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Simplify configuration.

Browse source 
Remove support for (outdated) 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 2005-09-28 21:49:26 +00:00
commit cf2a57dd88
46 changed files with 482 additions and 886 deletions
Download patch file Download diff file Expand all files Collapse all files

5
eo/app/gprop/mlp.h
View file

@ -245,6 +245,9 @@ namespace mlp {
load(is);
}
/** Virtual destructor */
virtual ~net() {};
void load(istream &is) {
unsigned num_inputs;
unsigned num_outputs;
@ -253,7 +256,7 @@ namespace mlp {
is >> num_inputs >> num_outputs >> num_hidden_layers;
std::vector<unsigned> layer_sizes;
for (int i=0; i<num_hidden_layers;i++) {
for (unsigned i=0; i<num_hidden_layers;i++) {
unsigned layer_size;
is >> layer_size;
layer_sizes.push_back(layer_size);

27
eo/configure.in
View file

@ -28,28 +28,27 @@ AC_PROG_MAKE_SET
AC_PROG_RANLIB
AC_CHECK_PROG(DOXYGEN, doxygen, doxygen, true)
dnl Checks for header files.
AC_HEADER_STDC
AC_CHECK_HEADERS(inttypes.h)
AC_CHECK_HEADERS(limits.h)
AC_CHECK_HEADERS(values.h)
AC_CXX_HAVE_NUMERIC_LIMITS
AC_CXX_HAVE_SSTREAM
dnl Checks for compiler characteristics.
AC_CXX_NAMESPACES
AC_TYPE_SIZE_T
dnl Checks for header files.
AC_LANG(C)
AC_HEADER_STDC
AC_CHECK_HEADERS(limits.h)
AC_LANG(C++)
AC_CHECK_HEADERS(sstream, [], AC_MSG_ERROR([Need sstream C++ include.]))
AC_CHECK_HEADERS(stdint.h, [], AC_MSG_WARN([Need C99 standard header.]))
AC_CXX_HAVE_NUMERIC_LIMITS
dnl Checks for typedefs, structures, and compiler characteristics.
AC_C_CONST
AC_C_INLINE
AC_CHECK_SIZEOF([unsigned long])
AC_CHECK_TYPES(uint32_t)
AC_TYPE_SIZE_T
AC_CHECK_SIZEOF(unsigned long)
AC_CHECK_TYPES(uint32_t, [], AC_MSG_WARN([Need uint32_t from C99 standard.]))
dnl Checks for libraries.
AC_CHECK_LIB(m, cos)
dnl Checks for library functions.
AC_CHECK_FUNCS(select)
dnl create makefiles
AC_OUTPUT(Makefile \

5
eo/src/Makefile.am
View file

@ -12,8 +12,6 @@ libeo_a_SOURCES = eoFunctorStore.cpp \
eoScalarFitnessAssembled.cpp
AM_CXXFLAGS = -I$(top_srcdir)/src
pkginclude_HEADERS = eo \
EO.h \
apply.h \
@ -114,3 +112,6 @@ pkginclude_HEADERS = eo \
es.h \
ga.h
AM_CXXFLAGS = -I$(top_srcdir)/src
AM_LIBS = -Lutils -leoutil

26
eo/src/do/make_checkpoint_pareto.h
View file

@ -32,11 +32,7 @@
#endif
#include <stdlib.h>
#ifdef HAVE_SSTREAM
#include <sstream>
#else
#include <strstream>
#endif
#include "EO.h"
#include "eoParetoFitness.h"
@ -124,32 +120,18 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
unsigned obj2 = atoi(fPlot.second[i+1].c_str());
eoMOFitnessStat<EOT>* fStat;
if (!bStat[obj1]) { // not already there: create it
#ifdef HAVE_SSTREAM
std::ostringstream os;
os << "Obj. " << obj1 << std::ends;
fStat = new eoMOFitnessStat<EOT>(obj1, os.str().c_str());
#else
char s[1024];
std::ostrstream os(s, 1022);
os << "Obj. " << obj1 << std::ends;
fStat = new eoMOFitnessStat<EOT>(obj1, s);
#endif
_state.storeFunctor(fStat);
bStat[obj1]=true;
theStats[obj1]=fStat;
checkpoint.add(*fStat);
}
if (!bStat[obj2]) { // not already there: create it
#ifdef HAVE_SSTREAM
std::ostringstream os;
os << "Obj. " << obj2 << std::ends;
fStat = new eoMOFitnessStat<EOT>(obj2, os.str().c_str());
#else
char s[1024];
std::ostrstream os2(s, 1022);
os2 << "Obj. " << obj2 << std::ends;
fStat = new eoMOFitnessStat<EOT>(obj2, s);
#endif
_state.storeFunctor(fStat);
bStat[obj2]=true;
theStats[obj2]=fStat;
@ -157,18 +139,10 @@ eoCheckPoint<EOT>& do_make_checkpoint_pareto(eoParser& _parser, eoState& _state,
}
// then the fileSnapshots
#ifdef HAVE_SSTREAM
std::ostringstream os;
os << "Front." << obj1 << "." << obj2 << "." << std::ends;
eoFileSnapshot& snapshot = _state.storeFunctor(
new eoFileSnapshot(dirName, frequency, os.str().c_str()));
#else
char s3[1024];
std::ostrstream os3(s3, 1022);
os3 << "Front." << obj1 << "." << obj2 << "." << std::ends;
eoFileSnapshot & snapshot = _state.storeFunctor(
new eoFileSnapshot(dirName, frequency, s3 ) );
#endif
checkpoint.add(snapshot);
snapshot.add(*theStats[obj1]);

1
eo/src/eoSequentialSelect.h
View file

@ -34,6 +34,7 @@
* starting with best, continuing shuffled (see G3 engine)
*/
#include <utils/eoData.h>
#include <utils/eoRNG.h>
#include <eoSelectOne.h>

11
eo/src/eoVariableLengthCrossover.h
View file

@ -155,16 +155,9 @@ public :
/** the inherited className */
virtual std::string className() const
{
#ifdef HAVE_SSTREAM
std::ostringstream os;
os << "eoVlAtomExchangeQuadOp(" << atomExchange.className() << ")";
return os.str()
#else
char s[1024];
std::ostrstream os(s, 1022);
os << "eoVlAtomExchangeQuadOp(" << atomExchange.className() << ")" << std::ends;
return std::string(s);
#endif
os << "eoVlAtomExchangeQuadOp(" << atomExchange.className() << ")";
return os.str()
}
private:

7
eo/src/eoVariableLengthMutation.h
View file

@ -142,16 +142,9 @@ public :
virtual std::string className() const
{
#ifdef HAVE_SSTREAM
std::ostringstream os;
os << "eoVlDelMutation("<<chooser.className() << ")";
return os.str();
#else
char s[1024];
std::ostrstream os(s, 1022);
os << "eoVlDelMutation(" << chooser.className() << ")" << std::ends;
return std::string(s);
#endif
}
private:

67
eo/src/es/eoEsMutationInit.h
View file

@ -1,4 +1,4 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; fill-column: 80 -*-
//-----------------------------------------------------------------------------
// eoEsMutationInit.h
@ -24,37 +24,48 @@
*/
//-----------------------------------------------------------------------------
#ifndef _eoEsInit_h
#define _eoEsInit_h
#ifndef _eoEsMutationInit_h
#define _eoEsMutationInit_h
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <utils/eoParser.h>
/**
\ingroup EvolutionStrategies
/** Initialize Mutation operator
eoESMutationInit. Proxy class that is used for initializing the mutation
operator. It provides an interface between eoEsMutate and the abstract
parameterLoader. It also provides the names for the parameters in this
class as virtual protected member functions.
@ingroup EvolutionStrategies
If you have more than a single ES in a project that need different
names in the configuration files, you might consider overriding this class
to change the names.
Proxy class that is used for initializing the mutation operator. It provides an
interface between eoEsMutate and the abstract parameterLoader. It also provides
the names for the parameters in this class as virtual protected member
functions.
@see eoEsMutate
If you have more than a single ES in a project that need different names in the
configuration files, you might consider overriding this class to change the
names.
@see eoEsMutate
*/
class eoEsMutationInit
{
public :
public :
/** Constructor
@param _parser Parser to read parameters from.
@param _section Parser section for \tau-parameters.
*/
eoEsMutationInit(eoParser& _parser,
std::string _section="ES mutation parameters" ) :
parser(_parser), repSection(_section),
TauLclParam(0), TauGlbParam(0), TauBetaParam(0) {}
parser(_parser), repSection(_section),
TauLclParam(0), TauGlbParam(0), TauBetaParam(0) {}
// because we have virtual function - size
virtual ~eoEsMutationInit(){}
/** Virtual destructor */
virtual ~eoEsMutationInit() {}
/** local \tau */
double TauLcl(void)
{
if (TauLclParam == 0)
@ -63,10 +74,10 @@ class eoEsMutationInit
"Local Tau (before normalization)",
TauLclShort(), section());
}
return TauLclParam->value();
}
/** global tau */
double TauGlb(void)
{
if (TauGlbParam == 0)
@ -75,10 +86,10 @@ class eoEsMutationInit
"Global Tau (before normalization)",
TauGlbShort(), section());
}
return TauGlbParam->value();
}
/** correlation's tau */
double TauBeta(void)
{
if (TauBetaParam == 0)
@ -86,14 +97,12 @@ class eoEsMutationInit
TauBetaParam = &parser.getORcreateParam(0.0873, TauBetaName(),
"Beta", TauBetaShort(), section());
}
return TauBetaParam->value();
}
protected :
virtual std::string section(void)
{ 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

18
eo/src/es/make_genotype_real.h
View file

@ -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

24
eo/src/gp/eoParseTree.h
View file

@ -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>
{

16
eo/src/pyeo/PyEO.cpp
View file

@ -18,15 +18,11 @@
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;
@ -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(); }

12
eo/src/pyeo/pickle.h
View file

@ -24,11 +24,7 @@
#include <config.h>
#include <boost/python.hpp>
#ifdef HAVE_SSTREAM
#include <sstream>
#else
#include <strstream>
#endif
/** Implements pickle support for eoPersistent derivatives */
@ -38,11 +34,7 @@ struct T_pickle_suite : boost::python::pickle_suite
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();
@ -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);
}
};

13
eo/src/pyeo/random_numbers.cpp
View file

@ -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);
}

10
eo/src/utils/Makefile.am
View file

@ -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
View 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:

38
eo/src/utils/eoData.h
View file

@ -25,47 +25,17 @@
#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>
#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
#ifdef MAXINT
#undef MAXINT
#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

18
eo/src/utils/eoFileSnapshot.h
View file

@ -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>
@ -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

17
eo/src/utils/eoGnuplot.h
View file

@ -26,10 +26,6 @@
#ifndef _eoGnuplot_H
#define _eoGnuplot_H
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <string>
/**
@ -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 $
* ----------------------------------------------------------------------
*/

15
eo/src/utils/eoGnuplot1DMonitor.h
View file

@ -28,10 +28,6 @@
#ifndef _eoGnuplot1DMonitor_H
#define _eoGnuplot1DMonitor_H
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <string>
#include <utils/eoMonitor.h>
@ -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

26
eo/src/utils/eoGnuplot1DSnapshot.h
View file

@ -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>
@ -107,13 +101,7 @@ 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;
os << "set autoscale\nset yrange [" ;
if (_bounds.isMinBounded(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);
}

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