+ lib utils

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)
+
+######################################################################################

src/TODO

@@ -1,2 +1 @@
-* deplacer les ecritures pour gnuplot dans des classes type eoContinue (eoMonitor)
 * integrer ACP

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_

src/doContinue.h

@@ -9,10 +9,9 @@
 #define _doContinue_h
 
 #include <eoFunctor.h>
-#include <eoPop.h>
 #include <eoPersistent.h>
 
-//! 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

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 >

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)
+
+######################################################################################

src/utils/doCheckPoint.h

@@ -0,0 +1,126 @@
+// (c) Thales group, 2010
+/*
+    Authors:
+             Johann Dreo <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+*/
+
+#ifndef _doCheckPoint_h
+#define _doCheckPoint_h
+
+#include <utils/eoUpdater.h>
+#include <utils/eoMonitor.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 );
+	    }
+
+	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 ) )
+		    {
+			bContinue = false;
+		    }
+	    }
+
+	if ( !bContinue )
+	    {
+		for ( unsigned int i = 0, size = _stats.size(); i < size; ++i )
+		    {
+			_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;
+    }
+
+    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"; }
+
+    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 += "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 )
+	    {
+		s += _continuators[i]->className() + "\n";
+	    }
+	s += "\n";
+
+	return s;
+    }
+
+private:
+    std::vector< doContinue< D >* > _continuators;
+    std::vector< doStatBase< D >* > _stats;
+    std::vector< eoMonitor* > _monitors;
+    std::vector< eoUpdater* > _updaters;
+};
+
+#endif // !_doCheckPoint_h

src/utils/doFileSnapshot.cpp

@@ -0,0 +1,121 @@
+//-----------------------------------------------------------------------------
+// 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 <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+ */
+//-----------------------------------------------------------------------------
+
+#include <cstdlib>
+
+#include <iostream>
+#include <fstream>
+#include <stdexcept>
+
+#include <utils/doFileSnapshot.h>
+#include <utils/compatibility.h>
+#include <utils/eoParam.h>
+
+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;
+}

src/utils/doFileSnapshot.h

@@ -0,0 +1,69 @@
+//-----------------------------------------------------------------------------
+// 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 <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+ */
+//-----------------------------------------------------------------------------
+
+#ifndef _doFileSnapshot_h
+#define _doFileSnapshot_h
+
+#include <string>
+#include <fstream>
+#include <stdexcept>
+
+#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);
+
+    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 _boolChanged;
+};
+
+#endif // !_doFileSnapshot

src/utils/doHyperVolume.h

@@ -0,0 +1,32 @@
+// (c) Thales group, 2010
+/*
+    Authors:
+             Johann Dreo <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+*/
+
+#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

src/utils/doPopStat.h

@@ -0,0 +1,75 @@
+// -*- 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 <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+ */
+//-----------------------------------------------------------------------------
+
+/** 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 <utils/eoStat.h>
+
+
+/** 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 EOT>
+class doPopStat : public eoStat<EOT, std::string>
+{
+public:
+
+    using eoStat<EOT, std::string>::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<EOT, std::string>("", _desc) {}
+
+    /** Fills the value() of the eoParam with the dump of the population. */
+    void operator()(const eoPop<EOT>& _pop)
+    {
+	std::ostringstream os;
+	os << _pop;
+	value() = os.str();
+    }
+};
+
+#endif // !_doPopStat_h

src/utils/doStat.h

@@ -0,0 +1,54 @@
+// (c) Thales group, 2010
+/*
+    Authors:
+             Johann Dreo <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+*/
+
+#ifndef _doStat_h
+#define _doStat_h
+
+#include <eoFunctor.h>
+
+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

src/utils/doStatNormalMono.h

@@ -0,0 +1,35 @@
+// (c) Thales group, 2010
+/*
+    Authors:
+             Johann Dreo <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+*/
+
+#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

src/utils/doStatNormalMulti.h

@@ -0,0 +1,48 @@
+// (c) Thales group, 2010
+/*
+    Authors:
+             Johann Dreo <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+*/
+
+#ifndef _doStatNormalMulti_h
+#define _doStatNormalMulti_h
+
+#include <boost/numeric/ublas/io.hpp>
+
+#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

src/utils/doStatUniform.h

@@ -0,0 +1,35 @@
+// (c) Thales group, 2010
+/*
+    Authors:
+             Johann Dreo <johann.dreo@thalesgroup.com>
+             Caner Candan <caner.candan@thalesgroup.com>
+*/
+
+#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