Simplify configuration.
Remove support for (outdated) <strstream>, require <sstream>. Require uint32_t for now, defined in stdint.h according to C99. Some general cleanup and more documentation.
This commit is contained in:
kuepper
parent
abe55a641a
commit
cf2a57dd88
46 changed files with 482 additions and 886 deletions
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@ -245,6 +245,9 @@ namespace mlp {
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load(is);
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}
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/** Virtual destructor */
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virtual ~net() {};
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void load(istream &is) {
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unsigned num_inputs;
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unsigned num_outputs;
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@ -253,7 +256,7 @@ namespace mlp {
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is >> num_inputs >> num_outputs >> num_hidden_layers;
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std::vector<unsigned> layer_sizes;
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for (int i=0; i<num_hidden_layers;i++) {
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for (unsigned i=0; i<num_hidden_layers;i++) {
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unsigned layer_size;
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is >> layer_size;
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layer_sizes.push_back(layer_size);
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@ -28,28 +28,27 @@ AC_PROG_MAKE_SET
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AC_PROG_RANLIB
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AC_CHECK_PROG(DOXYGEN, doxygen, doxygen, true)
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dnl Checks for header files.
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AC_HEADER_STDC
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AC_CHECK_HEADERS(inttypes.h)
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AC_CHECK_HEADERS(limits.h)
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AC_CHECK_HEADERS(values.h)
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AC_CXX_HAVE_NUMERIC_LIMITS
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AC_CXX_HAVE_SSTREAM
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dnl Checks for compiler characteristics.
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AC_CXX_NAMESPACES
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AC_TYPE_SIZE_T
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dnl Checks for header files.
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AC_LANG(C)
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AC_HEADER_STDC
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AC_CHECK_HEADERS(limits.h)
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AC_LANG(C++)
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AC_CHECK_HEADERS(sstream, [], AC_MSG_ERROR([Need sstream C++ include.]))
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AC_CHECK_HEADERS(stdint.h, [], AC_MSG_WARN([Need C99 standard header.]))
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AC_CXX_HAVE_NUMERIC_LIMITS
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dnl Checks for typedefs, structures, and compiler characteristics.
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AC_C_CONST
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AC_C_INLINE
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AC_CHECK_SIZEOF([unsigned long])
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AC_CHECK_TYPES(uint32_t)
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AC_TYPE_SIZE_T
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AC_CHECK_SIZEOF(unsigned long)
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AC_CHECK_TYPES(uint32_t, [], AC_MSG_WARN([Need uint32_t from C99 standard.]))
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dnl Checks for libraries.
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AC_CHECK_LIB(m, cos)
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dnl Checks for library functions.
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AC_CHECK_FUNCS(select)
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dnl create makefiles
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AC_OUTPUT(Makefile \
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@ -12,8 +12,6 @@ libeo_a_SOURCES = eoFunctorStore.cpp \
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eoScalarFitnessAssembled.cpp
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AM_CXXFLAGS = -I$(top_srcdir)/src
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pkginclude_HEADERS = eo \
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EO.h \
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apply.h \
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@ -114,3 +112,6 @@ pkginclude_HEADERS = eo \
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es.h \
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ga.h
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AM_CXXFLAGS = -I$(top_srcdir)/src
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AM_LIBS = -Lutils -leoutil
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@ -3,7 +3,7 @@
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//-----------------------------------------------------------------------------
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// make_checkpoint_pareto.h
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// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2000
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/*
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/*
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This library is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public
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License as published by the Free Software Foundation; either
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@ -32,11 +32,7 @@
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#endif
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#include <stdlib.h>
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#ifdef HAVE_SSTREAM
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#include <sstream>
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#else
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#include <strstream>
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#endif
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#include "EO.h"
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#include "eoParetoFitness.h"
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@ -55,7 +51,7 @@ template <class EOT>
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eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state, eoEvalFuncCounter<EOT>& _eval, eoContinue<EOT>& _continue)
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{
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// first, create a checkpoint from the eoContinue - and store in _state
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eoCheckPoint<EOT> & checkpoint =
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eoCheckPoint<EOT> & checkpoint =
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_state.storeFunctor(new eoCheckPoint<EOT>(_continue));
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/////// get number of obectives from Fitness - not very elegant
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@ -72,9 +68,9 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
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// Create anyway a generation-counter parameter WARNING: not stored anywhere!!!
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eoValueParam<unsigned> *generationCounter = new eoValueParam<unsigned>(0, "Gen.");
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// Create an incrementor (sub-class of eoUpdater).
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eoIncrementor<unsigned> & increment =
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eoIncrementor<unsigned> & increment =
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_state.storeFunctor(new eoIncrementor<unsigned>(generationCounter->value()) );
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// Add it to the checkpoint,
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// Add it to the checkpoint,
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checkpoint.add(increment);
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// dir for DISK output
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@ -109,7 +105,7 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
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unsigned frequency = atoi(fPlot.first.c_str());
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if (frequency) // something to plot
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{
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unsigned nbPlot = fPlot.second.size();
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unsigned nbPlot = fPlot.second.size();
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if ( nbPlot % 2 ) // odd!
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throw std::runtime_error("Odd number of front description in make_checkpoint_pareto");
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@ -124,32 +120,18 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
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unsigned obj2 = atoi(fPlot.second[i+1].c_str());
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eoMOFitnessStat<EOT>* fStat;
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if (!bStat[obj1]) { // not already there: create it
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#ifdef HAVE_SSTREAM
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std::ostringstream os;
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os << "Obj. " << obj1 << std::ends;
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os << "Obj. " << obj1 << std::ends;
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fStat = new eoMOFitnessStat<EOT>(obj1, os.str().c_str());
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#else
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char s[1024];
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std::ostrstream os(s, 1022);
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os << "Obj. " << obj1 << std::ends;
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fStat = new eoMOFitnessStat<EOT>(obj1, s);
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#endif
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_state.storeFunctor(fStat);
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bStat[obj1]=true;
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theStats[obj1]=fStat;
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checkpoint.add(*fStat);
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}
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if (!bStat[obj2]) { // not already there: create it
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#ifdef HAVE_SSTREAM
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std::ostringstream os;
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os << "Obj. " << obj2 << std::ends;
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os << "Obj. " << obj2 << std::ends;
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fStat = new eoMOFitnessStat<EOT>(obj2, os.str().c_str());
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#else
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char s[1024];
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std::ostrstream os2(s, 1022);
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os2 << "Obj. " << obj2 << std::ends;
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fStat = new eoMOFitnessStat<EOT>(obj2, s);
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#endif
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_state.storeFunctor(fStat);
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bStat[obj2]=true;
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theStats[obj2]=fStat;
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@ -157,26 +139,18 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
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}
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// then the fileSnapshots
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#ifdef HAVE_SSTREAM
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std::ostringstream os;
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os << "Front." << obj1 << "." << obj2 << "." << std::ends;
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os << "Front." << obj1 << "." << obj2 << "." << std::ends;
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eoFileSnapshot& snapshot = _state.storeFunctor(
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new eoFileSnapshot(dirName, frequency, os.str().c_str()));
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#else
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char s3[1024];
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std::ostrstream os3(s3, 1022);
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os3 << "Front." << obj1 << "." << obj2 << "." << std::ends;
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eoFileSnapshot & snapshot = _state.storeFunctor(
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new eoFileSnapshot(dirName, frequency, s3 ) );
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#endif
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checkpoint.add(snapshot);
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snapshot.add(*theStats[obj1]);
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snapshot.add(*theStats[obj2]);
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// and create the gnuplotter from the fileSnapshot
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#if !defined(NO_GNUPLOT)
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if (boolGnuplot)
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if (boolGnuplot)
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{
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eoGnuplot1DSnapshot & plotSnapshot = _state.storeFunctor(new
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eoGnuplot1DSnapshot(snapshot));
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@ -204,8 +178,8 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
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// do we want an eoStdoutMonitor?
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bool needStdoutMonitor = printPop ; // only this one at the moment
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// The Stdout monitor will print parameters to the screen ...
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if ( needStdoutMonitor )
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// The Stdout monitor will print parameters to the screen ...
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if ( needStdoutMonitor )
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{
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eoStdoutMonitor & monitor = _state.storeFunctor(new eoStdoutMonitor(false));
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@ -241,12 +215,12 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
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#else
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std::string stmp = dirName + "/generations";
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#endif
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eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
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eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
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_state.storeFunctor(stateSaver1);
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checkpoint.add(*stateSaver1);
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}
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// save state every T seconds
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// save state every T seconds
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eoValueParam<unsigned>& saveTimeIntervalParam = _parser.createParam(unsigned(0), "saveTimeInterval", "Save every T seconds (0 or absent = never)", '\0',"Persistence" );
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if (_parser.isItThere(saveTimeIntervalParam) && saveTimeIntervalParam.value()>0)
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{
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@ -259,7 +233,7 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
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#else
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std::string stmp = dirName + "/time";
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#endif
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eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
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eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
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_state.storeFunctor(stateSaver2);
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checkpoint.add(*stateSaver2);
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}
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@ -28,12 +28,13 @@
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#define eoSequential_h
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/** Contains the following classes:
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* - eoSequentialSelect, returns all individuals one by one,
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* - eoSequentialSelect, returns all individuals one by one,
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* either sorted or shuffled
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* - eoEliteSequentialSelect, returns all indivisuals one by one
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* starting with best, continuing shuffled (see G3 engine)
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*/
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#include <utils/eoData.h>
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#include <utils/eoRNG.h>
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#include <eoSelectOne.h>
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@ -129,7 +130,7 @@ template <class EOT> class eoEliteSequentialSelect: public eoSelectOne<EOT>
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const EOT *ptmp = eoPters[0];
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eoPters[0]=best;
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eoPters[ibest] = ptmp;
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// exit after setting current
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// exit after setting current
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current=0;
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}
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@ -3,7 +3,7 @@
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//-----------------------------------------------------------------------------
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// eoVariableLengthCrossover.h
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// (c) GeNeura Team, 2000 - EEAAX 1999 - Maarten Keijzer 2000
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/*
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/*
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This library is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public
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License as published by the Free Software Foundation; either
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@ -55,7 +55,7 @@ public:
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eoUniformAtomExchange(double _rate=0.5):rate(_rate){}
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/** randomize: fill the mask: the exchange will be simulated first
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* to see if sizes are OK, so it must be repeatable :
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* to see if sizes are OK, so it must be repeatable :
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* the mask has to be a private data, cannot be computed on the fly
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*/
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void randomize(unsigned _size1, unsigned _size2)
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@ -154,17 +154,10 @@ public :
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/** the inherited className */
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virtual std::string className() const
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{
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#ifdef HAVE_SSTREAM
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{
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std::ostringstream os;
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os << "eoVlAtomExchangeQuadOp(" << atomExchange.className() << ")";
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return os.str()
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#else
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char s[1024];
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std::ostrstream os(s, 1022);
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os << "eoVlAtomExchangeQuadOp(" << atomExchange.className() << ")" << std::ends;
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return std::string(s);
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#endif
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os << "eoVlAtomExchangeQuadOp(" << atomExchange.className() << ")";
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return os.str()
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}
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private:
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@ -172,7 +165,7 @@ private:
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eoAtomExchange<AtomType> & atomExchange;
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};
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/** Crossover using an AtomCrossover. Probably irrelevant in Variable Length -
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/** Crossover using an AtomCrossover. Probably irrelevant in Variable Length -
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see eoFlOrBinOp.h and eoFlOrQuadOp.h for the similar Fixed Length operators
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*/
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template <class EOT>
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@ -201,7 +194,7 @@ public :
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}
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virtual std::string className() const
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{
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{
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return "eoInnerExchangeQuadOp(" + op.className() + ")";
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}
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@ -142,16 +142,9 @@ public :
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virtual std::string className() const
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{
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#ifdef HAVE_SSTREAM
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std::ostringstream os;
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os << "eoVlDelMutation("<<chooser.className() << ")";
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return os.str();
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#else
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char s[1024];
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std::ostrstream os(s, 1022);
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os << "eoVlDelMutation(" << chooser.className() << ")" << std::ends;
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return std::string(s);
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#endif
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}
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private:
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@ -1,4 +1,4 @@
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; fill-column: 80 -*-
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//-----------------------------------------------------------------------------
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// eoEsMutationInit.h
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@ -24,37 +24,48 @@
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*/
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//-----------------------------------------------------------------------------
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#ifndef _eoEsInit_h
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#define _eoEsInit_h
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#ifndef _eoEsMutationInit_h
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#define _eoEsMutationInit_h
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#include <utils/eoParser.h>
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/**
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\ingroup EvolutionStrategies
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/** Initialize Mutation operator
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eoESMutationInit. Proxy class that is used for initializing the mutation
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operator. It provides an interface between eoEsMutate and the abstract
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parameterLoader. It also provides the names for the parameters in this
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class as virtual protected member functions.
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@ingroup EvolutionStrategies
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If you have more than a single ES in a project that need different
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names in the configuration files, you might consider overriding this class
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to change the names.
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Proxy class that is used for initializing the mutation operator. It provides an
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interface between eoEsMutate and the abstract parameterLoader. It also provides
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the names for the parameters in this class as virtual protected member
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functions.
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@see eoEsMutate
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If you have more than a single ES in a project that need different names in the
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configuration files, you might consider overriding this class to change the
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names.
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@see eoEsMutate
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*/
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class eoEsMutationInit
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{
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public :
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public :
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/** Constructor
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@param _parser Parser to read parameters from.
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@param _section Parser section for \tau-parameters.
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*/
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eoEsMutationInit(eoParser& _parser,
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std::string _section="ES mutation parameters" ) :
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parser(_parser), repSection(_section),
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TauLclParam(0), TauGlbParam(0), TauBetaParam(0) {}
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parser(_parser), repSection(_section),
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TauLclParam(0), TauGlbParam(0), TauBetaParam(0) {}
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// because we have virtual function - size
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virtual ~eoEsMutationInit(){}
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/** Virtual destructor */
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virtual ~eoEsMutationInit() {}
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/** local \tau */
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double TauLcl(void)
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{
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if (TauLclParam == 0)
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@ -63,10 +74,10 @@ class eoEsMutationInit
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"Local Tau (before normalization)",
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TauLclShort(), section());
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}
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return TauLclParam->value();
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}
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/** global tau */
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double TauGlb(void)
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{
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if (TauGlbParam == 0)
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@ -75,10 +86,10 @@ class eoEsMutationInit
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"Global Tau (before normalization)",
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TauGlbShort(), section());
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}
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return TauGlbParam->value();
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}
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/** correlation's tau */
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double TauBeta(void)
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{
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if (TauBetaParam == 0)
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@ -86,14 +97,12 @@ class eoEsMutationInit
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TauBetaParam = &parser.getORcreateParam(0.0873, TauBetaName(),
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"Beta", TauBetaShort(), section());
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}
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return TauBetaParam->value();
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}
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protected :
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virtual std::string section(void)
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{ return repSection; }
|
||||
virtual std::string section(void) { return repSection; }
|
||||
|
||||
virtual std::string TauLclName(void) const { return "TauLoc"; }
|
||||
virtual char TauLclShort(void) const { return 'l'; }
|
||||
|
|
@ -104,13 +113,13 @@ class eoEsMutationInit
|
|||
virtual std::string TauBetaName(void) const { return "Beta"; }
|
||||
virtual char TauBetaShort(void) const { return 'b'; }
|
||||
|
||||
private :
|
||||
private:
|
||||
|
||||
eoParser& parser;
|
||||
std::string repSection;
|
||||
eoValueParam<double>* TauLclParam;
|
||||
eoValueParam<double>* TauGlbParam;
|
||||
eoValueParam<double>* TauBetaParam;
|
||||
eoParser& parser;
|
||||
std::string repSection;
|
||||
eoValueParam<double>* TauLclParam;
|
||||
eoValueParam<double>* TauGlbParam;
|
||||
eoValueParam<double>* TauBetaParam;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -27,23 +27,13 @@
|
|||
#ifndef _make_genotype_h
|
||||
#define _make_genotype_h
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#ifdef HAVE_SSTREAM
|
||||
#include <sstream>
|
||||
#else
|
||||
#include <strstream>
|
||||
#endif
|
||||
|
||||
#include <iostream>
|
||||
#include <sstream>
|
||||
|
||||
#include "es/eoReal.h"
|
||||
#include "es/eoEsChromInit.h"
|
||||
#include "utils/eoRealVectorBounds.h"
|
||||
// also need the parser and param includes
|
||||
#include "utils/eoParser.h"
|
||||
#include "utils/eoRealVectorBounds.h"
|
||||
#include "utils/eoState.h"
|
||||
|
||||
|
||||
|
|
@ -102,11 +92,7 @@ eoEsChromInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT)
|
|||
to_scale = true;
|
||||
sigmaString.resize(pos);
|
||||
}
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::istringstream is(sigmaString);
|
||||
#else
|
||||
std::istrstream is(sigmaString.c_str());
|
||||
#endif
|
||||
double sigma;
|
||||
is >> sigma;
|
||||
// minimum check
|
||||
|
|
|
|||
|
|
@ -27,33 +27,29 @@
|
|||
#ifndef eoParseTree_h
|
||||
#define eoParseTree_h
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#include <iterator>
|
||||
|
||||
#include <list>
|
||||
|
||||
#include <EO.h>
|
||||
#include <eoInit.h>
|
||||
#include <eoOp.h>
|
||||
#include <gp/parse_tree.h>
|
||||
#include <eoInit.h>
|
||||
|
||||
using namespace gp_parse_tree;
|
||||
|
||||
/**
|
||||
\defgroup ParseTree
|
||||
/** @defgroup ParseTree
|
||||
|
||||
Various functions for tree-based Genetic Programming
|
||||
*/
|
||||
|
||||
/** eoParseTree : implementation of parse-tree for genetic programming
|
||||
\class eoParseTree eoParseTree.h gp/eoParseTree.h
|
||||
\ingroup ParseTree
|
||||
Various functions for tree-based Genetic Programming
|
||||
*/
|
||||
|
||||
|
||||
|
||||
/** Implementation of parse-tree for genetic programming
|
||||
|
||||
@class eoParseTree eoParseTree.h gp/eoParseTree.h
|
||||
|
||||
@ingroup ParseTree
|
||||
*/
|
||||
template <class FType, class Node>
|
||||
class eoParseTree : public EO<FType>, public parse_tree<Node>
|
||||
{
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
/*
|
||||
PyEO
|
||||
|
||||
|
||||
Copyright (C) 2003 Maarten Keijzer
|
||||
|
||||
This program is free software; you can redistribute it and/or modify
|
||||
|
|
@ -18,35 +18,31 @@
|
|||
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
||||
*/
|
||||
|
||||
#include <sstream>
|
||||
|
||||
#include "PyEO.h"
|
||||
#include <eoPop.h>
|
||||
|
||||
#ifdef HAVE_SSTREAM
|
||||
#include <sstream>
|
||||
#else
|
||||
#include <strstream>
|
||||
#endif
|
||||
|
||||
|
||||
using namespace std;
|
||||
//using namespace boost::python;
|
||||
|
||||
// static member, needs to be instantiated somewhere
|
||||
std::vector<int> PyFitness::objective_info;
|
||||
|
||||
|
||||
bool PyFitness::dominates(const PyFitness& oth) const
|
||||
{
|
||||
{
|
||||
bool dom = false;
|
||||
|
||||
for (unsigned i = 0; i < nObjectives(); ++i)
|
||||
{
|
||||
int objective = objective_info[i];
|
||||
|
||||
|
||||
if (objective == 0) // ignore
|
||||
continue;
|
||||
|
||||
bool maxim = objective > 0;
|
||||
|
||||
|
||||
double aval = maxim? (*this)[i] : -(*this)[i];
|
||||
double bval = maxim? oth[i] : -oth[i];
|
||||
|
||||
|
|
@ -103,17 +99,9 @@ struct pyPop_pickle_suite : boost::python::pickle_suite
|
|||
template <class T>
|
||||
boost::python::str to_string(T& _p)
|
||||
{
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::ostringstream os;
|
||||
_p.printOn(os);
|
||||
return boost::python::str(os.str().c_str());
|
||||
#else
|
||||
std::ostrstream os;
|
||||
_p.printOn(os);
|
||||
os << ends;
|
||||
std::string s(os.str());
|
||||
return boost::python::str(s.c_str());
|
||||
#endif
|
||||
}
|
||||
|
||||
void pop_sort(eoPop<PyEO>& pop) { pop.sort(); }
|
||||
|
|
@ -129,11 +117,11 @@ PyEO& pop_getitem(eoPop<PyEO>& pop, boost::python::object key)
|
|||
boost::python::extract<int> x(key);
|
||||
if (!x.check())
|
||||
throw index_error("Slicing not allowed");
|
||||
|
||||
|
||||
int i = x();
|
||||
|
||||
|
||||
if (static_cast<unsigned>(i) >= pop.size())
|
||||
{
|
||||
{
|
||||
throw index_error("Index out of bounds");
|
||||
}
|
||||
return pop[i];
|
||||
|
|
@ -144,14 +132,14 @@ void pop_setitem(eoPop<PyEO>& pop, boost::python::object key, PyEO& value)
|
|||
boost::python::extract<int> x(key);
|
||||
if (!x.check())
|
||||
throw index_error("Slicing not allowed");
|
||||
|
||||
|
||||
int i = x();
|
||||
|
||||
|
||||
if (static_cast<unsigned>(i) >= pop.size())
|
||||
{
|
||||
{
|
||||
throw index_error("Index out of bounds");
|
||||
}
|
||||
|
||||
|
||||
pop[i] = value;
|
||||
}
|
||||
|
||||
|
|
@ -179,7 +167,7 @@ BOOST_PYTHON_MODULE(PyEO)
|
|||
using namespace boost::python;
|
||||
|
||||
boost::python::register_exception_translator<index_error>(&translate_index_error);
|
||||
|
||||
|
||||
boost::python::class_<PyEO>("EO")
|
||||
.add_property("fitness", &PyEO::getFitness, &PyEO::setFitness)
|
||||
.add_property("genome", &PyEO::getGenome, &PyEO::setGenome)
|
||||
|
|
@ -204,8 +192,8 @@ BOOST_PYTHON_MODULE(PyEO)
|
|||
.def_pickle(pyPop_pickle_suite())
|
||||
;
|
||||
|
||||
|
||||
// Other definitions in different compilation units,
|
||||
|
||||
// Other definitions in different compilation units,
|
||||
// this to avoid having g++ to choke on the load
|
||||
random_numbers();
|
||||
valueParam();
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
/*
|
||||
PyEO
|
||||
|
||||
|
||||
Copyright (C) 2003 Maarten Keijzer
|
||||
|
||||
This program is free software; you can redistribute it and/or modify
|
||||
|
|
@ -24,30 +24,22 @@
|
|||
#include <config.h>
|
||||
|
||||
#include <boost/python.hpp>
|
||||
#ifdef HAVE_SSTREAM
|
||||
#include <sstream>
|
||||
#else
|
||||
#include <strstream>
|
||||
#endif
|
||||
/** Implements pickle support for eoPersistent derivatives */
|
||||
|
||||
|
||||
template <class T>
|
||||
struct T_pickle_suite : boost::python::pickle_suite
|
||||
{
|
||||
static
|
||||
static
|
||||
std::string print_to_string(const T& t)
|
||||
{
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::ostringstream os;
|
||||
#else
|
||||
std::ostrstream os;
|
||||
#endif
|
||||
t.printOn(os);
|
||||
os << std::ends;
|
||||
return os.str();
|
||||
}
|
||||
|
||||
|
||||
static
|
||||
boost::python::tuple getstate(const T& t)
|
||||
{
|
||||
|
|
@ -59,11 +51,7 @@ struct T_pickle_suite : boost::python::pickle_suite
|
|||
void setstate(T& t, boost::python::tuple pickled)
|
||||
{
|
||||
std::string s = boost::python::extract<std::string>(pickled[0]);
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::istringstream is(s);
|
||||
#else
|
||||
std::istrstream is(s.c_str(), s.size());
|
||||
#endif
|
||||
t.readFrom(is);
|
||||
}
|
||||
};
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
/*
|
||||
PyEO
|
||||
|
||||
|
||||
Copyright (C) 2003 Maarten Keijzer
|
||||
|
||||
This program is free software; you can redistribute it and/or modify
|
||||
|
|
@ -23,12 +23,7 @@
|
|||
|
||||
using namespace boost::python;
|
||||
|
||||
#ifdef HAVE_SSTREAM
|
||||
#include <sstream>
|
||||
#else
|
||||
#include <strstream>
|
||||
#endif
|
||||
|
||||
#include <boost/python/detail/api_placeholder.hpp>
|
||||
|
||||
using namespace boost::python;
|
||||
|
|
@ -43,11 +38,7 @@ double normal(eoRng& rng) { return rng.normal(); }
|
|||
|
||||
std::string rng_to_string(const eoRng& _rng)
|
||||
{
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::ostringstream os;
|
||||
#else
|
||||
std::ostrstream os;
|
||||
#endif
|
||||
_rng.printOn(os);
|
||||
os << std::ends;
|
||||
return os.str();
|
||||
|
|
@ -56,11 +47,7 @@ std::string rng_to_string(const eoRng& _rng)
|
|||
|
||||
void rng_from_string(eoRng& _rng, std::string s)
|
||||
{
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::istringstream is(s);
|
||||
#else
|
||||
std::istrstream is(s.c_str(), s.size());
|
||||
#endif
|
||||
_rng.readFrom(is);
|
||||
}
|
||||
|
||||
|
|
@ -91,7 +78,7 @@ int spin(eoRng& _rng, numeric::array values, double total)
|
|||
}
|
||||
|
||||
double chance = _rng.uniform() * total;
|
||||
|
||||
|
||||
int i = 0;
|
||||
while (chance >= 0.0)
|
||||
chance -= extract<double>(values[i++]);
|
||||
|
|
@ -115,6 +102,6 @@ void random_numbers()
|
|||
.def("roulette_wheel", spin)
|
||||
.def_pickle(RNG_pickle_suite())
|
||||
;
|
||||
|
||||
|
||||
def("rng", get_rng, return_value_policy<reference_existing_object>());
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,8 +1,9 @@
|
|||
## Makefile.am for eo/src/utils
|
||||
|
||||
lib_LIBRARIES = libeoutils.a
|
||||
lib_LIBRARIES = libeoutils.a
|
||||
|
||||
libeoutils_a_SOURCES = eoParser.cpp \
|
||||
libeoutils_a_SOURCES = eoData.cpp \
|
||||
eoParser.cpp \
|
||||
eoRNG.cpp \
|
||||
eoState.cpp \
|
||||
eoUpdater.cpp \
|
||||
|
|
@ -12,8 +13,6 @@ libeoutils_a_SOURCES = eoParser.cpp \
|
|||
eoIntBounds.cpp \
|
||||
make_help.cpp
|
||||
|
||||
AM_CXXFLAGS = -I$(top_srcdir)/src
|
||||
|
||||
utilsincludedir = $(pkgincludedir)/utils
|
||||
|
||||
utilsinclude_HEADERS = checkpointing \
|
||||
|
|
@ -50,3 +49,6 @@ utilsinclude_HEADERS = checkpointing \
|
|||
pipecom.h \
|
||||
rnd_generators.h \
|
||||
selectors.h
|
||||
|
||||
AM_CXXFLAGS = -I$(top_srcdir)/src
|
||||
|
||||
|
|
|
|||
30
eo/src/utils/eoData.cpp
Normal file
30
eo/src/utils/eoData.cpp
Normal file
|
|
@ -0,0 +1,30 @@
|
|||
// Copyright (C) 2005 Jochen Küpper <jochen@fhi-berlin.mpg.de>
|
||||
//
|
||||
// This program is free software; you can redistribute it and/or modify it under
|
||||
// the terms of the GNU General Public License as published by the Free Software
|
||||
// Foundation; either version 2 of the License, or (at your option) any later
|
||||
// version.
|
||||
//
|
||||
// This program is distributed in the hope that it will be useful, but WITHOUT
|
||||
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
|
||||
// FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
|
||||
//
|
||||
// You should have received a copy of the GNU General Public License along with
|
||||
// this program; see the file License. if not, write to the Free Software
|
||||
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
|
||||
|
||||
|
||||
#include "eoData.h"
|
||||
|
||||
#ifdef HAVE_NUMERIC_LIMITS
|
||||
int MAXINT = numeric_limits<int>::max();
|
||||
#else
|
||||
#include <limits.h>
|
||||
int MAXINT = INT_MAX;
|
||||
#endif
|
||||
|
||||
|
||||
// Local Variables:
|
||||
// c-file-style: "Stroustrup"
|
||||
// fill-column: 80
|
||||
// End:
|
||||
|
|
@ -25,61 +25,31 @@
|
|||
#ifndef EODATA_H
|
||||
#define EODATA_H
|
||||
|
||||
//-----------------------------------------------------------------------------
|
||||
|
||||
#include <vector> // std::vector
|
||||
#include <set> // set
|
||||
#include <string> // std::string
|
||||
|
||||
|
||||
#ifdef _MSC_VER
|
||||
#include <limits> // MAXDOUBLE
|
||||
#define MAXFLOAT numeric_limits<float>::max()
|
||||
#define MINFLOAT numeric_limits<float>::min()
|
||||
#define MAXDOUBLE numeric_limits<double>::max()
|
||||
#define MAXINT numeric_limits<int>::max()
|
||||
#else
|
||||
#include <float.h>
|
||||
#include <limits.h>
|
||||
#ifdef MAXINT
|
||||
#undef MAXINT
|
||||
#endif
|
||||
|
||||
#if !defined(_WIN32) && !defined(__CYGWIN__) && !(defined(__APPLE__) || defined(MACOSX)) && !defined(__FreeBSD__)
|
||||
#include <values.h>
|
||||
#endif
|
||||
|
||||
// for cygwin and windows (and possibly MacOsX)
|
||||
#ifndef MINFLOAT
|
||||
#define MINFLOAT ( (float)1e-127 )
|
||||
#endif
|
||||
#ifndef MAXFLOAT
|
||||
#define MAXFLOAT ( (float)1e127 )
|
||||
#endif
|
||||
#ifndef MAXINT
|
||||
#define MAXINT 2147483647
|
||||
#endif
|
||||
#ifndef MAXDOUBLE
|
||||
#define MAXDOUBLE (double)1.79769313486231570e+308
|
||||
#endif
|
||||
extern int MAXINT;
|
||||
|
||||
#ifndef _MSC_VER
|
||||
#include <math.h>
|
||||
#define _isnan isnan
|
||||
#endif
|
||||
|
||||
|
||||
//-----------------------------------------------------------------------------
|
||||
// some defines to make things easier to get at first sight
|
||||
|
||||
// tuning the amount of output using a boolean argument:
|
||||
// tuning the amount of output using a boolean argument:
|
||||
// true should always mean more output
|
||||
#define eo_verbose true
|
||||
#define eo_no_verbose false
|
||||
// to be used in selection / replacement procedures to indicate whether
|
||||
// to be used in selection / replacement procedures to indicate whether
|
||||
// the argument (rate, a double) shoudl be treated as a rate (number=rate*popSize)
|
||||
// or as an absolute integer (number=rate regardless of popsize).
|
||||
// the default value shoudl ALWAYS be true (eo_as_a_rate).
|
||||
//
|
||||
// this construct is mandatory because in some cases you might not know the
|
||||
// population size that will enter the replacement for instance - so you
|
||||
// this construct is mandatory because in some cases you might not know the
|
||||
// population size that will enter the replacement for instance - so you
|
||||
// cannot simply have a pre-computed (double) rate of 1/popSize
|
||||
#define eo_is_a_rate true
|
||||
#define eo_is_an_integer false
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
//-----------------------------------------------------------------------------
|
||||
// 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
|
||||
|
|
@ -27,10 +27,6 @@
|
|||
#ifndef _eoFileSnapshot_h
|
||||
#define _eoFileSnapshot_h
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#include <string>
|
||||
#include <fstream>
|
||||
#include <utils/eoParam.h>
|
||||
|
|
@ -39,15 +35,15 @@
|
|||
|
||||
|
||||
/**
|
||||
Prints snapshots of fitnesses to a (new) file every N generations
|
||||
Prints snapshots of fitnesses to a (new) file every N generations
|
||||
|
||||
Assumes that the parameters that are passed to the monitor
|
||||
Assumes that the parameters that are passed to the monitor
|
||||
(method add in eoMonitor.h) are eoValueParam<std::vector<double> > of same size.
|
||||
|
||||
A dir is created and one file per snapshot is created there -
|
||||
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
|
||||
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<std::vector<T> >
|
||||
|
|
@ -103,17 +99,9 @@ public :
|
|||
*/
|
||||
void setCurrentFileName()
|
||||
{
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::ostringstream oscount;
|
||||
oscount << counter;
|
||||
#else
|
||||
char buff[255];
|
||||
std::ostrstream oscount(buff, 254);
|
||||
oscount << counter;
|
||||
oscount << std::ends;
|
||||
#endif
|
||||
|
||||
currentFileName = dirname + "/" + filename + oscount.str();
|
||||
std::ostringstream oscount;
|
||||
oscount << counter;
|
||||
currentFileName = dirname + "/" + filename + oscount.str();
|
||||
}
|
||||
|
||||
/** The operator(void): opens the std::ostream and calls the write method
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
//-----------------------------------------------------------------------------
|
||||
// eoGnuplot1DMonitor.h
|
||||
// (c) Marc Schoenauer, 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
|
||||
|
|
@ -26,10 +26,6 @@
|
|||
#ifndef _eoGnuplot_H
|
||||
#define _eoGnuplot_H
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#include <string>
|
||||
|
||||
/**
|
||||
|
|
@ -52,13 +48,13 @@ class eoGnuplot
|
|||
{
|
||||
public:
|
||||
// Ctor
|
||||
eoGnuplot(std::string _title, std::string _extra = std::string("")) :
|
||||
eoGnuplot(std::string _title, std::string _extra = std::string("")) :
|
||||
firstTime(true)
|
||||
{
|
||||
// opens pipe with Gnuplot
|
||||
initGnuPlot(_title, _extra);
|
||||
}
|
||||
|
||||
|
||||
// Dtor
|
||||
virtual ~eoGnuplot() {
|
||||
// close - the gnuplot windows if pipe was correctly opened
|
||||
|
|
@ -109,24 +105,13 @@ private:
|
|||
inline void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
|
||||
/////////////////////////////////////////////////////////
|
||||
{
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::ostringstream os;
|
||||
os << "250x150-0+" << numWindow*170;
|
||||
#else
|
||||
char snum[255];
|
||||
std::ostrstream os(snum, 254);
|
||||
os << "250x150-0+" << numWindow*170 << std::ends;
|
||||
#endif
|
||||
|
||||
numWindow++;
|
||||
char *args[6];
|
||||
args[0] = strdup( "gnuplot" );
|
||||
args[1] = strdup( "-geometry" );
|
||||
#ifdef HAVE_SSTREAM
|
||||
args[2] = strdup( os.str().c_str());
|
||||
#else
|
||||
args[2] = strdup( os.str() );
|
||||
#endif
|
||||
args[3] = strdup( "-title" );
|
||||
args[4] = strdup( _title.c_str() );
|
||||
args[5] = 0;
|
||||
|
|
@ -154,7 +139,7 @@ inline void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
|
|||
* Created......: Mon Mar 13 13:50:11 1995
|
||||
* Description..: Communication par pipe bidirectionnel avec un autre process
|
||||
*
|
||||
* Ident........: $Id: eoGnuplot.h,v 1.12 2005-09-07 17:09:19 maartenkeijzer Exp $
|
||||
* Ident........: $Id: eoGnuplot.h,v 1.13 2005-09-28 21:49:26 kuepper Exp $
|
||||
* ----------------------------------------------------------------------
|
||||
*/
|
||||
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
//-----------------------------------------------------------------------------
|
||||
// eoGnuplot1DMonitor.h
|
||||
// (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2000
|
||||
/*
|
||||
/*
|
||||
This library is free software; you can redistribute it and/or
|
||||
modify it under the terms of the GNU Lesser General Public
|
||||
License as published by the Free Software Foundation; either
|
||||
|
|
@ -28,10 +28,6 @@
|
|||
#ifndef _eoGnuplot1DMonitor_H
|
||||
#define _eoGnuplot1DMonitor_H
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#include <string>
|
||||
|
||||
#include <utils/eoMonitor.h>
|
||||
|
|
@ -93,10 +89,10 @@ inline eoMonitor& eoGnuplot1DMonitor::operator() (void)
|
|||
FirstPlot();
|
||||
firstTime = false;
|
||||
}
|
||||
else
|
||||
else
|
||||
{
|
||||
if( gpCom ) {
|
||||
PipeComSend( gpCom, "replot\n" );
|
||||
PipeComSend( gpCom, "replot\n" );
|
||||
}
|
||||
}
|
||||
return *this;
|
||||
|
|
@ -110,13 +106,7 @@ inline void eoGnuplot1DMonitor::FirstPlot()
|
|||
{
|
||||
throw std::runtime_error("Must have some stats to plot!\n");
|
||||
}
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::ostringstream os;
|
||||
#else
|
||||
char buff[1024];
|
||||
std::ostrstream os(buff, 1024);
|
||||
#endif
|
||||
|
||||
os << "plot";
|
||||
for (unsigned i=1; i<vec.size(); i++) {
|
||||
os << " '" << getFileName().c_str() <<
|
||||
|
|
@ -125,12 +115,7 @@ inline void eoGnuplot1DMonitor::FirstPlot()
|
|||
os << ", ";
|
||||
}
|
||||
os << '\n';
|
||||
#ifdef HAVE_SSTREAM
|
||||
PipeComSend( gpCom, os.str().c_str());
|
||||
#else
|
||||
os << std::ends;
|
||||
PipeComSend( gpCom, buff );
|
||||
#endif
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
//-----------------------------------------------------------------------------
|
||||
// eoGnuplot1DSnapshot.h
|
||||
// (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2000
|
||||
/*
|
||||
/*
|
||||
This library is free software; you can redistribute it and/or
|
||||
modify it under the terms of the GNU Lesser General Public
|
||||
License as published by the Free Software Foundation; either
|
||||
|
|
@ -28,14 +28,8 @@
|
|||
#ifndef _eoGnuplot1DSnapshot_H
|
||||
#define _eoGnuplot1DSnapshot_H
|
||||
|
||||
#ifdef HAVE_CONFIG_H
|
||||
#include <config.h>
|
||||
#endif
|
||||
|
||||
#include <string>
|
||||
#ifdef HAVE_SSTREAM
|
||||
#include <sstream>
|
||||
#endif
|
||||
#include <string>
|
||||
|
||||
#include <utils/eoFileSnapshot.h>
|
||||
#include <utils/eoGnuplot.h>
|
||||
|
|
@ -57,7 +51,7 @@ This class plots through gnuplot the eoStat given as argument
|
|||
|
||||
|
||||
/** eoGnuplot1DSnapshot plots stats through gnuplot
|
||||
* assumes that the same file is re-written every so and so,
|
||||
* assumes that the same file is re-written every so and so,
|
||||
* and plots it from scratch everytime it's called
|
||||
*/
|
||||
class eoGnuplot1DSnapshot: public eoFileSnapshot, public eoGnuplot
|
||||
|
|
@ -107,14 +101,8 @@ class eoGnuplot1DSnapshot: public eoFileSnapshot, public eoGnuplot
|
|||
|
||||
virtual void handleBounds(eoRealVectorBounds & _bounds)
|
||||
{
|
||||
#ifdef HAVE_SSTREAM
|
||||
std::ostringstream os;
|
||||
#else
|
||||
// use strstream and not std::stringstream until strstream is in all distributions
|
||||
char buf[1024];
|
||||
std::ostrstream os(buf, 1023);
|
||||
#endif
|
||||
// std::ostrstream os;
|
||||
// std::ostrstream os;
|
||||
os << "set autoscale\nset yrange [" ;
|
||||
if (_bounds.isMinBounded(0))
|
||||
os << _bounds.minimum(0);
|
||||
|
|
@ -140,25 +128,13 @@ inline eoMonitor& eoGnuplot1DSnapshot::operator() (void)
|
|||
eoFileSnapshot::operator()();
|
||||
|
||||
// sends plot order to gnuplot
|
||||
#ifdef HAVE_SSTREAM
|
||||
//std::string buff; // need local memory
|
||||
std::ostringstream os;
|
||||
#else
|
||||
char buff[1024];
|
||||
std::ostrstream os(buff, 1024);
|
||||
#endif
|
||||
|
||||
os << "set title 'Gen. " << getCounter() << "'; plot '"
|
||||
// mk: had to use getFilename().c_str(), because it seems the string(stream) lib is screwed in gcc3.2
|
||||
<< getFileName().c_str() << "' notitle with points ps " << pointSize;
|
||||
os << std::endl;
|
||||
|
||||
#ifdef HAVE_SSTREAM
|
||||
PipeComSend( gpCom, os.str().c_str());
|
||||
#else
|
||||
os << std::ends;
|
||||
PipeComSend( gpCom, buff );
|
||||
#endif
|
||||
return (*this);
|
||||
}
|
||||
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show more
Reference in a new issue