance.size()); - } - - unsigned int size() - { - assert(_mean.size() == _variance.size()); - return _mean.size(); - } - - EOT mean(){return _mean;} - EOT variance(){return _variance;} - -private: - EOT _mean; - EOT _variance; -}; - -#endif // !_doNormalMono_h diff --git a/src/doNormalMonoCenter.h b/src/doNormalMonoCenter.h deleted file mode 100644 index 7786d347..00000000 --- a/src/doNormalMonoCenter.h +++ /dev/null @@ -1,26 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doNormalMonoCenter_h -#define _doNormalMonoCenter_h - -#include "doModifierMass.h" -#include "doNormalMono.h" - -template < typename EOT > -class doNormalMonoCenter : public doModifierMass< doNormalMono< EOT > > -{ -public: - typedef typename EOT::AtomType AtomType; - - void operator() ( doNormalMono< EOT >& distrib, EOT& mass ) - { - distrib.mean() = mass; - } -}; - -#endif // !_doNormalMonoCenter_h diff --git a/src/doNormalMultiCenter.h b/src/doNormalMultiCenter.h deleted file mode 100644 index bf52ecf1..00000000 --- a/src/doNormalMultiCenter.h +++ /dev/null @@ -1,28 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doNormalMultiCenter_h -#define _doNormalMultiCenter_h - -#include "doModifierMass.h" -#include "doNormalMulti.h" - -template < typename EOT > -class doNormalMultiCenter : public doModifierMass< doNormalMulti< EOT > > -{ -public: - typedef typename EOT::AtomType AtomType; - - void operator() ( doNormalMulti< EOT >& distrib, EOT& mass ) - { - ublas::vector< AtomType > mean( distrib.size() ); - std::copy( mass.begin(), mass.end(), mean.begin() ); - distrib.mean() = mean; - } -}; - -#endif // !_doNormalMultiCenter_h diff --git a/src/doSampler.h b/src/doSampler.h deleted file mode 100644 index 0d69223c..00000000 --- a/src/doSampler.h +++ /dev/null @@ -1,75 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doSampler_h -#define _doSampler_h - -#include - -#include "doBounder.h" -#include "doBounderNo.h" - -template < typename D > -class doSampler : public eoUF< D&, typename D::EOType > -{ -public: - typedef typename D::EOType EOType; - - doSampler(doBounder< EOType > & bounder) - : /*_dummy_bounder(),*/ _bounder(bounder) - {} - - /* - doSampler() - : _dummy_bounder(), _bounder( _dummy_bounder ) - {} - */ - - // virtual EOType operator()( D& ) = 0 (provided by eoUF< A1, R >) - - virtual EOType sample( D& ) = 0; - - EOType operator()( D& distrib ) - { - unsigned int size = distrib.size(); - assert(size > 0); - - - //------------------------------------------------------------- - // Point we want to sample to get higher a set of points - // (coordinates in n dimension) - // x = {x1, x2, ..., xn} - // the sample method is implemented in the derivated class - //------------------------------------------------------------- - - EOType solution(sample(distrib)); - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // Now we are bounding the distribution thanks to min and max - // parameters. - //------------------------------------------------------------- - - _bounder(solution); - - //------------------------------------------------------------- - - - return solution; - } - -private: - //doBounderNo _dummy_bounder; - - //! Bounder functor - doBounder< EOType > & _bounder; - -}; - -#endif // !_doSampler_h diff --git a/src/doSamplerNormalMono.h b/src/doSamplerNormalMono.h deleted file mode 100644 index b790ee6b..00000000 --- a/src/doSamplerNormalMono.h +++ /dev/null @@ -1,71 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doSamplerNormalMono_h -#define _doSamplerNormalMono_h - -#include - -#include "doSampler.h" -#include "doNormalMono.h" -#include "doBounder.h" - -/** - * doSamplerNormalMono - * This class uses the NormalMono distribution parameters (bounds) to return - * a random position used for population sampling. - */ -template < typename EOT > -class doSamplerNormalMono : public doSampler< doNormalMono< EOT > > -{ -public: - typedef typename EOT::AtomType AtomType; - - doSamplerNormalMono( doBounder< EOT > & bounder ) - : doSampler< doNormalMono< EOT > >( bounder ) - {} - - EOT sample( doNormalMono< EOT >& distrib ) - { - unsigned int size = distrib.size(); - assert(size > 0); - - - //------------------------------------------------------------- - // Point we want to sample to get higher a set of points - // (coordinates in n dimension) - // x = {x1, x2, ..., xn} - //------------------------------------------------------------- - - EOT solution; - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // Sampling all dimensions - //------------------------------------------------------------- - - for (unsigned int i = 0; i < size; ++i) - { - AtomType mean = distrib.mean()[i]; - AtomType variance = distrib.variance()[i]; - AtomType random = rng.normal(mean, variance); - - assert(variance >= 0); - - solution.push_back(random); - } - - //------------------------------------------------------------- - - - return solution; - } -}; - -#endif // !_doSamplerNormalMono_h diff --git a/src/doSamplerUniform.h b/src/doSamplerUniform.h deleted file mode 100644 index 6f79c138..00000000 --- a/src/doSamplerUniform.h +++ /dev/null @@ -1,76 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doSamplerUniform_h -#define _doSamplerUniform_h - -#include - -#include "doSampler.h" -#include "doUniform.h" - -/** - * doSamplerUniform - * This class uses the Uniform distribution parameters (bounds) to return - * a random position used for population sampling. - */ -template < typename EOT, class D=doUniform > // FIXME: D template name is there really used ?!? -class doSamplerUniform : public doSampler< doUniform< EOT > > -{ -public: - typedef D Distrib; - - doSamplerUniform(doBounder< EOT > & bounder) - : doSampler< doUniform >(bounder) // FIXME: Why D is not used here ? - {} - - /* - doSamplerUniform() - : doSampler< doUniform >() - {} - */ - - EOT sample( doUniform< EOT >& distrib ) - { - unsigned int size = distrib.size(); - assert(size > 0); - - - //------------------------------------------------------------- - // Point we want to sample to get higher a set of points - // (coordinates in n dimension) - // x = {x1, x2, ..., xn} - //------------------------------------------------------------- - - EOT solution; - - //------------------------------------------------------------- - - - //------------------------------------------------------------- - // Sampling all dimensions - //------------------------------------------------------------- - - for (unsigned int i = 0; i < size; ++i) - { - double min = distrib.min()[i]; - double max = distrib.max()[i]; - double random = rng.uniform(min, max); - - assert(min <= random && random <= max); - - solution.push_back(random); - } - - //------------------------------------------------------------- - - - return solution; - } -}; - -#endif // !_doSamplerUniform_h diff --git a/src/doUniform.h b/src/doUniform.h deleted file mode 100644 index 624fec1f..00000000 --- a/src/doUniform.h +++ /dev/null @@ -1,23 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doUniform_h -#define _doUniform_h - -#include "doDistrib.h" -#include "doVectorBounds.h" - -template < typename EOT > -class doUniform : public doDistrib< EOT >, public doVectorBounds< EOT > -{ -public: - doUniform(EOT min, EOT max) - : doVectorBounds< EOT >(min, max) - {} -}; - -#endif // !_doUniform_h diff --git a/src/doUniformCenter.h b/src/doUniformCenter.h deleted file mode 100644 index 8b0016bc..00000000 --- a/src/doUniformCenter.h +++ /dev/null @@ -1,35 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doUniformCenter_h -#define _doUniformCenter_h - -#include "doModifierMass.h" -#include "doUniform.h" - -template < typename EOT > -class doUniformCenter : public doModifierMass< doUniform< EOT > > -{ -public: - typedef typename EOT::AtomType AtomType; - - void operator() ( doUniform< EOT >& distrib, EOT& mass ) - { - for (unsigned int i = 0, n = mass.size(); i < n; ++i) - { - AtomType& min = distrib.min()[i]; - AtomType& max = distrib.max()[i]; - - AtomType range = (max - min) / 2; - - min = mass[i] - range; - max = mass[i] + range; - } - } -}; - -#endif // !_doUniformCenter_h diff --git a/src/doVectorBounds.h b/src/doVectorBounds.h deleted file mode 100644 index 4e23d486..00000000 --- a/src/doVectorBounds.h +++ /dev/null @@ -1,36 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doVectorBounds_h -#define _doVectorBounds_h - -template < typename EOT > -class doVectorBounds -{ -public: - doVectorBounds(EOT min, EOT max) - : _min(min), _max(max) - { - assert(_min.size() > 0); - assert(_min.size() == _max.size()); - } - - EOT min(){return _min;} - EOT max(){return _max;} - - unsigned int size() - { - assert(_min.size() == _max.size()); - return _min.size(); - } - -private: - EOT _min; - EOT _max; -}; - -#endif // !_doVectorBounds_h diff --git a/src/edo b/src/edo new file mode 100644 index 00000000..54f20284 --- /dev/null +++ b/src/edo @@ -0,0 +1,79 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edo_ +#define _edo_ + +#include "edoAlgo.h" +#include "edoEDASA.h" +#include "edoEDA.h" + +#include "edoDistrib.h" +#include "edoUniform.h" +#include "edoNormalMono.h" +#include "edoNormalMulti.h" + +#include "edoEstimator.h" +#include "edoEstimatorUniform.h" +#include "edoEstimatorNormalMono.h" +#include "edoEstimatorNormalMulti.h" + +#include "edoModifier.h" +#include "edoModifierDispersion.h" +#include "edoModifierMass.h" +#include "edoUniformCenter.h" +#include "edoNormalMonoCenter.h" +#include "edoNormalMultiCenter.h" + +#include "edoSampler.h" +#include "edoSamplerUniform.h" +#include "edoSamplerNormalMono.h" +#include "edoSamplerNormalMulti.h" + +#include "edoVectorBounds.h" + +#include "edoBounder.h" +#include "edoBounderNo.h" +#include "edoBounderBound.h" +#include "edoBounderRng.h" + +#include "edoContinue.h" +#include "utils/edoCheckPoint.h" + +#include "utils/edoStat.h" +#include "utils/edoStatUniform.h" +#include "utils/edoStatNormalMono.h" +#include "utils/edoStatNormalMulti.h" + +#include "utils/edoFileSnapshot.h" +#include "utils/edoPopStat.h" + +#endif // !_edo_ + +// Local Variables: +// mode: C++ +// End: diff --git a/src/edo.cpp b/src/edo.cpp new file mode 100644 index 00000000..ff2bd2f9 --- /dev/null +++ b/src/edo.cpp @@ -0,0 +1,28 @@ +/* +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: + Caner Candan +*/ + +#include "edo" + diff --git a/src/edoAlgo.h b/src/edoAlgo.h new file mode 100644 index 00000000..249e42dd --- /dev/null +++ b/src/edoAlgo.h @@ -0,0 +1,44 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + + +#ifndef _edoAlgo_h +#define _edoAlgo_h + +#include + +template < typename D > +class edoAlgo : public eoAlgo< typename D::EOType > +{ + //! Alias for the type + typedef typename D::EOType EOT; + +public: + virtual ~edoAlgo(){} +}; + +#endif // !_edoAlgo_h diff --git a/src/edoBounder.h b/src/edoBounder.h new file mode 100644 index 00000000..98bfc1a8 --- /dev/null +++ b/src/edoBounder.h @@ -0,0 +1,54 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoBounder_h +#define _edoBounder_h + +#include + +template < typename EOT > +class edoBounder : public eoUF< EOT&, void > +{ +public: + edoBounder( EOT min = EOT(1, 0), EOT max = EOT(1, 0) ) + : _min(min), _max(max) + { + assert(_min.size() > 0); + assert(_min.size() == _max.size()); + } + + // virtual void operator()( EOT& ) = 0 (provided by eoUF< A1, R >) + + EOT& min(){return _min;} + EOT& max(){return _max;} + +private: + EOT _min; + EOT _max; +}; + +#endif // !_edoBounder_h diff --git a/src/edoBounderBound.h b/src/edoBounderBound.h new file mode 100644 index 00000000..8d5e52be --- /dev/null +++ b/src/edoBounderBound.h @@ -0,0 +1,62 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoBounderBound_h +#define _edoBounderBound_h + +#include "edoBounder.h" + +template < typename EOT > +class edoBounderBound : public edoBounder< EOT > +{ +public: + edoBounderBound( EOT min, EOT max ) + : edoBounder< EOT >( min, max ) + {} + + void operator()( EOT& x ) + { + unsigned int size = x.size(); + assert(size > 0); + + for (unsigned int d = 0; d < size; ++d) // browse all dimensions + { + if (x[d] < this->min()[d]) + { + x[d] = this->min()[d]; + continue; + } + + if (x[d] > this->max()[d]) + { + x[d] = this->max()[d]; + } + } + } +}; + +#endif // !_edoBounderBound_h diff --git a/src/edoBounderNo.h b/src/edoBounderNo.h new file mode 100644 index 00000000..27d65e6c --- /dev/null +++ b/src/edoBounderNo.h @@ -0,0 +1,40 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoBounderNo_h +#define _edoBounderNo_h + +#include "edoBounder.h" + +template < typename EOT > +class edoBounderNo : public edoBounder< EOT > +{ +public: + void operator()( EOT& ) {} +}; + +#endif // !_edoBounderNo_h diff --git a/src/edoBounderRng.h b/src/edoBounderRng.h new file mode 100644 index 00000000..e1e3617f --- /dev/null +++ b/src/edoBounderRng.h @@ -0,0 +1,63 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoBounderRng_h +#define _edoBounderRng_h + +#include "edoBounder.h" + +template < typename EOT > +class edoBounderRng : public edoBounder< EOT > +{ +public: + edoBounderRng( EOT min, EOT max, eoRndGenerator< double > & rng ) + : edoBounder< EOT >( min, max ), _rng(rng) + {} + + void operator()( EOT& x ) + { + unsigned int size = x.size(); + assert(size > 0); + + for (unsigned int d = 0; d < size; ++d) // browse all dimensions + { + + // FIXME: attention: les bornes RNG ont les memes bornes quelque soit les dimensions idealement on voudrait avoir des bornes differentes pour chaque dimensions. + + if (x[d] < this->min()[d] || x[d] > this->max()[d]) + { + x[d] = _rng(); + } + } + } + +private: + eoRndGenerator< double> & _rng; +}; + +#endif // !_edoBounderRng_h + diff --git a/src/edoBounderUniform.h b/src/edoBounderUniform.h new file mode 100644 index 00000000..fef1674d --- /dev/null +++ b/src/edoBounderUniform.h @@ -0,0 +1,55 @@ +/* +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: + Johann Dréo +*/ + +#ifndef _edoBounderUniform_h +#define _edoBounderUniform_h + +#include "edoBounder.h" + +template < typename EOT > +class edoBounderUniform : public edoBounder< EOT > +{ +public: + edoBounderUniform( EOT min, EOT max ) + : edoBounder< EOT >( min, max ) + {} + + void operator()( EOT& sol ) + { + unsigned int size = sol.size(); + assert(size > 0); + + for (unsigned int d = 0; d < size; ++d) { + + if ( sol[d] < this->min()[d] || sol[d] > this->max()[d]) { + // use EO's global "rng" + sol[d] = rng.uniform( this->min()[d], this->max()[d] ); + } + } // for d in size + } +}; + +#endif // !_edoBounderUniform_h diff --git a/src/edoContinue.h b/src/edoContinue.h new file mode 100644 index 00000000..2f7dff5a --- /dev/null +++ b/src/edoContinue.h @@ -0,0 +1,61 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _doContinue_h +#define _doContinue_h + +#include +#include + +//! edoContinue< EOT > classe fitted to Distribution Object library + +template < typename D > +class edoContinue : public eoUF< const D&, bool >, public eoPersistent +{ +public: + virtual std::string className(void) const { return "edoContinue"; } + + void readFrom(std::istream&) + { + /* It should be implemented by subclasses ! */ + } + + void printOn(std::ostream&) const + { + /* It should be implemented by subclasses ! */ + } +}; + +template < typename D > +class edoDummyContinue : public edoContinue< D > +{ + bool operator()(const D&){ return true; } + + virtual std::string className() const { return "edoDummyContinue"; } +}; + +#endif // !_edoContinue_h diff --git a/src/edoDistrib.h b/src/edoDistrib.h new file mode 100644 index 00000000..29ff500d --- /dev/null +++ b/src/edoDistrib.h @@ -0,0 +1,43 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoDistrib_h +#define _edoDistrib_h + +#include + +template < typename EOT > +class edoDistrib : public eoFunctorBase +{ +public: + //! Alias for the type + typedef EOT EOType; + + virtual ~edoDistrib(){} +}; + +#endif // !_edoDistrib_h diff --git a/src/doEDA.h b/src/edoEDA.h similarity index 79% rename from src/doEDA.h rename to src/edoEDA.h index 6873e5da..dde0bb3a 100644 --- a/src/doEDA.h +++ b/src/edoEDA.h @@ -1,26 +1,46 @@ -// (c) Thales group, 2010 /* - Authors: - Johann Dreo - Caner Candan +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: + Johann Dréo + Caner Candan */ -#ifndef _doEDA_h -#define _doEDA_h +#ifndef _edoEDA_h +#define _edoEDA_h #include #include #include -#include "doAlgo.h" -#include "doEstimator.h" -#include "doModifierMass.h" -#include "doSampler.h" -#include "doContinue.h" +#include "edoAlgo.h" +#include "edoEstimator.h" +#include "edoModifierMass.h" +#include "edoSampler.h" +#include "edoContinue.h" template < typename D > -class doEDA : public doAlgo< D > +class edoEDA : public edoAlgo< D > { public: //! Alias for the type EOT @@ -34,7 +54,7 @@ public: public: - //! doEDA constructor + //! edoEDA constructor /*! All the boxes used by a EDASA need to be given. @@ -51,13 +71,13 @@ public: \param initial_temperature The initial temperature. \param replacor Population replacor */ - doEDA (eoSelect< EOT > & selector, - doEstimator< D > & estimator, + edoEDA (eoSelect< EOT > & selector, + edoEstimator< D > & estimator, eoSelectOne< EOT > & selectone, - doModifierMass< D > & modifier, - doSampler< D > & sampler, + edoModifierMass< D > & modifier, + edoSampler< D > & sampler, eoContinue< EOT > & pop_continue, - doContinue< D > & distribution_continue, + edoContinue< D > & distribution_continue, eoEvalFunc < EOT > & evaluation, //moContinuator< moDummyNeighbor > & sa_continue, //moCoolingSchedule & cooling_schedule, @@ -216,22 +236,22 @@ private: eoSelect < EOT > & _selector; //! A EOT estimator. It is going to estimate distribution parameters. - doEstimator< D > & _estimator; + edoEstimator< D > & _estimator; //! SelectOne eoSelectOne< EOT > & _selectone; //! A D modifier - doModifierMass< D > & _modifier; + edoModifierMass< D > & _modifier; //! A D sampler - doSampler< D > & _sampler; + edoSampler< D > & _sampler; //! A EOT population continuator eoContinue < EOT > & _pop_continue; //! A D continuator - doContinue < D > & _distribution_continue; + edoContinue < D > & _distribution_continue; //! A full evaluation function. eoEvalFunc < EOT > & _evaluation; @@ -249,4 +269,4 @@ private: eoReplacement < EOT > & _replacor; }; -#endif // !_doEDA_h +#endif // !_edoEDA_h diff --git a/src/doEDASA.h b/src/edoEDASA.h similarity index 79% rename from src/doEDASA.h rename to src/edoEDASA.h index c6fb4927..b77daa07 100644 --- a/src/doEDASA.h +++ b/src/edoEDASA.h @@ -1,26 +1,46 @@ -// (c) Thales group, 2010 /* - Authors: - Johann Dreo - Caner Candan +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: + Johann Dréo + Caner Candan */ -#ifndef _doEDASA_h -#define _doEDASA_h +#ifndef _edoEDASA_h +#define _edoEDASA_h #include #include #include -#include "doAlgo.h" -#include "doEstimator.h" -#include "doModifierMass.h" -#include "doSampler.h" -#include "doContinue.h" +#include "edoAlgo.h" +#include "edoEstimator.h" +#include "edoModifierMass.h" +#include "edoSampler.h" +#include "edoContinue.h" template < typename D > -class doEDASA : public doAlgo< D > +class edoEDASA : public edoAlgo< D > { public: //! Alias for the type EOT @@ -34,7 +54,7 @@ public: public: - //! doEDASA constructor + //! edoEDASA constructor /*! All the boxes used by a EDASA need to be given. @@ -51,13 +71,13 @@ public: \param initial_temperature The initial temperature. \param replacor Population replacor */ - doEDASA (eoSelect< EOT > & selector, - doEstimator< D > & estimator, + edoEDASA (eoSelect< EOT > & selector, + edoEstimator< D > & estimator, eoSelectOne< EOT > & selectone, - doModifierMass< D > & modifier, - doSampler< D > & sampler, + edoModifierMass< D > & modifier, + edoSampler< D > & sampler, eoContinue< EOT > & pop_continue, - doContinue< D > & distribution_continue, + edoContinue< D > & distribution_continue, eoEvalFunc < EOT > & evaluation, moContinuator< moDummyNeighbor > & sa_continue, moCoolingSchedule & cooling_schedule, @@ -214,22 +234,22 @@ private: eoSelect < EOT > & _selector; //! A EOT estimator. It is going to estimate distribution parameters. - doEstimator< D > & _estimator; + edoEstimator< D > & _estimator; //! SelectOne eoSelectOne< EOT > & _selectone; //! A D modifier - doModifierMass< D > & _modifier; + edoModifierMass< D > & _modifier; //! A D sampler - doSampler< D > & _sampler; + edoSampler< D > & _sampler; //! A EOT population continuator eoContinue < EOT > & _pop_continue; //! A D continuator - doContinue < D > & _distribution_continue; + edoContinue < D > & _distribution_continue; //! A full evaluation function. eoEvalFunc < EOT > & _evaluation; @@ -247,4 +267,4 @@ private: eoReplacement < EOT > & _replacor; }; -#endif // !_doEDASA_h +#endif // !_edoEDASA_h diff --git a/src/edoEstimator.h b/src/edoEstimator.h new file mode 100644 index 00000000..6a2be7a3 --- /dev/null +++ b/src/edoEstimator.h @@ -0,0 +1,43 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoEstimator_h +#define _edoEstimator_h + +#include +#include + +template < typename D > +class edoEstimator : public eoUF< eoPop< typename D::EOType >&, D > +{ +public: + typedef typename D::EOType EOType; + + // virtual D operator() ( eoPop< EOT >& )=0 (provided by eoUF< A1, R >) +}; + +#endif // !_edoEstimator_h diff --git a/src/edoEstimatorNormalMono.h b/src/edoEstimatorNormalMono.h new file mode 100644 index 00000000..1ef61ab7 --- /dev/null +++ b/src/edoEstimatorNormalMono.h @@ -0,0 +1,97 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoEstimatorNormalMono_h +#define _edoEstimatorNormalMono_h + +#include "edoEstimator.h" +#include "edoNormalMono.h" + +template < typename EOT > +class edoEstimatorNormalMono : public edoEstimator< edoNormalMono< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + class Variance + { + public: + Variance() : _sumvar(0){} + + void update(AtomType v) + { + _n++; + + AtomType d = v - _mean; + + _mean += 1 / _n * d; + _sumvar += (_n - 1) / _n * d * d; + } + + AtomType get_mean() const {return _mean;} + AtomType get_var() const {return _sumvar / (_n - 1);} + AtomType get_std() const {return sqrt( get_var() );} + + private: + AtomType _n; + AtomType _mean; + AtomType _sumvar; + }; + +public: + edoNormalMono< EOT > operator()(eoPop& pop) + { + unsigned int popsize = pop.size(); + assert(popsize > 0); + + unsigned int dimsize = pop[0].size(); + assert(dimsize > 0); + + std::vector< Variance > var( dimsize ); + + for (unsigned int i = 0; i < popsize; ++i) + { + for (unsigned int d = 0; d < dimsize; ++d) + { + var[d].update( pop[i][d] ); + } + } + + EOT mean( dimsize ); + EOT variance( dimsize ); + + for (unsigned int d = 0; d < dimsize; ++d) + { + mean[d] = var[d].get_mean(); + variance[d] = var[d].get_var(); + } + + return edoNormalMono< EOT >( mean, variance ); + } +}; + +#endif // !_edoEstimatorNormalMono_h diff --git a/src/doEstimatorNormalMulti.h b/src/edoEstimatorNormalMulti.h similarity index 68% rename from src/doEstimatorNormalMulti.h rename to src/edoEstimatorNormalMulti.h index 286c752f..f06fadd8 100644 --- a/src/doEstimatorNormalMulti.h +++ b/src/edoEstimatorNormalMulti.h @@ -1,18 +1,39 @@ -// (c) Thales group, 2010 /* - Authors: - Johann Dreo - Caner Candan +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: + Johann Dréo + Caner Candan */ -#ifndef _doEstimatorNormalMulti_h -#define _doEstimatorNormalMulti_h -#include "doEstimator.h" -#include "doNormalMulti.h" +#ifndef _edoEstimatorNormalMulti_h +#define _edoEstimatorNormalMulti_h + +#include "edoEstimator.h" +#include "edoNormalMulti.h" template < typename EOT > -class doEstimatorNormalMulti : public doEstimator< doNormalMulti< EOT > > +class edoEstimatorNormalMulti : public edoEstimator< edoNormalMulti< EOT > > { public: class CovMatrix @@ -112,7 +133,7 @@ public: public: typedef typename EOT::AtomType AtomType; - doNormalMulti< EOT > operator()(eoPop& pop) + edoNormalMulti< EOT > operator()(eoPop& pop) { unsigned int popsize = pop.size(); assert(popsize > 0); @@ -122,8 +143,8 @@ public: CovMatrix cov( pop ); - return doNormalMulti< EOT >( cov.get_mean(), cov.get_varcovar() ); + return edoNormalMulti< EOT >( cov.get_mean(), cov.get_varcovar() ); } }; -#endif // !_doEstimatorNormalMulti_h +#endif // !_edoEstimatorNormalMulti_h diff --git a/src/edoEstimatorUniform.h b/src/edoEstimatorUniform.h new file mode 100644 index 00000000..7c5779ff --- /dev/null +++ b/src/edoEstimatorUniform.h @@ -0,0 +1,71 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoEstimatorUniform_h +#define _edoEstimatorUniform_h + +#include "edoEstimator.h" +#include "edoUniform.h" + +// TODO: calcule de la moyenne + covariance dans une classe derivee + +template < typename EOT > +class edoEstimatorUniform : public edoEstimator< edoUniform< EOT > > +{ +public: + edoUniform< EOT > operator()(eoPop& pop) + { + unsigned int size = pop.size(); + + assert(size > 0); + + EOT min = pop[0]; + EOT max = pop[0]; + + for (unsigned int i = 1; i < size; ++i) + { + unsigned int size = pop[i].size(); + + assert(size > 0); + + // possibilité d'utiliser std::min_element et std::max_element mais exige 2 pass au lieu d'1. + + for (unsigned int d = 0; d < size; ++d) + { + if (pop[i][d] < min[d]) + min[d] = pop[i][d]; + + if (pop[i][d] > max[d]) + max[d] = pop[i][d]; + } + } + + return edoUniform< EOT >(min, max); + } +}; + +#endif // !_edoEstimatorUniform_h diff --git a/src/edoModifier.h b/src/edoModifier.h new file mode 100644 index 00000000..5aac0bb5 --- /dev/null +++ b/src/edoModifier.h @@ -0,0 +1,41 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoModifier_h +#define _edoModifier_h + +template < typename D > +class edoModifier +{ +public: + virtual ~edoModifier(){} + + typedef typename D::EOType EOType; +}; + +#endif // !_edoModifier_h + diff --git a/src/edoModifierDispersion.h b/src/edoModifierDispersion.h new file mode 100644 index 00000000..81a6b541 --- /dev/null +++ b/src/edoModifierDispersion.h @@ -0,0 +1,43 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoModifierDispersion_h +#define _edoModifierDispersion_h + +#include +#include + +#include "edoModifier.h" + +template < typename D > +class edoModifierDispersion : public edoModifier< D >, public eoBF< D&, eoPop< typename D::EOType >&, void > +{ +public: + // virtual void operator() ( D&, eoPop< D::EOType >& )=0 (provided by eoBF< A1, A2, R >) +}; + +#endif // !_edoModifierDispersion_h diff --git a/src/edoModifierMass.h b/src/edoModifierMass.h new file mode 100644 index 00000000..fee69d2d --- /dev/null +++ b/src/edoModifierMass.h @@ -0,0 +1,45 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoModifierMass_h +#define _edoModifierMass_h + +#include + +#include "edoModifier.h" + +template < typename D > +class edoModifierMass : public edoModifier< D >, public eoBF< D&, typename D::EOType&, void > +{ +public: + //typedef typename D::EOType::AtomType AtomType; // does not work !!! + + // virtual void operator() ( D&, D::EOType& )=0 (provided by eoBF< A1, A2, R >) +}; + +#endif // !_edoModifierMass_h + diff --git a/src/edoNormalMono.h b/src/edoNormalMono.h new file mode 100644 index 00000000..0850386c --- /dev/null +++ b/src/edoNormalMono.h @@ -0,0 +1,58 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoNormalMono_h +#define _edoNormalMono_h + +#include "edoDistrib.h" + +template < typename EOT > +class edoNormalMono : public edoDistrib< EOT > +{ +public: + edoNormalMono( const EOT& mean, const EOT& variance ) + : _mean(mean), _variance(variance) + { + assert(_mean.size() > 0); + assert(_mean.size() == _variance.size()); + } + + unsigned int size() + { + assert(_mean.size() == _variance.size()); + return _mean.size(); + } + + EOT mean(){return _mean;} + EOT variance(){return _variance;} + +private: + EOT _mean; + EOT _variance; +}; + +#endif // !_edoNormalMono_h diff --git a/src/edoNormalMonoCenter.h b/src/edoNormalMonoCenter.h new file mode 100644 index 00000000..8bd990a7 --- /dev/null +++ b/src/edoNormalMonoCenter.h @@ -0,0 +1,47 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoNormalMonoCenter_h +#define _edoNormalMonoCenter_h + +#include "edoModifierMass.h" +#include "edoNormalMono.h" + +template < typename EOT > +class edoNormalMonoCenter : public edoModifierMass< edoNormalMono< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + void operator() ( edoNormalMono< EOT >& distrib, EOT& mass ) + { + distrib.mean() = mass; + } +}; + +#endif // !_edoNormalMonoCenter_h + diff --git a/src/doNormalMulti.h b/src/edoNormalMulti.h similarity index 86% rename from src/doNormalMulti.h rename to src/edoNormalMulti.h index 1b3e3f16..54f695b1 100644 --- a/src/doNormalMulti.h +++ b/src/edoNormalMulti.h @@ -5,23 +5,23 @@ Caner Candan */ -#ifndef _doNormalMulti_h -#define _doNormalMulti_h +#ifndef _edoNormalMulti_h +#define _edoNormalMulti_h #include #include -#include "doDistrib.h" +#include "edoDistrib.h" namespace ublas = boost::numeric::ublas; template < typename EOT > -class doNormalMulti : public doDistrib< EOT > +class edoNormalMulti : public edoDistrib< EOT > { public: typedef typename EOT::AtomType AtomType; - doNormalMulti + edoNormalMulti ( const ublas::vector< AtomType >& mean, const ublas::symmetric_matrix< AtomType, ublas::lower >& varcovar @@ -48,4 +48,4 @@ private: ublas::symmetric_matrix< AtomType, ublas::lower > _varcovar; }; -#endif // !_doNormalMulti_h +#endif // !_edoNormalMulti_h diff --git a/src/edoNormalMultiCenter.h b/src/edoNormalMultiCenter.h new file mode 100644 index 00000000..e59c5634 --- /dev/null +++ b/src/edoNormalMultiCenter.h @@ -0,0 +1,48 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoNormalMultiCenter_h +#define _edoNormalMultiCenter_h + +#include "edoModifierMass.h" +#include "edoNormalMulti.h" + +template < typename EOT > +class edoNormalMultiCenter : public edoModifierMass< edoNormalMulti< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + void operator() ( edoNormalMulti< EOT >& distrib, EOT& mass ) + { + ublas::vector< AtomType > mean( distrib.size() ); + std::copy( mass.begin(), mass.end(), mean.begin() ); + distrib.mean() = mean; + } +}; + +#endif // !_edoNormalMultiCenter_h diff --git a/src/edoSampler.h b/src/edoSampler.h new file mode 100644 index 00000000..efd77649 --- /dev/null +++ b/src/edoSampler.h @@ -0,0 +1,95 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoSampler_h +#define _edoSampler_h + +#include + +#include "edoBounder.h" +#include "edoBounderNo.h" + +template < typename D > +class edoSampler : public eoUF< D&, typename D::EOType > +{ +public: + typedef typename D::EOType EOType; + + edoSampler(edoBounder< EOType > & bounder) + : /*_dummy_bounder(),*/ _bounder(bounder) + {} + + /* + edoSampler() + : _dummy_bounder(), _bounder( _dummy_bounder ) + {} + */ + + // virtual EOType operator()( D& ) = 0 (provided by eoUF< A1, R >) + + virtual EOType sample( D& ) = 0; + + EOType operator()( D& distrib ) + { + unsigned int size = distrib.size(); + assert(size > 0); + + + //------------------------------------------------------------- + // Point we want to sample to get higher a set of points + // (coordinates in n dimension) + // x = {x1, x2, ..., xn} + // the sample method is implemented in the derivated class + //------------------------------------------------------------- + + EOType solution(sample(distrib)); + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Now we are bounding the distribution thanks to min and max + // parameters. + //------------------------------------------------------------- + + _bounder(solution); + + //------------------------------------------------------------- + + + return solution; + } + +private: + //edoBounderNo _dummy_bounder; + + //! Bounder functor + edoBounder< EOType > & _bounder; + +}; + +#endif // !_edoSampler_h diff --git a/src/edoSamplerNormalMono.h b/src/edoSamplerNormalMono.h new file mode 100644 index 00000000..d628ba2f --- /dev/null +++ b/src/edoSamplerNormalMono.h @@ -0,0 +1,91 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoSamplerNormalMono_h +#define _edoSamplerNormalMono_h + +#include + +#include "edoSampler.h" +#include "edoNormalMono.h" +#include "edoBounder.h" + +/** + * edoSamplerNormalMono + * This class uses the NormalMono distribution parameters (bounds) to return + * a random position used for population sampling. + */ +template < typename EOT > +class edoSamplerNormalMono : public edoSampler< edoNormalMono< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + edoSamplerNormalMono( edoBounder< EOT > & bounder ) + : edoSampler< edoNormalMono< EOT > >( bounder ) + {} + + EOT sample( edoNormalMono< EOT >& distrib ) + { + unsigned int size = distrib.size(); + assert(size > 0); + + + //------------------------------------------------------------- + // Point we want to sample to get higher a set of points + // (coordinates in n dimension) + // x = {x1, x2, ..., xn} + //------------------------------------------------------------- + + EOT solution; + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Sampling all dimensions + //------------------------------------------------------------- + + for (unsigned int i = 0; i < size; ++i) + { + AtomType mean = distrib.mean()[i]; + AtomType variance = distrib.variance()[i]; + AtomType random = rng.normal(mean, variance); + + assert(variance >= 0); + + solution.push_back(random); + } + + //------------------------------------------------------------- + + + return solution; + } +}; + +#endif // !_edoSamplerNormalMono_h diff --git a/src/doSamplerNormalMulti.h b/src/edoSamplerNormalMulti.h similarity index 67% rename from src/doSamplerNormalMulti.h rename to src/edoSamplerNormalMulti.h index 2378634a..c1ce5745 100644 --- a/src/doSamplerNormalMulti.h +++ b/src/edoSamplerNormalMulti.h @@ -1,30 +1,39 @@ -// (c) Thales group, 2010 /* - Authors: - Johann Dreo - Caner Candan +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: + Johann Dréo + Caner Candan */ -#ifndef _doSamplerNormalMulti_h -#define _doSamplerNormalMulti_h +#ifndef _edoSamplerNormalMulti_h +#define _edoSamplerNormalMulti_h -#include -#include +#include #include +#include -#include - -#include "doSampler.h" -#include "doNormalMulti.h" -#include "doBounder.h" - -/** - * doSamplerNormalMulti - * This class uses the Normal distribution parameters (bounds) to return - * a random position used for population sampling. - */ -template < typename EOT > -class doSamplerNormalMulti : public doSampler< doNormalMulti< EOT > > +template< class EOT > +class edoSamplerNormalMulti : public edoSampler< edoNormalMulti< EOT > > { public: typedef typename EOT::AtomType AtomType; @@ -96,11 +105,11 @@ public: ublas::symmetric_matrix< AtomType, ublas::lower > _L; }; - doSamplerNormalMulti( doBounder< EOT > & bounder ) - : doSampler< doNormalMulti< EOT > >( bounder ) + edoSamplerNormalMulti( edoBounder< EOT > & bounder ) + : edoSampler< edoNormalMulti< EOT > >( bounder ) {} - EOT sample( doNormalMulti< EOT >& distrib ) + EOT sample( edoNormalMulti< EOT >& distrib ) { unsigned int size = distrib.size(); @@ -162,4 +171,4 @@ public: } }; -#endif // !_doSamplerNormalMulti_h +#endif // !_edoSamplerNormalMulti_h diff --git a/src/edoSamplerUniform.h b/src/edoSamplerUniform.h new file mode 100644 index 00000000..a7b4c316 --- /dev/null +++ b/src/edoSamplerUniform.h @@ -0,0 +1,96 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoSamplerUniform_h +#define _edoSamplerUniform_h + +#include + +#include "edoSampler.h" +#include "edoUniform.h" + +/** + * edoSamplerUniform + * This class uses the Uniform distribution parameters (bounds) to return + * a random position used for population sampling. + */ +template < typename EOT, class D=edoUniform > // FIXME: D template name is there really used ?!? +class edoSamplerUniform : public edoSampler< edoUniform< EOT > > +{ +public: + typedef D Distrib; + + edoSamplerUniform(edoBounder< EOT > & bounder) + : edoSampler< edoUniform >(bounder) // FIXME: Why D is not used here ? + {} + + /* + edoSamplerUniform() + : edoSampler< edoUniform >() + {} + */ + + EOT sample( edoUniform< EOT >& distrib ) + { + unsigned int size = distrib.size(); + assert(size > 0); + + + //------------------------------------------------------------- + // Point we want to sample to get higher a set of points + // (coordinates in n dimension) + // x = {x1, x2, ..., xn} + //------------------------------------------------------------- + + EOT solution; + + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Sampling all dimensions + //------------------------------------------------------------- + + for (unsigned int i = 0; i < size; ++i) + { + double min = distrib.min()[i]; + double max = distrib.max()[i]; + double random = rng.uniform(min, max); + + assert(min <= random && random <= max); + + solution.push_back(random); + } + + //------------------------------------------------------------- + + + return solution; + } +}; + +#endif // !_edoSamplerUniform_h diff --git a/src/edoUniform.h b/src/edoUniform.h new file mode 100644 index 00000000..93d3b537 --- /dev/null +++ b/src/edoUniform.h @@ -0,0 +1,43 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoUniform_h +#define _edoUniform_h + +#include "edoDistrib.h" +#include "edoVectorBounds.h" + +template < typename EOT > +class edoUniform : public edoDistrib< EOT >, public edoVectorBounds< EOT > +{ +public: + edoUniform(EOT min, EOT max) + : edoVectorBounds< EOT >(min, max) + {} +}; + +#endif // !_edoUniform_h diff --git a/src/edoUniformCenter.h b/src/edoUniformCenter.h new file mode 100644 index 00000000..8284439b --- /dev/null +++ b/src/edoUniformCenter.h @@ -0,0 +1,55 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoUniformCenter_h +#define _edoUniformCenter_h + +#include "edoModifierMass.h" +#include "edoUniform.h" + +template < typename EOT > +class edoUniformCenter : public edoModifierMass< edoUniform< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + void operator() ( edoUniform< EOT >& distrib, EOT& mass ) + { + for (unsigned int i = 0, n = mass.size(); i < n; ++i) + { + AtomType& min = distrib.min()[i]; + AtomType& max = distrib.max()[i]; + + AtomType range = (max - min) / 2; + + min = mass[i] - range; + max = mass[i] + range; + } + } +}; + +#endif // !_edoUniformCenter_h diff --git a/src/edoVectorBounds.h b/src/edoVectorBounds.h new file mode 100644 index 00000000..3c00995f --- /dev/null +++ b/src/edoVectorBounds.h @@ -0,0 +1,56 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoVectorBounds_h +#define _edoVectorBounds_h + +template < typename EOT > +class edoVectorBounds +{ +public: + edoVectorBounds(EOT min, EOT max) + : _min(min), _max(max) + { + assert(_min.size() > 0); + assert(_min.size() == _max.size()); + } + + EOT min(){return _min;} + EOT max(){return _max;} + + unsigned int size() + { + assert(_min.size() == _max.size()); + return _min.size(); + } + +private: + EOT _min; + EOT _max; +}; + +#endif // !_edoVectorBounds_h diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt index 48a65519..490adc1a 100644 --- a/src/utils/CMakeLists.txt +++ b/src/utils/CMakeLists.txt @@ -5,10 +5,10 @@ FILE(GLOB SOURCES *.cpp) SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) -ADD_LIBRARY(doutils ${SOURCES}) -INSTALL(TARGETS doutils ARCHIVE DESTINATION lib COMPONENT libraries) +ADD_LIBRARY(edoutils ${SOURCES}) +INSTALL(TARGETS edoutils ARCHIVE DESTINATION lib COMPONENT libraries) FILE(GLOB HDRS *.h utils) -INSTALL(FILES ${HDRS} DESTINATION include/do/utils COMPONENT headers) +INSTALL(FILES ${HDRS} DESTINATION include/edo/utils COMPONENT headers) ###################################################################################### diff --git a/src/utils/doFileSnapshot.h b/src/utils/doFileSnapshot.h deleted file mode 100644 index ea0ffeb6..00000000 --- a/src/utils/doFileSnapshot.h +++ /dev/null @@ -1,74 +0,0 @@ -//----------------------------------------------------------------------------- -// doFileSnapshot.h -// (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2001 -/* - 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 - Marc.Schoenauer@polytechnique.fr - mkeijzer@dhi.dk - Johann Dreo - Caner Candan - */ -//----------------------------------------------------------------------------- - -#ifndef _doFileSnapshot_h -#define _doFileSnapshot_h - -#include -#include -#include - -#include "utils/eoMonitor.h" - -class doFileSnapshot : public eoMonitor -{ -public: - - doFileSnapshot(std::string dirname, - unsigned int frequency = 1, - std::string filename = "gen", - std::string delim = " ", - unsigned int counter = 0, - bool rmFiles = true, - bool saveFilenames = true); - - virtual ~doFileSnapshot(); - - virtual bool hasChanged() {return _boolChanged;} - virtual std::string getDirName() { return _dirname; } - virtual unsigned int getCounter() { return _counter; } - virtual const std::string baseFileName() { return _filename;} - std::string getFileName() {return _currentFileName;} - - void setCurrentFileName(); - - virtual eoMonitor& operator()(void); - - virtual eoMonitor& operator()(std::ostream& os); - -private : - std::string _dirname; - unsigned int _frequency; - std::string _filename; - std::string _delim; - std::string _currentFileName; - unsigned int _counter; - bool _saveFilenames; - std::ofstream* _descOfFiles; - bool _boolChanged; -}; - -#endif // !_doFileSnapshot diff --git a/src/utils/doHyperVolume.h b/src/utils/doHyperVolume.h deleted file mode 100644 index 2a1be37f..00000000 --- a/src/utils/doHyperVolume.h +++ /dev/null @@ -1,32 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doHyperVolume_h -#define _doHyperVolume_h - -template < typename EOT > -class doHyperVolume -{ -public: - typedef typename EOT::AtomType AtomType; - - doHyperVolume() : _hv(1) {} - - void update(AtomType v) - { - _hv *= ::sqrt( v ); - - assert( _hv <= std::numeric_limits< AtomType >::max() ); - } - - AtomType get_hypervolume() const { return _hv; } - -protected: - AtomType _hv; -}; - -#endif // !_doHyperVolume_h diff --git a/src/utils/doPopStat.h b/src/utils/doPopStat.h deleted file mode 100644 index a3ae4575..00000000 --- a/src/utils/doPopStat.h +++ /dev/null @@ -1,75 +0,0 @@ -// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*- - -//----------------------------------------------------------------------------- -// doPopStat.h -// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001 -/* - 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 - Marc.Schoenauer@polytechnique.fr - mkeijzer@dhi.dk - Johann Dreo - Caner Candan - */ -//----------------------------------------------------------------------------- - -/** WARNING: this file contains 2 classes: - -eoPopString and eoSortedPopString - -that transform the population into a std::string -that can be used to dump to the screen -*/ - -#ifndef _doPopStat_h -#define _doPopStat_h - -#include - - -/** Thanks to MS/VC++, eoParam mechanism is unable to handle std::vectors of stats. -This snippet is a workaround: -This class will "print" a whole population into a std::string - that you can later -send to any stream -This is the plain version - see eoPopString for the Sorted version - -Note: this Stat should probably be used only within eoStdOutMonitor, and not -inside an eoFileMonitor, as the eoState construct will work much better there. -*/ -template -class doPopStat : public eoStat -{ -public: - - using eoStat::value; - - /** default Ctor, void std::string by default, as it appears - on the description line once at beginning of evolution. and - is meaningless there. _howMany defaults to 0, that is, the whole - population*/ - doPopStat(std::string _desc ="") - : eoStat("", _desc) {} - - /** Fills the value() of the eoParam with the dump of the population. */ - void operator()(const eoPop& _pop) - { - std::ostringstream os; - os << _pop; - value() = os.str(); - } -}; - -#endif // !_doPopStat_h diff --git a/src/utils/doStat.h b/src/utils/doStat.h deleted file mode 100644 index 5a6056a9..00000000 --- a/src/utils/doStat.h +++ /dev/null @@ -1,54 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doStat_h -#define _doStat_h - -#include - -template < typename D > -class doStatBase : public eoUF< const D&, void > -{ -public: - // virtual void operator()( const D& ) = 0 (provided by eoUF< A1, R >) - - virtual void lastCall( const D& ) {} - virtual std::string className() const { return "doStatBase"; } -}; - -template < typename D > class doCheckPoint; - -template < typename D, typename T > -class doStat : public eoValueParam< T >, public doStatBase< D > -{ -public: - doStat(T value, std::string description) - : eoValueParam< T >(value, description) - {} - - virtual std::string className(void) const { return "doStat"; } - - doStat< D, T >& addTo(doCheckPoint< D >& cp) { cp.add(*this); return *this; } - - // TODO: doStat< D, T >& addTo(eoMonitor& mon) { mon.add(*this); return *this; } -}; - - -//! A parent class for any kind of distribution to dump parameter to std::string type - -template < typename D > -class doDistribStat : public doStat< D, std::string > -{ -public: - using doStat< D, std::string >::value; - - doDistribStat(std::string desc) - : doStat< D, std::string >("", desc) - {} -}; - -#endif // !_doStat_h diff --git a/src/utils/doStatNormalMono.h b/src/utils/doStatNormalMono.h deleted file mode 100644 index 1eab0d53..00000000 --- a/src/utils/doStatNormalMono.h +++ /dev/null @@ -1,35 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doStatNormalMono_h -#define _doStatNormalMono_h - -#include "doStat.h" -#include "doNormalMono.h" - -template < typename EOT > -class doStatNormalMono : public doDistribStat< doNormalMono< EOT > > -{ -public: - using doDistribStat< doNormalMono< EOT > >::value; - - doStatNormalMono( std::string desc = "" ) - : doDistribStat< doNormalMono< EOT > >( desc ) - {} - - void operator()( const doNormalMono< EOT >& distrib ) - { - value() = "\n# ====== mono normal distribution dump =====\n"; - - std::ostringstream os; - os << distrib.mean() << " " << distrib.variance() << std::endl; - - value() += os.str(); - } -}; - -#endif // !_doStatNormalMono_h diff --git a/src/utils/doStatNormalMulti.h b/src/utils/doStatNormalMulti.h deleted file mode 100644 index d433e40e..00000000 --- a/src/utils/doStatNormalMulti.h +++ /dev/null @@ -1,48 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doStatNormalMulti_h -#define _doStatNormalMulti_h - -#include - -#include "doStat.h" -#include "doNormalMulti.h" - -template < typename EOT > -class doStatNormalMulti : public doDistribStat< doNormalMulti< EOT > > -{ -public: - typedef typename EOT::AtomType AtomType; - - using doDistribStat< doNormalMulti< EOT > >::value; - - doStatNormalMulti( std::string desc = "" ) - : doDistribStat< doNormalMulti< EOT > >( desc ) - {} - - void operator()( const doNormalMulti< EOT >& distrib ) - { - value() = "\n# ====== multi normal distribution dump =====\n"; - - std::ostringstream os; - - os << distrib.mean() << " " << distrib.varcovar() << std::endl; - - // ublas::vector< AtomType > mean = distrib.mean(); - // std::copy(mean.begin(), mean.end(), std::ostream_iterator< std::string >( os, " " )); - - // ublas::symmetric_matrix< AtomType, ublas::lower > varcovar = distrib.varcovar(); - // std::copy(varcovar.begin(), varcovar.end(), std::ostream_iterator< std::string >( os, " " )); - - // os << std::endl; - - value() += os.str(); - } -}; - -#endif // !_doStatNormalMulti_h diff --git a/src/utils/doStatUniform.h b/src/utils/doStatUniform.h deleted file mode 100644 index 808750f7..00000000 --- a/src/utils/doStatUniform.h +++ /dev/null @@ -1,35 +0,0 @@ -// (c) Thales group, 2010 -/* - Authors: - Johann Dreo - Caner Candan -*/ - -#ifndef _doStatUniform_h -#define _doStatUniform_h - -#include "doStat.h" -#include "doUniform.h" - -template < typename EOT > -class doStatUniform : public doDistribStat< doUniform< EOT > > -{ -public: - using doDistribStat< doUniform< EOT > >::value; - - doStatUniform( std::string desc = "" ) - : doDistribStat< doUniform< EOT > >( desc ) - {} - - void operator()( const doUniform< EOT >& distrib ) - { - value() = "\n# ====== uniform distribution dump =====\n"; - - std::ostringstream os; - os << distrib.min() << " " << distrib.max() << std::endl; - - value() += os.str(); - } -}; - -#endif // !_doStatUniform_h diff --git a/src/utils/doCheckPoint.h b/src/utils/edoCheckPoint.h similarity index 57% rename from src/utils/doCheckPoint.h rename to src/utils/edoCheckPoint.h index d424e184..90ba72e6 100644 --- a/src/utils/doCheckPoint.h +++ b/src/utils/edoCheckPoint.h @@ -1,28 +1,48 @@ -// (c) Thales group, 2010 /* - Authors: - Johann Dreo - Caner Candan +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: + Johann Dréo + Caner Candan */ -#ifndef _doCheckPoint_h -#define _doCheckPoint_h +#ifndef _edoCheckPoint_h +#define _edoCheckPoint_h #include #include -#include "doContinue.h" -#include "doStat.h" +#include "edoContinue.h" +#include "edoStat.h" //! eoCheckPoint< EOT > classe fitted to Distribution Object library template < typename D > -class doCheckPoint : public doContinue< D > +class edoCheckPoint : public edoContinue< D > { public: typedef typename D::EOType EOType; - doCheckPoint(doContinue< D >& _cont) + edoCheckPoint(edoContinue< D >& _cont) { _continuators.push_back( &_cont ); } @@ -74,12 +94,12 @@ public: return bContinue; } - void add(doContinue< D >& cont) { _continuators.push_back( &cont ); } - void add(doStatBase< D >& stat) { _stats.push_back( &stat ); } + void add(edoContinue< D >& cont) { _continuators.push_back( &cont ); } + void add(edoStatBase< D >& stat) { _stats.push_back( &stat ); } void add(eoMonitor& mon) { _monitors.push_back( &mon ); } void add(eoUpdater& upd) { _updaters.push_back( &upd ); } - virtual std::string className(void) const { return "doCheckPoint"; } + virtual std::string className(void) const { return "edoCheckPoint"; } std::string allClassNames() const { @@ -117,10 +137,10 @@ public: } private: - std::vector< doContinue< D >* > _continuators; - std::vector< doStatBase< D >* > _stats; + std::vector< edoContinue< D >* > _continuators; + std::vector< edoStatBase< D >* > _stats; std::vector< eoMonitor* > _monitors; std::vector< eoUpdater* > _updaters; }; -#endif // !_doCheckPoint_h +#endif // !_edoCheckPoint_h diff --git a/src/utils/doFileSnapshot.cpp b/src/utils/edoFileSnapshot.cpp similarity index 57% rename from src/utils/doFileSnapshot.cpp rename to src/utils/edoFileSnapshot.cpp index 268cfe82..40f1db68 100644 --- a/src/utils/doFileSnapshot.cpp +++ b/src/utils/edoFileSnapshot.cpp @@ -1,28 +1,33 @@ -//----------------------------------------------------------------------------- -// doFileSnapshot.cpp -// (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2001 /* - 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. +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 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 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. - 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 +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. - Contact: todos@geneura.ugr.es, http://geneura.ugr.es - Marc.Schoenauer@polytechnique.fr - mkeijzer@dhi.dk - Johann Dreo - Caner Candan - */ -//----------------------------------------------------------------------------- +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) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2001 +Copyright (C) 2010 Thales group +*/ +/* +Authors: + todos@geneura.ugr.es + Marc Schoenauer + Martin Keijzer + Johann Dréo + Caner Candan +*/ #include @@ -30,11 +35,11 @@ #include #include -#include +#include #include #include -doFileSnapshot::doFileSnapshot(std::string dirname, +edoFileSnapshot::edoFileSnapshot(std::string dirname, unsigned int frequency /*= 1*/, std::string filename /*= "gen"*/, std::string delim /*= " "*/, @@ -79,19 +84,19 @@ doFileSnapshot::doFileSnapshot(std::string dirname, } -doFileSnapshot::~doFileSnapshot() +edoFileSnapshot::~edoFileSnapshot() { delete _descOfFiles; } -void doFileSnapshot::setCurrentFileName() +void edoFileSnapshot::setCurrentFileName() { std::ostringstream oscount; oscount << _counter; _currentFileName = _dirname + "/" + _filename + oscount.str(); } -eoMonitor& doFileSnapshot::operator()(void) +eoMonitor& edoFileSnapshot::operator()(void) { if (_counter % _frequency) { @@ -107,7 +112,7 @@ eoMonitor& doFileSnapshot::operator()(void) if (!os) { - std::string str = "doFileSnapshot: Could not open " + _currentFileName; + std::string str = "edoFileSnapshot: Could not open " + _currentFileName; throw std::runtime_error(str); } @@ -119,7 +124,7 @@ eoMonitor& doFileSnapshot::operator()(void) return operator()(os); } -eoMonitor& doFileSnapshot::operator()(std::ostream& os) +eoMonitor& edoFileSnapshot::operator()(std::ostream& os) { iterator it = vec.begin(); diff --git a/src/utils/edoFileSnapshot.h b/src/utils/edoFileSnapshot.h new file mode 100644 index 00000000..43e6f088 --- /dev/null +++ b/src/utils/edoFileSnapshot.h @@ -0,0 +1,79 @@ +/* +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) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2001 +Copyright (C) 2010 Thales group +*/ +/* +Authors: + todos@geneura.ugr.es + Marc Schoenauer + Martin Keijzer + Johann Dréo + Caner Candan +*/ + +#ifndef _edoFileSnapshot_h +#define _edoFileSnapshot_h + +#include +#include +#include + +#include "utils/eoMonitor.h" + +class edoFileSnapshot : public eoMonitor +{ +public: + + edoFileSnapshot(std::string dirname, + unsigned int frequency = 1, + std::string filename = "gen", + std::string delim = " ", + unsigned int counter = 0, + bool rmFiles = true, + bool saveFilenames = true); + + virtual ~edoFileSnapshot(); + + virtual bool hasChanged() {return _boolChanged;} + virtual std::string getDirName() { return _dirname; } + virtual unsigned int getCounter() { return _counter; } + virtual const std::string baseFileName() { return _filename;} + std::string getFileName() {return _currentFileName;} + + void setCurrentFileName(); + + virtual eoMonitor& operator()(void); + + virtual eoMonitor& operator()(std::ostream& os); + +private : + std::string _dirname; + unsigned int _frequency; + std::string _filename; + std::string _delim; + std::string _currentFileName; + unsigned int _counter; + bool _saveFilenames; + std::ofstream* _descOfFiles; + bool _boolChanged; +}; + +#endif // !_edoFileSnapshot diff --git a/src/utils/edoHyperVolume.h b/src/utils/edoHyperVolume.h new file mode 100644 index 00000000..a1bf4e59 --- /dev/null +++ b/src/utils/edoHyperVolume.h @@ -0,0 +1,52 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoHyperVolume_h +#define _edoHyperVolume_h + +template < typename EOT > +class edoHyperVolume +{ +public: + typedef typename EOT::AtomType AtomType; + + edoHyperVolume() : _hv(1) {} + + void update(AtomType v) + { + _hv *= ::sqrt( v ); + + assert( _hv <= std::numeric_limits< AtomType >::max() ); + } + + AtomType get_hypervolume() const { return _hv; } + +protected: + AtomType _hv; +}; + +#endif // !_edoHyperVolume_h diff --git a/src/utils/edoPopStat.h b/src/utils/edoPopStat.h new file mode 100644 index 00000000..c8df5f96 --- /dev/null +++ b/src/utils/edoPopStat.h @@ -0,0 +1,70 @@ +/* +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) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2001 +Copyright (C) 2010 Thales group +*/ +/* +Authors: + todos@geneura.ugr.es + Marc Schoenauer + Martin Keijzer + Johann Dréo + Caner Candan +*/ + +#ifndef _edoPopStat_h +#define _edoPopStat_h + +#include + + +/** Thanks to MS/VC++, eoParam mechanism is unable to handle std::vectors of stats. +This snippet is a workaround: +This class will "print" a whole population into a std::string - that you can later +send to any stream +This is the plain version - see eoPopString for the Sorted version + +Note: this Stat should probably be used only within eoStdOutMonitor, and not +inside an eoFileMonitor, as the eoState construct will work much better there. +*/ +template +class edoPopStat : public eoStat +{ +public: + + using eoStat::value; + + /** default Ctor, void std::string by default, as it appears + on the description line once at beginning of evolution. and + is meaningless there. _howMany defaults to 0, that is, the whole + population*/ + edoPopStat(std::string _desc ="") + : eoStat("", _desc) {} + + /** Fills the value() of the eoParam with the dump of the population. */ + void operator()(const eoPop& _pop) + { + std::ostringstream os; + os << _pop; + value() = os.str(); + } +}; + +#endif // !_edoPopStat_h diff --git a/src/utils/edoStat.h b/src/utils/edoStat.h new file mode 100644 index 00000000..24dce9c4 --- /dev/null +++ b/src/utils/edoStat.h @@ -0,0 +1,74 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoStat_h +#define _edoStat_h + +#include + +template < typename D > +class edoStatBase : public eoUF< const D&, void > +{ +public: + // virtual void operator()( const D& ) = 0 (provided by eoUF< A1, R >) + + virtual void lastCall( const D& ) {} + virtual std::string className() const { return "edoStatBase"; } +}; + +template < typename D > class edoCheckPoint; + +template < typename D, typename T > +class edoStat : public eoValueParam< T >, public edoStatBase< D > +{ +public: + edoStat(T value, std::string description) + : eoValueParam< T >(value, description) + {} + + virtual std::string className(void) const { return "edoStat"; } + + edoStat< D, T >& addTo(edoCheckPoint< D >& cp) { cp.add(*this); return *this; } + + // TODO: edoStat< D, T >& addTo(eoMonitor& mon) { mon.add(*this); return *this; } +}; + + +//! A parent class for any kind of distribution to dump parameter to std::string type + +template < typename D > +class edoDistribStat : public edoStat< D, std::string > +{ +public: + using edoStat< D, std::string >::value; + + edoDistribStat(std::string desc) + : edoStat< D, std::string >("", desc) + {} +}; + +#endif // !_edoStat_h diff --git a/src/utils/edoStatNormalMono.h b/src/utils/edoStatNormalMono.h new file mode 100644 index 00000000..8cb28553 --- /dev/null +++ b/src/utils/edoStatNormalMono.h @@ -0,0 +1,55 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoStatNormalMono_h +#define _edoStatNormalMono_h + +#include "edoStat.h" +#include "edoNormalMono.h" + +template < typename EOT > +class edoStatNormalMono : public edoDistribStat< edoNormalMono< EOT > > +{ +public: + using edoDistribStat< edoNormalMono< EOT > >::value; + + edoStatNormalMono( std::string desc = "" ) + : edoDistribStat< edoNormalMono< EOT > >( desc ) + {} + + void operator()( const edoNormalMono< EOT >& distrib ) + { + value() = "\n# ====== mono normal distribution dump =====\n"; + + std::ostringstream os; + os << distrib.mean() << " " << distrib.variance() << std::endl; + + value() += os.str(); + } +}; + +#endif // !_edoStatNormalMono_h diff --git a/src/utils/edoStatNormalMulti.h b/src/utils/edoStatNormalMulti.h new file mode 100644 index 00000000..74adb0ba --- /dev/null +++ b/src/utils/edoStatNormalMulti.h @@ -0,0 +1,68 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoStatNormalMulti_h +#define _edoStatNormalMulti_h + +#include + +#include "edoStat.h" +#include "edoNormalMulti.h" + +template < typename EOT > +class edoStatNormalMulti : public edoDistribStat< edoNormalMulti< EOT > > +{ +public: + typedef typename EOT::AtomType AtomType; + + using edoDistribStat< edoNormalMulti< EOT > >::value; + + edoStatNormalMulti( std::string desc = "" ) + : edoDistribStat< edoNormalMulti< EOT > >( desc ) + {} + + void operator()( const edoNormalMulti< EOT >& distrib ) + { + value() = "\n# ====== multi normal distribution dump =====\n"; + + std::ostringstream os; + + os << distrib.mean() << " " << distrib.varcovar() << std::endl; + + // ublas::vector< AtomType > mean = distrib.mean(); + // std::copy(mean.begin(), mean.end(), std::ostream_iterator< std::string >( os, " " )); + + // ublas::symmetric_matrix< AtomType, ublas::lower > varcovar = distrib.varcovar(); + // std::copy(varcovar.begin(), varcovar.end(), std::ostream_iterator< std::string >( os, " " )); + + // os << std::endl; + + value() += os.str(); + } +}; + +#endif // !_edoStatNormalMulti_h diff --git a/src/utils/edoStatUniform.h b/src/utils/edoStatUniform.h new file mode 100644 index 00000000..ab75e66b --- /dev/null +++ b/src/utils/edoStatUniform.h @@ -0,0 +1,55 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + +#ifndef _edoStatUniform_h +#define _edoStatUniform_h + +#include "edoStat.h" +#include "edoUniform.h" + +template < typename EOT > +class edoStatUniform : public edoDistribStat< edoUniform< EOT > > +{ +public: + using edoDistribStat< edoUniform< EOT > >::value; + + edoStatUniform( std::string desc = "" ) + : edoDistribStat< edoUniform< EOT > >( desc ) + {} + + void operator()( const edoUniform< EOT >& distrib ) + { + value() = "\n# ====== uniform distribution dump =====\n"; + + std::ostringstream os; + os << distrib.min() << " " << distrib.max() << std::endl; + + value() += os.str(); + } +}; + +#endif // !_edoStatUniform_h diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 74ad84ac..aea8eaee 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -33,7 +33,7 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/application/common) SET(SOURCES - t-doEstimatorNormalMulti + t-edoEstimatorNormalMulti t-mean-distance t-bounderno t-uniform @@ -43,8 +43,8 @@ SET(SOURCES FOREACH(current ${SOURCES}) ADD_EXECUTABLE(${current} ${current}.cpp) ADD_TEST(${current} ${current}) - TARGET_LINK_LIBRARIES(${current} do doutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) - INSTALL(TARGETS ${current} RUNTIME DESTINATION share/do/test COMPONENT test) + TARGET_LINK_LIBRARIES(${current} edo edoutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) + INSTALL(TARGETS ${current} RUNTIME DESTINATION share/edo/test COMPONENT test) ENDFOREACH() ###################################################################################### diff --git a/test/t-bounderno.cpp b/test/t-bounderno.cpp index 0898520b..3f7a189b 100644 --- a/test/t-bounderno.cpp +++ b/test/t-bounderno.cpp @@ -1,5 +1,32 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + #include -#include +#include #include "Rosenbrock.h" @@ -7,7 +34,7 @@ typedef eoReal< eoMinimizingFitness > EOT; int main(void) { - doBounderNo< EOT > bounder; + edoBounderNo< EOT > bounder; return 0; } diff --git a/test/t-continue.cpp b/test/t-continue.cpp index 5cae79ff..7206a0c3 100644 --- a/test/t-continue.cpp +++ b/test/t-continue.cpp @@ -1,16 +1,43 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + #include -#include +#include #include "Rosenbrock.h" typedef eoReal< eoMinimizingFitness > EOT; -typedef doUniform< EOT > Distrib; +typedef edoUniform< EOT > Distrib; int main(void) { eoState state; - doContinue< Distrib >* continuator = new doDummyContinue< Distrib >(); + edoContinue< Distrib >* continuator = new edoDummyContinue< Distrib >(); state.storeFunctor(continuator); return 0; diff --git a/test/t-doEstimatorNormalMulti.cpp b/test/t-edoEstimatorNormalMulti.cpp similarity index 78% rename from test/t-doEstimatorNormalMulti.cpp rename to test/t-edoEstimatorNormalMulti.cpp index 71b07e2a..23324eef 100644 --- a/test/t-doEstimatorNormalMulti.cpp +++ b/test/t-edoEstimatorNormalMulti.cpp @@ -1,3 +1,30 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + #include #include @@ -7,13 +34,13 @@ #include #include -#include +#include #include "Rosenbrock.h" #include "Sphere.h" typedef eoReal< eoMinimizingFitness > EOT; -typedef doNormalMulti< EOT > Distrib; +typedef edoNormalMulti< EOT > Distrib; typedef EOT::AtomType AtomType; int main(int ac, char** av) @@ -37,7 +64,7 @@ int main(int ac, char** av) AtomType covar3_value = parser.createParam((AtomType)1.0, "covar3", "Covar value 3", '3', section).value(); std::ostringstream ss; - ss << p_size << "_" << fixed << setprecision(1) + ss << p_size << "_" << std::fixed << std::setprecision(1) << mean_value << "_" << covar1_value << "_" << covar2_value << "_" << covar3_value << "_gen"; std::string gen_filename = ss.str(); @@ -101,18 +128,18 @@ int main(int ac, char** av) // (3a) distribution output preparation //----------------------------------------------------------------------------- - doDummyContinue< Distrib >* distrib_dummy_continue = new doDummyContinue< Distrib >(); + edoDummyContinue< Distrib >* distrib_dummy_continue = new edoDummyContinue< Distrib >(); state.storeFunctor(distrib_dummy_continue); - doCheckPoint< Distrib >* distrib_continue = new doCheckPoint< Distrib >( *distrib_dummy_continue ); + edoCheckPoint< Distrib >* distrib_continue = new edoCheckPoint< Distrib >( *distrib_dummy_continue ); state.storeFunctor(distrib_continue); - doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); + edoDistribStat< Distrib >* distrib_stat = new edoStatNormalMulti< EOT >(); state.storeFunctor(distrib_stat); distrib_continue->add( *distrib_stat ); - doFileSnapshot* distrib_file_snapshot = new doFileSnapshot( "TestResDistrib", 1, gen_filename ); + edoFileSnapshot* distrib_file_snapshot = new edoFileSnapshot( "TestResDistrib", 1, gen_filename ); state.storeFunctor(distrib_file_snapshot); distrib_file_snapshot->add(*distrib_stat); distrib_continue->add(*distrib_file_snapshot); @@ -131,10 +158,10 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- // Prepare bounder class to set bounds of sampling. - // This is used by doSampler. + // This is used by edoSampler. //----------------------------------------------------------------------------- - doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + edoBounder< EOT >* bounder = new edoBounderRng< EOT >(EOT(pop[0].size(), -5), EOT(pop[0].size(), 5), *gen); state.storeFunctor(bounder); @@ -146,7 +173,7 @@ int main(int ac, char** av) // Prepare sampler class with a specific distribution //----------------------------------------------------------------------------- - doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); + edoSampler< Distrib >* sampler = new edoSamplerNormalMulti< EOT >( *bounder ); state.storeFunctor(sampler); //----------------------------------------------------------------------------- @@ -177,11 +204,11 @@ int main(int ac, char** av) eoCheckPoint< EOT >* pop_continue = new eoCheckPoint< EOT >( *pop_cont ); state.storeFunctor(pop_continue); - doPopStat< EOT >* pop_stat = new doPopStat; + edoPopStat< EOT >* pop_stat = new edoPopStat; state.storeFunctor(pop_stat); pop_continue->add(*pop_stat); - doFileSnapshot* pop_file_snapshot = new doFileSnapshot( "TestResPop", 1, gen_filename ); + edoFileSnapshot* pop_file_snapshot = new edoFileSnapshot( "TestResPop", 1, gen_filename ); state.storeFunctor(pop_file_snapshot); pop_file_snapshot->add(*pop_stat); pop_continue->add(*pop_file_snapshot); @@ -195,7 +222,7 @@ int main(int ac, char** av) // (6) estimation phase //----------------------------------------------------------------------------- - doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); + edoEstimator< Distrib >* estimator = new edoEstimatorNormalMulti< EOT >(); state.storeFunctor(estimator); distrib = (*estimator)( pop ); diff --git a/test/t-mean-distance.cpp b/test/t-mean-distance.cpp index 46173883..40a95c99 100644 --- a/test/t-mean-distance.cpp +++ b/test/t-mean-distance.cpp @@ -1,3 +1,30 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + #include #include @@ -11,13 +38,16 @@ #include #include -#include +#include + +#include +#include #include "Rosenbrock.h" #include "Sphere.h" typedef eoReal< eoMinimizingFitness > EOT; -typedef doNormalMulti< EOT > Distrib; +typedef edoNormalMulti< EOT > Distrib; typedef EOT::AtomType AtomType; int main(int ac, char** av) @@ -121,10 +151,10 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- // Prepare bounder class to set bounds of sampling. - // This is used by doSampler. + // This is used by edoSampler. //----------------------------------------------------------------------------- - doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + edoBounder< EOT >* bounder = new edoBounderRng< EOT >(EOT(pop[0].size(), -5), EOT(pop[0].size(), 5), *gen); state.storeFunctor(bounder); @@ -136,7 +166,7 @@ int main(int ac, char** av) // Prepare sampler class with a specific distribution //----------------------------------------------------------------------------- - doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); + edoSampler< Distrib >* sampler = new edoSamplerNormalMulti< EOT >( *bounder ); state.storeFunctor(sampler); //----------------------------------------------------------------------------- @@ -161,7 +191,7 @@ int main(int ac, char** av) // (6) estimation phase //----------------------------------------------------------------------------- - doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); + edoEstimator< Distrib >* estimator = new edoEstimatorNormalMulti< EOT >(); state.storeFunctor(estimator); distrib = (*estimator)( pop ); diff --git a/test/t-uniform.cpp b/test/t-uniform.cpp index d7aedfea..ec01ec7a 100644 --- a/test/t-uniform.cpp +++ b/test/t-uniform.cpp @@ -1,5 +1,32 @@ +/* +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: + Johann Dréo + Caner Candan +*/ + #include -#include +#include #include "Rosenbrock.h" @@ -9,7 +36,7 @@ int main(void) { eoState state; - doUniform< EOT >* distrib = new doUniform< EOT >( EOT(3, -1), EOT(3, 1) ); + edoUniform< EOT >* distrib = new edoUniform< EOT >( EOT(3, -1), EOT(3, 1) ); state.storeFunctor(distrib); return 0; diff --git a/test/test_cov_parameters.py b/test/test_cov_parameters.py index f9199a9e..7a90f167 100755 --- a/test/test_cov_parameters.py +++ b/test/test_cov_parameters.py @@ -2,7 +2,7 @@ PSIZE = 10000 MEAN = 0 -CMD = "./test/t-doEstimatorNormalMulti -P=%s -m=%.1f -1=%.1f -2=%.1f -3=%.1f && ./gplot.py -r TestResPop -p -w 5 -u -g %s -G results_for_test_cov_parameters -f %s_gen1" +CMD = "./test/t-edoEstimatorNormalMulti -P=%s -m=%.1f -1=%.1f -2=%.1f -3=%.1f && ./gplot.py -r TestResPop -p -w 5 -u -g %s -G results_for_test_cov_parameters -f %s_gen1" from os import system from numpy import arange

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z;B`(+xXSgTfhMz_;%El;WTjL5y%q9Qh!5PLeL{XbMg8+NSG;h()@X|Fm9r4}#tbW~ zb`RPR1xPl%=3FWEc9iGr*Lw+Y+hz0>AW4GJYVy43TO>FOfdVDDu5{_dc@bDnet)Q< z!u)TsHxZ@9l(`#r;KyLku@km7erC;l4*th3&BrVJBx-Q}Z!C*Gvqez3ma%ozXXjFJR{ Q1p+=&V)CMYgbf1!7XhnDZU6uP literal 0 HcmV?d00001 From 15ae721ceae936f7a9f2aa0e3473e41f21a4a181 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Thu, 9 Sep 2010 13:55:18 +0200 Subject: [PATCH 60/74] * added some comments --- src/doEstimatorNormalMulti.h | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/src/doEstimatorNormalMulti.h b/src/doEstimatorNormalMulti.h index e1c907b2..098eb8f5 100644 --- a/src/doEstimatorNormalMulti.h +++ b/src/doEstimatorNormalMulti.h @@ -22,14 +22,23 @@ public: CovMatrix( const eoPop< EOT >& pop ) { - unsigned int p_size = pop.size(); // population size + //------------------------------------------------------------- + // Some checks before starting to estimate covar + //------------------------------------------------------------- + unsigned int p_size = pop.size(); // population size assert(p_size > 0); unsigned int s_size = pop[0].size(); // solution size - assert(s_size > 0); + //------------------------------------------------------------- + + + //------------------------------------------------------------- + // Copy the population to an ublas matrix + //------------------------------------------------------------- + ublas::matrix< AtomType > sample( p_size, s_size ); for (unsigned int i = 0; i < p_size; ++i) @@ -40,6 +49,9 @@ public: } } + //------------------------------------------------------------- + + _varcovar.resize(s_size, s_size); @@ -52,6 +64,8 @@ public: ublas::symmetric_matrix< AtomType, ublas::lower > var = ublas::prod( ublas::trans( sample ), sample ); + // Be sure that the symmetric matrix got the good size + assert(var.size1() == s_size); assert(var.size2() == s_size); assert(var.size1() == _varcovar.size1()); @@ -60,6 +74,8 @@ public: //------------------------------------------------------------- + // TODO: to remove the comment below + // for (unsigned int i = 0; i < s_size; ++i) // { // // triangular LOWER matrix, thus j is not going further than i @@ -72,7 +88,7 @@ public: _varcovar = var / p_size; - _mean.resize(s_size); + _mean.resize(s_size); // FIXME: check if it is really used because of the assignation below // unit vector ublas::scalar_vector< AtomType > u( p_size, 1 ); From e70464630e6c8d8820df13a7515fcaea4debb9f8 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 10 Sep 2010 01:09:16 +0200 Subject: [PATCH 61/74] + test/t-doEstimatorNormalMulti --- application/eda_sa/gplot.py | 26 ++-- application/eda_sa/main.cpp | 10 +- src/doEstimatorNormalMulti.h | 2 +- test/CMakeLists.txt | 15 ++- test/t-doEstimatorNormalMulti.cpp | 199 ++++++++++++++++++++++++++++++ 5 files changed, 228 insertions(+), 24 deletions(-) create mode 100644 test/t-doEstimatorNormalMulti.cpp diff --git a/application/eda_sa/gplot.py b/application/eda_sa/gplot.py index 159c1caf..2d012e16 100755 --- a/application/eda_sa/gplot.py +++ b/application/eda_sa/gplot.py @@ -39,6 +39,7 @@ def logger(level_name, filename='plot.log'): def parser(parser=optparse.OptionParser()): parser.add_option('-v', '--verbose', choices=LEVELS.keys(), default='warning', help='set a verbose level') parser.add_option('-f', '--files', help='give some input sample files separated by comma (cf. gen1,gen2,...)', default='') + parser.add_option('-r', '--respop', help='define the population results containing folder', default='./ResPop') parser.add_option('-o', '--output', help='give an output filename for logging', default='plot.log') parser.add_option('-d', '--dimension', help='give a dimension size', default=2) parser.add_option('-m', '--multiplot', action="store_true", help='plot all graphics in one window', dest="multiplot", default=True) @@ -252,6 +253,7 @@ def main(): n = int(options.dimension) w = int(options.windowid) + r = options.respop if options.multiplot: g = Gnuplot.Gnuplot() @@ -270,56 +272,56 @@ def main(): g('set origin 0.0, 0.5') if n >= 1: - plotXPointYFitness('./ResPop', state=gstate, g=g) + plotXPointYFitness(r, state=gstate, g=g) g('set size 0.5, 0.5') g('set origin 0.0, 0.0') if n >= 2: - plotXPointYFitness('./ResPop', '4:1', state=gstate, g=g) + plotXPointYFitness(r, '4:1', state=gstate, g=g) g('set size 0.5, 0.5') g('set origin 0.5, 0.5') if n >= 2: - plotXYPointZFitness('./ResPop', state=gstate, g=g) + plotXYPointZFitness(r, state=gstate, g=g) g('set size 0.5, 0.5') g('set origin 0.5, 0.0') if n >= 2: - plotXYPoint('./ResPop', state=gstate, g=g) + plotXYPoint(r, state=gstate, g=g) elif n >= 3: - plotXYZPoint('./ResPop', state=gstate, g=g) + plotXYZPoint(r, state=gstate, g=g) g('set nomultiplot') else: if n >= 1 and w in [0, 1]: - plotXPointYFitness('./ResPop', state=gstate) + plotXPointYFitness(r, state=gstate) if n >= 2 and w in [0, 2]: - plotXPointYFitness('./ResPop', '4:1', state=gstate) + plotXPointYFitness(r, '4:1', state=gstate) if n >= 2 and w in [0, 3]: - plotXYPointZFitness('./ResPop', state=gstate) + plotXYPointZFitness(r, state=gstate) if n >= 3 and w in [0, 4]: - plotXYZPoint('./ResPop', state=gstate) + plotXYZPoint(r, state=gstate) if n >= 2 and w in [0, 5]: - plotXYPoint('./ResPop', state=gstate) + plotXYPoint(r, state=gstate) # if n >= 1: # plotParams('./ResParams.txt', state=gstate) # if n >= 2: # plot2DRectFromFiles('./ResBounds', state=gstate) - # plotXYPoint('./ResPop', state=gstate) + # plotXYPoint(r, state=gstate) # g = plot2DRectFromFiles('./ResBounds', state=gstate, plot=False) - # plotXYPoint('./ResPop', g=g) + # plotXYPoint(r, g=g) wait(prompt='Press return to end the plot.\n') diff --git a/application/eda_sa/main.cpp b/application/eda_sa/main.cpp index b873c1d6..00cbea6f 100644 --- a/application/eda_sa/main.cpp +++ b/application/eda_sa/main.cpp @@ -154,7 +154,7 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- - // general output + // population output //----------------------------------------------------------------------------- eoCheckPoint< EOT >& pop_continue = do_make_checkpoint(parser, state, eval, eo_continue); @@ -171,14 +171,6 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- - //----------------------------------------------------------------------------- - // population output - //----------------------------------------------------------------------------- - - - //----------------------------------------------------------------------------- - - //----------------------------------------------------------------------------- // distribution output //----------------------------------------------------------------------------- diff --git a/src/doEstimatorNormalMulti.h b/src/doEstimatorNormalMulti.h index e1c907b2..19ad7828 100644 --- a/src/doEstimatorNormalMulti.h +++ b/src/doEstimatorNormalMulti.h @@ -9,7 +9,7 @@ #define _doEstimatorNormalMulti_h #include "doEstimator.h" -#include "doUniform.h" +#include "doNormalMulti.h" template < typename EOT > class doEstimatorNormalMulti : public doEstimator< doNormalMulti< EOT > > diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 674dac15..cf1c0b4f 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -23,13 +23,24 @@ ### 3) Define your targets and link the librairies ###################################################################################### +FIND_PACKAGE(Boost 1.33.0) + +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) + +INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) +LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) + +INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/application/eda_sa) + SET(SOURCES + t-doEstimatorNormalMulti ) FOREACH(current ${SOURCES}) ADD_EXECUTABLE(${current} ${current}.cpp) - TARGET_LINK_LIBRARIES(${current} ${PROJECT_NAME} ${EO_LIBRARIES}) - ADD_CURRENT(${current} ${current}) + ADD_TEST(${current} ${current}) + TARGET_LINK_LIBRARIES(${current} do doutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES}) + INSTALL(TARGETS ${current} RUNTIME DESTINATION share/do/test COMPONENT test) ENDFOREACH() ###################################################################################### diff --git a/test/t-doEstimatorNormalMulti.cpp b/test/t-doEstimatorNormalMulti.cpp new file mode 100644 index 00000000..398cdcbf --- /dev/null +++ b/test/t-doEstimatorNormalMulti.cpp @@ -0,0 +1,199 @@ +#include +#include + +#include +#include + +#include + +#include "Rosenbrock.h" +#include "Sphere.h" + +typedef eoReal< eoMinimizingFitness > EOT; +typedef doNormalMulti< EOT > Distrib; +typedef EOT::AtomType AtomType; + +int main(int ac, char** av) +{ + //----------------------------------------------------- + // (0) parser + eo routines + //----------------------------------------------------- + + eoParserLogger parser(ac, av); + + std::string section("Algorithm parameters"); + + unsigned int p_size = parser.createParam((unsigned int)100, "popSize", "Population Size", 'P', section).value(); // P + + unsigned int s_size = parser.createParam((unsigned int)2, "dimension-size", "Dimension size", 'd', section).value(); // d + + AtomType mean_value = parser.createParam((AtomType)0, "mean", "Mean value", 'm', section).value(); // m + + AtomType covar1_value = parser.createParam((AtomType)1, "covar1", "Covar value 1", '1', section).value(); + AtomType covar2_value = parser.createParam((AtomType)0.5, "covar2", "Covar value 2", '2', section).value(); + AtomType covar3_value = parser.createParam((AtomType)1, "covar3", "Covar value 3", '3', section).value(); + + if (parser.userNeedsHelp()) + { + parser.printHelp(std::cout); + exit(1); + } + + make_verbose(parser); + make_help(parser); + + + assert(p_size > 0); + assert(s_size > 0); + + + eoState state; + + //----------------------------------------------------- + + + //----------------------------------------------------- + // (1) Population init and sampler + //----------------------------------------------------- + + eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5); + state.storeFunctor(gen); + + eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( s_size, *gen ); + state.storeFunctor(init); + + // create an empty pop and let the state handle the memory + // fill population thanks to eoInit instance + eoPop< EOT >& pop = state.takeOwnership( eoPop< EOT >( p_size, *init ) ); + + //----------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (2) distribution initial parameters + //----------------------------------------------------------------------------- + + ublas::vector< AtomType > mean( s_size, mean_value ); + ublas::symmetric_matrix< AtomType, ublas::lower > varcovar( s_size, s_size ); + + varcovar( 0, 0 ) = covar1_value; + varcovar( 0, 1 ) = covar2_value; + varcovar( 1, 1 ) = covar3_value; + + Distrib distrib( mean, varcovar ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (3) distribution output + //----------------------------------------------------------------------------- + + doDummyContinue< Distrib >* dummy_continue = new doDummyContinue< Distrib >(); + state.storeFunctor(dummy_continue); + + doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue ); + state.storeFunctor(distribution_continue); + + doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); + state.storeFunctor(distrib_stat); + + distribution_continue->add( *distrib_stat ); + + eoMonitor* stdout_monitor = new eoStdoutMonitor(); + state.storeFunctor(stdout_monitor); + stdout_monitor->add(*distrib_stat); + distribution_continue->add( *stdout_monitor ); + + (*distribution_continue)( distrib ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare bounder class to set bounds of sampling. + // This is used by doSampler. + //----------------------------------------------------------------------------- + + doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5), + EOT(pop[0].size(), 5), + *gen); + state.storeFunctor(bounder); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // Prepare sampler class with a specific distribution + //----------------------------------------------------------------------------- + + doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder ); + state.storeFunctor(sampler); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (4) sampling phase + //----------------------------------------------------------------------------- + + pop.clear(); + + for (unsigned int i = 0; i < p_size; ++i) + { + EOT candidate_solution = (*sampler)( distrib ); + pop.push_back( candidate_solution ); + } + + // pop.sort(); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (5) population output + //----------------------------------------------------------------------------- + + eoContinue< EOT >* cont = new eoGenContinue< EOT >( 2 ); // never reached fitness + state.storeFunctor(cont); + + eoCheckPoint< EOT >* pop_continue = new eoCheckPoint< EOT >( *cont ); + state.storeFunctor(pop_continue); + + doPopStat< EOT >* popStat = new doPopStat; + state.storeFunctor(popStat); + pop_continue->add(*popStat); + + doFileSnapshot* fileSnapshot = new doFileSnapshot("TestResPop"); + state.storeFunctor(fileSnapshot); + fileSnapshot->add(*popStat); + pop_continue->add(*fileSnapshot); + + (*pop_continue)( pop ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (6) estimation phase + //----------------------------------------------------------------------------- + + doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >(); + state.storeFunctor(estimator); + + distrib = (*estimator)( pop ); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (7) distribution output + //----------------------------------------------------------------------------- + + (*distribution_continue)( distrib ); + + //----------------------------------------------------------------------------- + + + return 0; +} From 7845ba50c7ac4efe55a8d81f1daed65d5e440d43 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 10 Sep 2010 15:48:16 +0200 Subject: [PATCH 62/74] + test_cov_parameters.py: script to execute the estimator testor (t-EstimatorNormalMulti) in using all combinaison parameters values for 2-D cov-matrix --- application/eda_sa/gplot.py | 91 ++++++++++++++++++++++++++----- test/t-doEstimatorNormalMulti.cpp | 58 ++++++++++++-------- test/test_cov_parameters.py | 17 ++++++ 3 files changed, 130 insertions(+), 36 deletions(-) create mode 100755 test/test_cov_parameters.py diff --git a/application/eda_sa/gplot.py b/application/eda_sa/gplot.py index 2d012e16..55e95cb0 100755 --- a/application/eda_sa/gplot.py +++ b/application/eda_sa/gplot.py @@ -44,7 +44,11 @@ def parser(parser=optparse.OptionParser()): parser.add_option('-d', '--dimension', help='give a dimension size', default=2) parser.add_option('-m', '--multiplot', action="store_true", help='plot all graphics in one window', dest="multiplot", default=True) parser.add_option('-p', '--plot', action="store_false", help='plot graphics separetly, one by window', dest="multiplot") - parser.add_option('-w', '--windowid', help='give the window id you want to display, 0 means we display all ones', default=0) + parser.add_option('-w', '--windowid', help='give the window id you want to display, 0 means we display all ones, this option should be combined with -p', default=0) + parser.add_option('-G', '--graphicsdirectory', help='give a directory name for graphics, this option should be combined with -u', default='plot') + parser.add_option('-g', '--graphicsprefixname', help='give a prefix name for graphics, this option should be combined with -u', default='plot') + parser.add_option('-t', '--terminal', action="store_true", help='display graphics on gnuplot windows', dest="terminal", default=True) + parser.add_option('-u', '--png', action="store_false", help='display graphics on png files', dest="terminal") options, args = parser.parse_args() @@ -95,10 +99,26 @@ def getSortedFiles(path): filelist = options.files.split(',') + checkFileErrors(path, filelist) + return filelist +def checkFileErrors(path, filelist): + for filename in filelist: + for line in open('%s/%s' % (path, filename)): + if '-nan' in line: + logging.warning("checkFileErrors: %s/%s file contains bad value, it is going to be skipped" % (path, filename)) + filelist.remove(filename) + break + def plotXPointYFitness(path, fields='3:1', state=None, g=None): - if g == None: g = Gnuplot.Gnuplot() + if g == None: + g = Gnuplot.Gnuplot() + + if not options.terminal: + g('set terminal png') + g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXPointYFitness')) + if state != None: state.append(g) g.title('Fitness observation') @@ -114,12 +134,19 @@ def plotXPointYFitness(path, fields='3:1', state=None, g=None): ) ) - g.plot(*files) + if len(files) > 0: + g.plot(*files) return g def plotXYPointZFitness(path, fields='4:3:1', state=None, g=None): - if g == None: g = Gnuplot.Gnuplot() + if g == None: + g = Gnuplot.Gnuplot() + + if not options.terminal: + g('set terminal png') + g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYPointZFitness')) + if state != None: state.append(g) g.title('Fitness observation in 3-D') @@ -136,12 +163,19 @@ def plotXYPointZFitness(path, fields='4:3:1', state=None, g=None): ) ) - g.splot(*files) + if len(files) > 0: + g.splot(*files) return g def plotXYPoint(path, fields='3:4', state=None, g=None): - if g == None: g = Gnuplot.Gnuplot() + if g == None: + g = Gnuplot.Gnuplot() + + if not options.terminal: + g('set terminal png') + g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYPoint')) + if state != None: state.append(g) g.title('Points observation in 2-D') @@ -157,12 +191,19 @@ def plotXYPoint(path, fields='3:4', state=None, g=None): ) ) - g.plot(*files) + if len(files) > 0: + g.plot(*files) return g def plotXYZPoint(path, fields='3:4:5', state=None, g=None): - if g == None: g = Gnuplot.Gnuplot() + if g == None: + g = Gnuplot.Gnuplot() + + if not options.terminal: + g('set terminal png') + g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYZPoint')) + if state != None: state.append(g) g.title('Points observation in 3-D') @@ -179,12 +220,19 @@ def plotXYZPoint(path, fields='3:4:5', state=None, g=None): ) ) - g.splot(*files) + if len(files) > 0: + g.splot(*files) return g def plotParams(path, field='1', state=None, g=None): - if g == None: g = Gnuplot.Gnuplot() + if g == None: + g = Gnuplot.Gnuplot() + + if not options.terminal: + g('set terminal png') + g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYZPoint')) + if state != None: state.append(g) g.title('Hyper-volume comparaison through all dimensions') @@ -197,7 +245,13 @@ def plotParams(path, field='1', state=None, g=None): return g def plot2DRectFromFiles(path, state=None, g=None, plot=True): - if g == None: g = Gnuplot.Gnuplot() + if g == None: + g = Gnuplot.Gnuplot() + + if not options.terminal: + g('set terminal png') + g('set output \'%s_%s.png\'' % (options.graphicsprefixname, 'plot2DRectFromFiles')) + if state != None: state.append(g) g.title('Rectangle drawing observation') @@ -255,9 +309,19 @@ def main(): w = int(options.windowid) r = options.respop + if not options.terminal: + try: + os.mkdir(options.graphicsdirectory) + except OSError: + pass + if options.multiplot: g = Gnuplot.Gnuplot() + if not options.terminal: + g('set terminal png') + g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'multiplot')) + g('set parametric') g('set nokey') g('set noxtic') @@ -323,9 +387,8 @@ def main(): # g = plot2DRectFromFiles('./ResBounds', state=gstate, plot=False) # plotXYPoint(r, g=g) - wait(prompt='Press return to end the plot.\n') - - pass + if options.terminal: + wait(prompt='Press return to end the plot.\n') # when executed, just run main(): if __name__ == '__main__': diff --git a/test/t-doEstimatorNormalMulti.cpp b/test/t-doEstimatorNormalMulti.cpp index 398cdcbf..2ba3c968 100644 --- a/test/t-doEstimatorNormalMulti.cpp +++ b/test/t-doEstimatorNormalMulti.cpp @@ -1,3 +1,5 @@ +#include + #include #include @@ -33,6 +35,7 @@ int main(int ac, char** av) AtomType covar2_value = parser.createParam((AtomType)0.5, "covar2", "Covar value 2", '2', section).value(); AtomType covar3_value = parser.createParam((AtomType)1, "covar3", "Covar value 3", '3', section).value(); + if (parser.userNeedsHelp()) { parser.printHelp(std::cout); @@ -86,26 +89,37 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- - // (3) distribution output + // (3a) distribution output preparation //----------------------------------------------------------------------------- - doDummyContinue< Distrib >* dummy_continue = new doDummyContinue< Distrib >(); - state.storeFunctor(dummy_continue); + doDummyContinue< Distrib >* distrib_dummy_continue = new doDummyContinue< Distrib >(); + state.storeFunctor(distrib_dummy_continue); - doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue ); - state.storeFunctor(distribution_continue); + doCheckPoint< Distrib >* distrib_continue = new doCheckPoint< Distrib >( *distrib_dummy_continue ); + state.storeFunctor(distrib_continue); doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >(); state.storeFunctor(distrib_stat); - distribution_continue->add( *distrib_stat ); + distrib_continue->add( *distrib_stat ); - eoMonitor* stdout_monitor = new eoStdoutMonitor(); - state.storeFunctor(stdout_monitor); - stdout_monitor->add(*distrib_stat); - distribution_continue->add( *stdout_monitor ); + std::ostringstream ss; + ss << p_size << "_" << mean_value << "_" << covar1_value << "_" + << covar2_value << "_" << covar3_value << "_gen"; - (*distribution_continue)( distrib ); + doFileSnapshot* distrib_file_snapshot = new doFileSnapshot("TestResDistrib", 1, ss.str()); + state.storeFunctor(distrib_file_snapshot); + distrib_file_snapshot->add(*distrib_stat); + distrib_continue->add(*distrib_file_snapshot); + + //----------------------------------------------------------------------------- + + + //----------------------------------------------------------------------------- + // (3b) distribution output + //----------------------------------------------------------------------------- + + (*distrib_continue)( distrib ); //----------------------------------------------------------------------------- @@ -154,20 +168,20 @@ int main(int ac, char** av) // (5) population output //----------------------------------------------------------------------------- - eoContinue< EOT >* cont = new eoGenContinue< EOT >( 2 ); // never reached fitness - state.storeFunctor(cont); + eoContinue< EOT >* pop_cont = new eoGenContinue< EOT >( 2 ); // never reached fitness + state.storeFunctor(pop_cont); - eoCheckPoint< EOT >* pop_continue = new eoCheckPoint< EOT >( *cont ); + eoCheckPoint< EOT >* pop_continue = new eoCheckPoint< EOT >( *pop_cont ); state.storeFunctor(pop_continue); - doPopStat< EOT >* popStat = new doPopStat; - state.storeFunctor(popStat); - pop_continue->add(*popStat); + doPopStat< EOT >* pop_stat = new doPopStat; + state.storeFunctor(pop_stat); + pop_continue->add(*pop_stat); - doFileSnapshot* fileSnapshot = new doFileSnapshot("TestResPop"); - state.storeFunctor(fileSnapshot); - fileSnapshot->add(*popStat); - pop_continue->add(*fileSnapshot); + doFileSnapshot* pop_file_snapshot = new doFileSnapshot("TestResPop"); + state.storeFunctor(pop_file_snapshot); + pop_file_snapshot->add(*pop_stat); + pop_continue->add(*pop_file_snapshot); (*pop_continue)( pop ); @@ -190,7 +204,7 @@ int main(int ac, char** av) // (7) distribution output //----------------------------------------------------------------------------- - (*distribution_continue)( distrib ); + (*distrib_continue)( distrib ); //----------------------------------------------------------------------------- diff --git a/test/test_cov_parameters.py b/test/test_cov_parameters.py new file mode 100755 index 00000000..c73c9fbb --- /dev/null +++ b/test/test_cov_parameters.py @@ -0,0 +1,17 @@ +#!/usr/bin/env python + +PSIZE = 10000 +MEAN = 0 +CMD = "./test/t-doEstimatorNormalMulti -P=%s -m=%.1f -1=%.1f -2=%.1f -3=%.1f && ./gplot.py -r TestResPop -p -w 5 -u -g %s -G results_for_test_cov_parameters" + +from os import system +from numpy import arange + +if __name__ == '__main__': + + for p1 in list(arange(0.1, 1.1, 0.1)): + for p2 in list(arange(-1., 0., 0.1)) + list(arange(0., 1.1, 0.1)): + for p3 in list(arange(0.1, 1.1, 0.1)): + cmd = CMD % ( PSIZE, MEAN, p1, p2, p3, '%d_%.1f_%.1f_%.1f_%.1f' % (PSIZE, MEAN, p1, p2, p3) ) + print cmd + system( cmd ) From b7f8934517d25cc2c8f99052c7c880354b2d6f1b Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 10 Sep 2010 15:52:54 +0200 Subject: [PATCH 63/74] replaced generated prefix name in result folder --- test/t-doEstimatorNormalMulti.cpp | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/test/t-doEstimatorNormalMulti.cpp b/test/t-doEstimatorNormalMulti.cpp index 2ba3c968..661fe474 100644 --- a/test/t-doEstimatorNormalMulti.cpp +++ b/test/t-doEstimatorNormalMulti.cpp @@ -35,6 +35,9 @@ int main(int ac, char** av) AtomType covar2_value = parser.createParam((AtomType)0.5, "covar2", "Covar value 2", '2', section).value(); AtomType covar3_value = parser.createParam((AtomType)1, "covar3", "Covar value 3", '3', section).value(); + std::ostringstream ss; + ss << p_size << "_" << mean_value << "_" << covar1_value << "_" << covar2_value << "_" << covar3_value << "_gen"; + std::string gen_filename = ss.str(); if (parser.userNeedsHelp()) { @@ -103,11 +106,7 @@ int main(int ac, char** av) distrib_continue->add( *distrib_stat ); - std::ostringstream ss; - ss << p_size << "_" << mean_value << "_" << covar1_value << "_" - << covar2_value << "_" << covar3_value << "_gen"; - - doFileSnapshot* distrib_file_snapshot = new doFileSnapshot("TestResDistrib", 1, ss.str()); + doFileSnapshot* distrib_file_snapshot = new doFileSnapshot( "TestResDistrib", 1, gen_filename ); state.storeFunctor(distrib_file_snapshot); distrib_file_snapshot->add(*distrib_stat); distrib_continue->add(*distrib_file_snapshot); @@ -178,7 +177,7 @@ int main(int ac, char** av) state.storeFunctor(pop_stat); pop_continue->add(*pop_stat); - doFileSnapshot* pop_file_snapshot = new doFileSnapshot("TestResPop"); + doFileSnapshot* pop_file_snapshot = new doFileSnapshot( "TestResPop", 1, gen_filename ); state.storeFunctor(pop_file_snapshot); pop_file_snapshot->add(*pop_stat); pop_continue->add(*pop_file_snapshot); From 492451f247561ee977257fd3f52cf0adfc2635c7 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 10 Sep 2010 17:04:02 +0200 Subject: [PATCH 64/74] * bugfixed on test_cov_parameters --- test/t-doEstimatorNormalMulti.cpp | 9 ++++++--- test/test_cov_parameters.py | 5 +++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/test/t-doEstimatorNormalMulti.cpp b/test/t-doEstimatorNormalMulti.cpp index 661fe474..c6fdeabc 100644 --- a/test/t-doEstimatorNormalMulti.cpp +++ b/test/t-doEstimatorNormalMulti.cpp @@ -1,4 +1,5 @@ #include +#include #include #include @@ -31,12 +32,14 @@ int main(int ac, char** av) AtomType mean_value = parser.createParam((AtomType)0, "mean", "Mean value", 'm', section).value(); // m - AtomType covar1_value = parser.createParam((AtomType)1, "covar1", "Covar value 1", '1', section).value(); + AtomType covar1_value = parser.createParam((AtomType)1.0, "covar1", "Covar value 1", '1', section).value(); AtomType covar2_value = parser.createParam((AtomType)0.5, "covar2", "Covar value 2", '2', section).value(); - AtomType covar3_value = parser.createParam((AtomType)1, "covar3", "Covar value 3", '3', section).value(); + AtomType covar3_value = parser.createParam((AtomType)1.0, "covar3", "Covar value 3", '3', section).value(); std::ostringstream ss; - ss << p_size << "_" << mean_value << "_" << covar1_value << "_" << covar2_value << "_" << covar3_value << "_gen"; + ss << p_size << "_" << fixed << setprecision(1) + << mean_value << "_" << covar1_value << "_" << covar2_value << "_" + << covar3_value << "_gen"; std::string gen_filename = ss.str(); if (parser.userNeedsHelp()) diff --git a/test/test_cov_parameters.py b/test/test_cov_parameters.py index c73c9fbb..f9199a9e 100755 --- a/test/test_cov_parameters.py +++ b/test/test_cov_parameters.py @@ -2,7 +2,7 @@ PSIZE = 10000 MEAN = 0 -CMD = "./test/t-doEstimatorNormalMulti -P=%s -m=%.1f -1=%.1f -2=%.1f -3=%.1f && ./gplot.py -r TestResPop -p -w 5 -u -g %s -G results_for_test_cov_parameters" +CMD = "./test/t-doEstimatorNormalMulti -P=%s -m=%.1f -1=%.1f -2=%.1f -3=%.1f && ./gplot.py -r TestResPop -p -w 5 -u -g %s -G results_for_test_cov_parameters -f %s_gen1" from os import system from numpy import arange @@ -12,6 +12,7 @@ if __name__ == '__main__': for p1 in list(arange(0.1, 1.1, 0.1)): for p2 in list(arange(-1., 0., 0.1)) + list(arange(0., 1.1, 0.1)): for p3 in list(arange(0.1, 1.1, 0.1)): - cmd = CMD % ( PSIZE, MEAN, p1, p2, p3, '%d_%.1f_%.1f_%.1f_%.1f' % (PSIZE, MEAN, p1, p2, p3) ) + gen = '%d_%.1f_%.1f_%.1f_%.1f' % (PSIZE, MEAN, p1, p2, p3) + cmd = CMD % ( PSIZE, MEAN, p1, p2, p3, gen, gen ) print cmd system( cmd ) From 0f4e43c0e7c41a1fbac512032af83aa27697cebc Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Fri, 10 Sep 2010 23:21:31 +0200 Subject: [PATCH 65/74] t-doEstimatorNormalMulti: display means and distance --- test/t-doEstimatorNormalMulti.cpp | 26 ++++++++++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/test/t-doEstimatorNormalMulti.cpp b/test/t-doEstimatorNormalMulti.cpp index c6fdeabc..4dbc658c 100644 --- a/test/t-doEstimatorNormalMulti.cpp +++ b/test/t-doEstimatorNormalMulti.cpp @@ -161,8 +161,6 @@ int main(int ac, char** av) pop.push_back( candidate_solution ); } - // pop.sort(); - //----------------------------------------------------------------------------- @@ -211,5 +209,29 @@ int main(int ac, char** av) //----------------------------------------------------------------------------- + //----------------------------------------------------------------------------- + // (8) euclidianne distance estimation + //----------------------------------------------------------------------------- + + ublas::vector< AtomType > new_mean = distrib.mean(); + ublas::symmetric_matrix< AtomType, ublas::lower > new_varcovar = distrib.varcovar(); + + AtomType distance = 0; + + for ( unsigned int d = 0; d < s_size; ++d ) + { + distance += pow( mean[ d ] - new_mean[ d ], 2 ); + } + + distance = sqrt( distance ); + + eo::log << eo::logging + << "mean: " << mean << std::endl + << "new mean: " << new_mean << std::endl + << "distance: " << distance << std::endl + ; + + //----------------------------------------------------------------------------- + return 0; } From 86b7538263c096ae50a3b7cd893ef67930ede2f1 Mon Sep 17 00:00:00 2001 From: Caner Candan Date: Mon, 13 Sep 2010 06:17:44 +0200 Subject: [PATCH 66/74] - screenshots --- screenshots/gplot-eda_sa-P-1000-d-10-a-0.9.png | Bin 78493 -> 0 bytes screenshots/gplot-eda_sa-P-10000-d-10-a-0.1.png | Bin 82590 -> 0 bytes screenshots/gplot-eda_sa-P-10000-d-2-a-0.1.png | Bin 50871 -> 0 bytes 3 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 screenshots/gplot-eda_sa-P-1000-d-10-a-0.9.png delete mode 100644 screenshots/gplot-eda_sa-P-10000-d-10-a-0.1.png delete mode 100644 screenshots/gplot-eda_sa-P-10000-d-2-a-0.1.png diff --git a/screenshots/gplot-eda_sa-P-1000-d-10-a-0.9.png 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