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move paradiseo/eo to deprecated/ before merge with eodev

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Johann Dreo 2012-10-05 15:12:12 +02:00
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Pedro Angel Castillo Valdivieso
Juan Julian Merelo Guervos
Victor Manuel Rivas Santos
Gustavo Romero Lopez
Maarten Keijzer
Marc Schoenauer
Jeroen Eggermont
Jochen K<>pper
Thomas Legrand
Clive Canape
Johann Dréo <johann.dreo@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>

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# the user should choose the build type on windows environments,excepted under cygwin (default=none)
#SET(CMAKE_DEFAULT_BUILD_TYPE "Release" CACHE STRING "Variable that stores the default CMake build type" FORCE)
#SET(CMAKE_BUILD_TYPE Debug) # allows to enable assert calls and -g flag
FIND_PROGRAM(MEMORYCHECK_COMMAND
NAMES purify valgrind
PATHS
"/usr/local/bin /usr/bin [HKEY_LOCAL_MACHINE\\SOFTWARE\\Rational Software\\Purify\\Setup;InstallFolder]"
DOC "Path to the memory checking command, used for memory error detection.")
IF(NOT CMAKE_BUILD_TYPE)
SET( CMAKE_BUILD_TYPE
${CMAKE_DEFAULT_BUILD_TYPE} CACHE STRING
"Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel."
FORCE)
ENDIF(NOT CMAKE_BUILD_TYPE)
IF(WIN32 AND NOT CYGWIN)
IF(CMAKE_CXX_COMPILER MATCHES cl)
IF(NOT WITH_SHARED_LIBS)
IF(CMAKE_GENERATOR STREQUAL "Visual Studio 8 2005" OR CMAKE_GENERATOR STREQUAL "Visual Studio 9 2008")
SET(CMAKE_CXX_FLAGS "/nologo /Gy")
SET(CMAKE_CXX_FLAGS_DEBUG "/W3 /MTd /Z7 /Od")
SET(CMAKE_CXX_FLAGS_RELEASE "/w /MT /O2 /wd4530")
SET(CMAKE_CXX_FLAGS_MINSIZEREL "/MT /O2")
SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "/MTd /Z7 /Od")
SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /SUBSYSTEM:CONSOLE")
ENDIF(CMAKE_GENERATOR STREQUAL "Visual Studio 8 2005" OR CMAKE_GENERATOR STREQUAL "Visual Studio 9 2008")
ENDIF(NOT WITH_SHARED_LIBS)
ENDIF(CMAKE_CXX_COMPILER MATCHES cl)
ELSE(WIN32 AND NOT CYGWIN)
IF(CMAKE_COMPILER_IS_GNUCXX)
# SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g -fprofile-arcs -ftest-coverage -Wall -Wextra -Wno-unused-parameter")
SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g -Wall -Wextra -Wno-unused-parameter -Wunknown-pragmas")
SET(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -Wunknown-pragmas")
SET(CMAKE_CXX_FLAGS_MINSIZEREL "${CMAKE_CXX_FLAGS_MINSIZEREL} -O6 -Wunknown-pragmas")
ENDIF(CMAKE_COMPILER_IS_GNUCXX)
ENDIF(WIN32 AND NOT CYGWIN)
IF(CMAKE_BUILD_TYPE MATCHES Debug)
ADD_DEFINITIONS(-DCMAKE_VERBOSE_MAKEFILE=ON)
ENDIF(CMAKE_BUILD_TYPE MATCHES Debug)

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CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
######################################################################################
### 0) If you want to set your variables in eo-conf.cmake and avoid the cmd line
######################################################################################
#INCLUDE(eo-conf.cmake OPTIONAL)
######################################################################################
######################################################################################
### 1) Main project config
######################################################################################
# set the project namef and other variables
PROJECT(EO)
# CMake > 2.8 is needed, because of the FindOpenMP feature
#cmake_minimum_required(VERSION 2.8)
#SET(PROJECT_VERSION_MAJOR 1)
#SET(PROJECT_VERSION_MINOR 1)
#SET(PROJECT_VERSION_PATCH 1)
SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}" CACHE STRING "Package version" FORCE)
SET(VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}${PROJECT_VERSION_MISC}" CACHE STRING "Global version" FORCE)
SET(GLOBAL_VERSION "${VERSION}")
SET(PACKAGE_BUGREPORT "eodev-help@sourceforge.net" CACHE STRING "Package bug report" FORCE)
SET(PACKAGE_NAME "Evolving Objects" CACHE STRING "Package name" FORCE)
SET(PACKAGE_STRING "${PACKAGE_NAME} ${PACKAGE_VERSION}"CACHE STRING "Package string full name" FORCE)
SET(PACKAGE_TARNAME "eo" CACHE STRING "Package tar name" FORCE)
# regular expression checking
INCLUDE_REGULAR_EXPRESSION("^.*$" "^$")
# set a language for the entire project.
ENABLE_LANGUAGE(CXX)
ENABLE_LANGUAGE(C)
######################################################################################
#####################################################################################
### 2) Include required modules / configuration files
#####################################################################################
FIND_PACKAGE(OpenMP)
IF(OPENMP_FOUND)
SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
ENDIF()
INCLUDE(CMakeBackwardCompatibilityCXX)
INCLUDE(FindDoxygen)
INCLUDE(FindGnuplot)
INCLUDE(CheckLibraryExists)
IF(UNIX)
INCLUDE(ConfigureChecks.cmake)
ENDIF(UNIX)
INCLUDE(Dart OPTIONNAL)
# now create config headers
CONFIGURE_FILE(config.h.cmake ${CMAKE_CURRENT_BINARY_DIR}/config.h)
# now create config install_symlink script file
CONFIGURE_FILE(install_symlink.py.cmake ${CMAKE_CURRENT_BINARY_DIR}/install_symlink.py)
# now create PKGBUILD file for archlinux package manager
CONFIGURE_FILE(PKGBUILD.cmake ${CMAKE_CURRENT_BINARY_DIR}/PKGBUILD)
# Set a special flag if the environment is windows (should do the same in a config.g file)
IF (WIN32)
ADD_DEFINITIONS(-D_WINDOWS=1)
ENDIF (WIN32)
######################################################################################
######################################################################################
######################################################################################
### compilation of examples?
######################################################################################
#SET(ENABLE_CMAKE_EXAMPLE TRUE CACHE BOOL "Enable copy of benchs and parameters file?")
######################################################################################
######################################################################################
### 4) Test config
######################################################################################
#IF (ENABLE_CMAKE_TESTING)
# ENABLE_TESTING()
#ENDIF (ENABLE_CMAKE_TESTING)
######################################################################################
######################################################################################
### 5) Where must cmake go now ?
######################################################################################
#ADD_SUBDIRECTORY(app)
ADD_SUBDIRECTORY(doc)
ADD_SUBDIRECTORY(src)
ADD_SUBDIRECTORY(test)
ADD_SUBDIRECTORY(tutorial)
######################################################################################
######################################################################################
### 6) Install pkg-config config file for EO
######################################################################################
SET(PCPREFIX "/usr")
SET(PCFLAGS "-leoutils -leo -les -lga -lcma -lgcov")
SET(PCINCLUDEDIR "eo")
CONFIGURE_FILE(pc.cmake ${CMAKE_CURRENT_BINARY_DIR}/eo.pc)
INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/eo.pc DESTINATION local/${LIB}/pkgconfig COMPONENT headers)
######################################################################################
######################################################################################
### 7) Include packaging
######################################################################################
#INCLUDE(Packaging.cmake)
######################################################################################

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Copyright (C) <year> <name of author>
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
Also add information on how to contact you by electronic and paper mail.
You should also get your employer (if you work as a programmer) or your
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Yoyodyne, Inc., hereby disclaims all copyright interest in the
library `Frob' (a library for tweaking knobs) written by James Random Hacker.
<signature of Ty Coon>, 1 April 1990
Ty Coon, President of Vice
That's all there is to it!

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set(CTEST_PROJECT_NAME "ParadisEO")
set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
set(CTEST_DROP_METHOD "http")
set(CTEST_DROP_SITE "cdash.inria.fr")
set(CTEST_DROP_LOCATION "/CDash/submit.php?project=ParadisEO")
set(CTEST_DROP_SITE_CDASH TRUE)

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# NOTE: only add something here if it is really needed by EO
INCLUDE(CheckIncludeFile)
INCLUDE(CheckIncludeFiles)
INCLUDE(CheckSymbolExists)
INCLUDE(CheckFunctionExists)
INCLUDE(CheckLibraryExists)
CHECK_LIBRARY_EXISTS(m cos "/usr/lib" HAVE_LIBM)
CHECK_INCLUDE_FILES(math.h "math.h" HAVE_MATH_H)
CHECK_INCLUDE_FILES(stdio.h "stdio.h" HAVE_STDIO_H)
CHECK_INCLUDE_FILES(stdlib.h "stdlib.h" HAVE_STDLIB_H)
CHECK_INCLUDE_FILES(string.h "string.h" HAVE_STRING_H)
CHECK_INCLUDE_FILES(strings.h "strings.h" HAVE_STRINGS_H)
CHECK_INCLUDE_FILES(malloc.h "malloc.h" HAVE_MALLOC_H)
CHECK_INCLUDE_FILES(limits.h "limits.h" HAVE_LIMITS_H)
CHECK_INCLUDE_FILES(unistd.h "unistd.h" HAVE_UNISTD_H)
CHECK_INCLUDE_FILES(stdint.h "stdint.h" HAVE_STDINT_H)
# Use check_symbol_exists to check for symbols in a reliable
# cross-platform manner. It accounts for different calling
# conventions and the possibility that the symbol is defined as a
# macro. Note that some symbols require multiple includes in a
# specific order. Refer to the man page for each symbol for which a
# check is to be added to get the proper set of headers. Example :
#check_symbol_exists(asymbol "symbole.h" HAVE_SYMBOLE)

45
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In order to create a new release from the current repository, perform the
following steps:
- If necessary, create a branch named "eo_x.y.z"
- Set version number in eo-conf.cmake
- Check/update NEWS file, set release date and version in NEWS.
- use the "archive_current.sh" script to create the source archive
- Build the packages
- Put source archive and packages files at SourceForge
- Post news on SourceForge project-page
- Send announcement to mailing lists
- Bump version number to next "x.y.z-edge" in eo-conf.cmake
When reaching stable versions:
- prepare a message with the following template:
-----8<-----
A new version of the "Evolving Objects" framework is available.
EO is a template-based, C++ evolutionary computation library which
helps you to write your own stochastic optimization algorithms
insanely fast.
Learn more about EO on the official website:
http://eodev.sourceforge.net/
You will find the release x.y.z at the following address:
https://sourceforge.net/projects/eodev/files/eo/
Here is a summary of the change log:
- XXXXX
- and more…
Do not hesitate to submit the bugs you will face:
https://sourceforge.net/apps/trac/eodev/wiki/WikiStart
Happy evolutionary hacking.
-----8<-----
- Post the message to:
- EO news https://sourceforge.net/news/?group_id=9775
- EO mailing list: eodev-main@lists.sourceforge.net
- ParadisEO mailing list: paradiseo-users@lists.gforge.inria.fr
- EC-digest maling list: ec-digest-l@listserv.gmu.edu
- JET mailing list: jet@inria.fr

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Basic Installation
==================
The simplest way to compile the libraries or the provided softwares is to run
one of the script beginnig with "build_". Each script permits to build different
parts of the framework, with different options.
To compile EO you will need CMake and a compiler for your system.
So far the available scripts for posix systems using g++ are the following:
* build_gcc_linux_release : the most usefull script, build the core libraries in release mode
* build_gcc_linux_debug : build the core libraries with debugging informations in the binaries
* build_gcc_linux_tutorial : build the core libraries and the tutorials
* build_gcc_linux_unittest : build the core libraries and the tests executables
* build_gcc_linux_stl_parallel : build the core libraries enabling STL parallel algorithms (like sorting)
* build_gcc_linux_pyeo : build the core libraries and the python module
* distclean : remove the "release/" and "debug/" directories where the build scripts put the binaries
For Windows systems using Visual Studio:
* build_vs2008_release.bat
You may need to adapt the ID to your version of Visual Studio, edit
the "Visual Studio 9 2008" string accordingly.
The libraries are in the "release/lib/" or "debug/lib/" directories.
Compilers and Options
=====================
The build scripts are really simple, take a look at them to see how to use the
build system.
Basically, the steps are:
0. remove any old build directory that's on the way:
rm -rf build/
1. create a directory in which to put build files:
mkdir build/
2. go in this directory:
cd build/
3. call cmake with the options you want, using the "-D" option and passing the
EO directory as an argument, for example:
cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_CMAKE_TESTING =1 ..
4. now type your favorite "make" command, like:
make -j # use several processors at once when possible
5. enjoy:
./debug/test/t-eofitness
Some of the available options are:
* CMAKE_BUILD_TYPE :
* "Debug" : embed debugging informations in the binaries) or
* "Release" : no debugging info and some optimizations (the default)
* ENABLE_EO_TUTORIAL : build the tutorial ("no" by default)
* ENABLE_CMAKE_TESTING : build the tests executables ("no" by default)
* ENABLE_PYEO : build the python module ("no" by default)
You can pass generic options to the compiler, like:
* _GLIBCXX_PARALLEL : use the parallel version of the STL
Installation using packages
===========================
To construct a dummy template of the EO package you will need CPack. Be warned
that those do not guarantee correct dependencies and version management.
Use the "package_*" scripts:
* package_deb : for debian-like systems
* package_rpm : for red-hat-like systems
Or go through the following steps:
1. go in the build directory where your binaries are:
cd build/
2. call CPack specifying the desired package system:
cpack -G DEB
3. install the package:
sudo dpkg -i EO-1.1.1-Linux.deb
Basic installation
==================
To install the framework system-wide, copy the "eo/" directory somewhere in your
path. The "lib/" directory should be reachable for the linker and the "src/"
directory must be in the compiler include path.

502
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GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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To apply these terms, attach the following notices to the library. It is
safest to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least the
"copyright" line and a pointer to where the full notice is found.
<one line to give the library's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
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
Also add information on how to contact you by electronic and paper mail.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the library, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the
library `Frob' (a library for tweaking knobs) written by James Random Hacker.
<signature of Ty Coon>, 1 April 1990
Ty Coon, President of Vice
That's all there is to it!

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* current version
* release 1.2 (16. May. 2011)
- fixed the incremental allocation issue in variation operators which were
taking too much time for big population sizes
- new class eoParallel enabling parallelization in EO using OpenMP. At this
time, it only concerns the evaluation operator, for advanced details go to
the file test/t-eoParallel.cpp. The default parallelization mode is off, to
switch it on, see the parameters prefixed by --parallelize-*
- pyeo compatible with the last version of Boost and Python libraries
- script installing EO manually in using symbolic links
- evaluators that throw an exception if a maximum time has been reached
(wallclock and CPU user time for POSIX systems), independently of the number of generations
- merged parser and parser-logger
- some bugfixes for windows systems
* release 1.1 (8. Nov. 2010)
- provide cmake build system, remove the old autotools one
- package generation system
- GCC 4.3 compatibility
- new versatile log system with several nested verbose levels
- classes using intern verbose parameters marked as deprecated, please update your code accordingly if you use one of the following files:
eo/src/eoCombinedInit.h
eo/src/eoGenContinue.h
eo/src/eoProportionalCombinedOp.h
eo/src/utils/eoData.h
eo/src/utils/eoStdoutMonitor.h
- an evaluator that throw an exception if a maximum eval numbers has been reached, independently of the number of generations
- new monitor that can write on any ostream
- new continuator that can catch POSIX system user signals
- dual fitness class to handle feasibility of individual with guarantee that feasible fitness will always be better than unfeasible one
- feasible fitness ratio stat
- interquartile range stat
- average size of individuals stat
- uniform(min,max) random function
- compatibility macros for compiling paradiseo with CUDACC
- removed old multi-objective classes, deprecated by the Paradiseo-MOEO project
- new website, switch from CVS to GIT, and a cool logo!
* release 1.0.1 (23. Jan. 2006)
- Templates/ improvements
* release 1.0 (29. Dec. 2006)
- Implement CMA-ES.
- Update introductory pages of documentation and webpage.
- Add Microsoft Visual C++ project support files (for Visual Studio 2003 and 2005)
- Upgrade Teamplates/ script to create a complete standalone EO project (using autotools)
- Remove support for pre-standard C++ compiler (i.e. gcc-2.x), which allows to
clean up the code considerably.
Assume availability of sstream and limits.
* release 0.9.3z.1 (1. Oct. 2005)
- Support gcc-3.4 and gcc.4.x.
- Provide full automake/autoconf/configure support.

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# $Id: pkgbuild-mode.el,v 1.23 2007/10/20 16:02:14 juergen Exp $
# Maintainer: Caner Candan <caner@candan.fr>
pkgname=libeo
pkgver=@PROJECT_VERSION@
pkgrel=1
pkgdesc="Evolving Objects is a template-based, ANSI-C++ evolutionary computation library which helps you to write your own stochastic optimization algorithms insanely fast."
url=""
arch=('i686' 'x86_64')
license=('LGPL')
depends=()
makedepends=('make' 'cmake')
conflicts=()
replaces=()
backup=()
install=
source=($pkgname-$pkgver.tar.gz)
md5sums=()
build() {
cd $startdir/src/$pkgname-$pkgver
cmake -DCMAKE_INSTALL_PREFIX=/usr .
make || return 1
make DESTDIR=$startdir/pkg install
}

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EO README FILE
=======================================================================
check latest news at http://eodev.sourceforge.net/
=======================================================================
Welcome to EO, the Evolving Objects library.
The latest news about EO can be found on the sourceforge repository at
http://eodev.sourceforge.net/
In case of any problem, please e-mail us at
eodev-main@lists.sourceforge.net
To get started, take a look at the tutorial, starting with
./tutorial/html/eoTutorial.html
The easiest way to start programming a new genome with all EO
evolution engines handy is to create a new standalone EO project from
the tutorial/Templates/ directory. Read Lesson 5 of the tutorial for
an introduction ;)
==================================================================
BUILDING EO
==================================================================
The basic installation procedure goes the following:
Go to the "eo/" and run one of the "build_*" script. 
Using the "build_gcc_linux_release" script is generally what you want. The
binaries are then located in the "release/" directory.
Now you should probably go to the tutorial and start learning about EO
features and programming.
In case of problems or if you want advanced options, you can read the INSTALL file.
===================================================================
DIRECTORY STRUCTURE
===================================================================
After unpacking the archive file, you should end up with the following
structure:
.../ the MAIN EO dir, created when unpacking
|
+-- src SOURCE dir. Contains most EO .h files
| |
| +- utils general utilities (e.g. RNG-related source files)
| |
| +- ga bistring-genotypes source files
| |
| +- es real-valued-genotypes source files
| |
| +- gp Genetic Programming source files
| |
| +- obsolete files from old versions - for upward compatibility
|
|
|
+-- tutorial TUTORIAL dir (indeed :-)
| |
| +- html all html files - start by browsing index.html
| |
| +- LessonX for X=1, 2, 3, ... : example of increasing complexity
|
|
|
+-- doc DOCUMENTATION dir (generated by Doxygen)
| |
| +- html HTML files - start at index.html (see also tutorial)
| |
| +- latex latex files - use to generate Poatscript doc.
| |
| +- man Unix man format documentation
|
|
+-- test TEST files - for debugging purposes only
|
|
+-- app APPLICATIONS - one dir per separate application
| |
| +- gprop GA/backpropagation for neural nets
| |
| +- mastermind the wellknown MasterMind game
|
|
+-- win WINDOWS dir: project files for MS/VC5+

0
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See the code-documentation for details.
General ToDos should be documented at the end of doc/index.h.

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######################################################################################
### 1) Where must cmake go now ?
######################################################################################
#ADD_SUBDIRECTORY(gprop)
#ADD_SUBDIRECTORY(gpsymreg)
ADD_SUBDIRECTORY(mastermind)
######################################################################################

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######################################################################################
### 1) Include the sources
######################################################################################
INCLUDE_DIRECTORIES(${EO_SOURCE_DIR}/src)
INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
######################################################################################
### 2) Specify where CMake can find the libraries (mandatory: before 3) )
######################################################################################
LINK_DIRECTORIES(${EO_BINARY_DIR}/lib)
######################################################################################
### 3) Define your target(s): just an executable here
######################################################################################
SET (GPROP_SOURCES gprop.cpp)
# especially for Visual Studio
IF(NOT WIN32 OR CYGWIN)
ADD_EXECUTABLE(gprop ${GPROP_SOURCES})
ADD_DEPENDENCIES(gprop eo eoutils)
TARGET_LINK_LIBRARIES(gprop eo eoutils)
SET(GPROP_VERSION ${GLOBAL_VERSION})
SET_TARGET_PROPERTIES(gprop PROPERTIES VERSION "${GPROP_VERSION}")
ENDIF(NOT WIN32 OR CYGWIN)
######################################################################################

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//-----------------------------------------------------------------------------
// gprop
//-----------------------------------------------------------------------------
#include <stdlib.h> // EXIT_SUCCESS EXIT_FAILURE
#include <stdexcept> // exception
#include <iostream> // cerr cout
#include <fstream> // ifstream
#include <string> // string
#include <eo> // all usefull eo stuff
#include "gprop.h" // Chrom eoChromInit eoChromMutation eoChromXover eoChromEvaluator
using namespace std;
//-----------------------------------------------------------------------------
// global variables
//-----------------------------------------------------------------------------
unsigned in, out, hidden;
mlp::set train, validate, test;
//-----------------------------------------------------------------------------
// parameters
//-----------------------------------------------------------------------------
eoValueParam<unsigned> pop_size(10, "pop_size", "population size", 'p');
eoValueParam<unsigned> generations(10, "generations", "number of generation", 'g');
eoValueParam<double> mut_rate(0.25, "mut_rate", "mutation rate", 'm');
eoValueParam<double> xover_rate(0.25, "xover_rate", "default crossover rate", 'x');
eoValueParam<string> file("", "file", "common start of patterns filenames *.trn *.val and *.tst", 'f');
eoValueParam<unsigned> hiddenp(0, "hidden", "number of neurons in hidden layer", 'd');
//-----------------------------------------------------------------------------
// auxiliar functions
//-----------------------------------------------------------------------------
void arg(int argc, char** argv);
void load_file(mlp::set& s1, const string& s2);
void ga();
//-----------------------------------------------------------------------------
// main
//-----------------------------------------------------------------------------
int main(int argc, char** argv)
{
try
{
arg(argc, argv);
ga();
}
catch (exception& e)
{
cerr << argv[0] << ": " << e.what() << endl;
exit(EXIT_FAILURE);
}
return 0;
}
//-----------------------------------------------------------------------------
// implementation
//-----------------------------------------------------------------------------
void arg(int argc, char** argv)
{
eoParser parser(argc, argv);
parser.processParam(pop_size, "genetic operators");
parser.processParam(generations, "genetic operators");
parser.processParam(mut_rate, "genetic operators");
parser.processParam(xover_rate, "genetic operators");
parser.processParam(file, "files");
parser.processParam(hiddenp, "genetic operators");
if (parser.userNeedsHelp())
{
parser.printHelp(cout);
exit(EXIT_SUCCESS);
}
load_file(train, "trn");
load_file(validate, "val");
load_file(test, "tst");
phenotype::trn_max = train.size();
phenotype::val_max = validate.size();
phenotype::tst_max = test.size();
in = train.front().input.size();
out = train.front().output.size();
gprop_use_datasets(&train, &validate, &test);
hidden = hiddenp.value();
}
//-----------------------------------------------------------------------------
void load_file(mlp::set& set, const string& ext)
{
string filename = file.value(); filename += "." + ext;
ifstream ifs(filename.c_str());
if (!ifs)
{
cerr << "can't open file \"" << filename << "\"" << endl;
exit(EXIT_FAILURE);
}
ifs >> set;
if (set.size() == 0)
{
cerr << filename << " data file is empty!";
exit(EXIT_FAILURE);
}
}
//-----------------------------------------------------------------------------
void ga()
{
// create population
eoInitChrom init;
eoPop<Chrom> pop(pop_size.value(), init);
// evaluate population
eoEvalFuncPtr<Chrom> evaluator(eoChromEvaluator);
apply<Chrom>(evaluator, pop);
// selector
eoStochTournamentSelect<Chrom> select;
// genetic operators
eoChromMutation mutation;
eoChromXover xover;
// stop condition
eoGenContinue<Chrom> continuator1(generations.value());
phenotype p; p.val_ok = validate.size() - 1; p.mse_error = 0;
eoFitContinue<Chrom> continuator2(p);
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
// checkpoint
eoCheckPoint<Chrom> checkpoint(continuator);
// monitor
eoStdoutMonitor monitor;
checkpoint.add(monitor);
// statistics
eoBestFitnessStat<Chrom> stats;
checkpoint.add(stats);
monitor.add(stats);
// genetic algorithm
eoSGA<Chrom> sga(select,
xover, xover_rate.value(),
mutation, mut_rate.value(),
evaluator,
checkpoint);
sga(pop);
cout << "best: " << *max_element(pop.begin(), pop.end()) << endl;
}
//-----------------------------------------------------------------------------
// Local Variables:
// mode:C++
// End:

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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// gprop.h
// (c) GeNeura Team 1998
/*
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
*/
//-----------------------------------------------------------------------------
#ifndef gprop_h
#define gprop_h
//-----------------------------------------------------------------------------
#include <iostream> // istream ostream
#include <iomanip> // setprecision
#include <string> // string
#include <EO.h> // EO
#include <eoOp.h> // eoMonOp eoQuadraticOp
#include <eoInit.h> // eoInit
#include <utils/rnd_generators.h> // normal_generator
#include "mlp.h" // mlp::net mlp::set
#include "qp.h" // qp::set
#include "mse.h" // mse::error
//-----------------------------------------------------------------------------
// phenotype
//-----------------------------------------------------------------------------
struct phenotype
{
int trn_ok, val_ok, tst_ok;
double mse_error;
static int trn_max, val_max, tst_max;
friend bool operator<(const phenotype& a, const phenotype& b)
{
return (a.val_ok < b.val_ok) || ((!(b.val_ok < a.val_ok)) && (b.mse_error < a.mse_error));
}
friend bool operator==(const phenotype& a, const phenotype& b)
{
return (a.val_ok == b.val_ok) && (b.mse_error == a.mse_error);
}
friend bool operator>=(const phenotype& a, const phenotype& b)
{
return !(a < b);
}
friend bool operator>(const phenotype& a, const phenotype& b)
{
return (!(a == b)) && (!(a < b));
}
friend std::ostream& operator<<(std::ostream& os, const phenotype& p)
{
return os << p.trn_ok << "/" << p.trn_max << " "
<< p.val_ok << "/" << p.val_max << " "
<< p.tst_ok << "/" << p.tst_max << " "
<< p.mse_error;
}
friend std::istream& operator>>(std::istream& is, phenotype& p)
{
return is; // complete me
}
};
int phenotype::trn_max = 0, phenotype::val_max = 0, phenotype::tst_max = 0;
//-----------------------------------------------------------------------------
// genotype
//-----------------------------------------------------------------------------
#ifndef GPROP_GENOTYPE
#define GPROP_GENOTYPE mlp::net
#endif
typedef GPROP_GENOTYPE genotype;
//-----------------------------------------------------------------------------
// Chrom
//-----------------------------------------------------------------------------
extern unsigned in, out, hidden;
class Chrom: public EO<phenotype>, public genotype
{
public:
Chrom(): genotype(in, out, std::vector<unsigned>(hidden < 1 ? 0 : 1, hidden)) {}
std::string className() const { return "Chrom"; }
void printOn (std::ostream& os) const
{
os << std::setprecision(3) << static_cast<genotype>(*this) << " \t"
<< fitness();
// os << fitness();
}
void readFrom (std::istream& is)
{
invalidate(); // complete me
}
};
//-----------------------------------------------------------------------------
// eoChromInit
//-----------------------------------------------------------------------------
class eoInitChrom: public eoInit<Chrom>
{
public:
void operator()(Chrom& chrom)
{
chrom.reset();
chrom.invalidate();
}
};
//-----------------------------------------------------------------------------
// global variables
//-----------------------------------------------------------------------------
mlp::set *trn_set = 0, *val_set = 0, *tst_set = 0;
void gprop_use_datasets(mlp::set *trn, mlp::set *val, mlp::set *tst) {
trn_set = trn;
val_set = val;
tst_set = tst;
}
void ensure_datasets_initialized() {
if (!trn_set) {
std::cerr << "trn_set is not initialized. Must call gprop_use_datasets before training\n";
std::cerr.flush();
abort();
}
}
//-----------------------------------------------------------------------------
// eoChromMutation
//-----------------------------------------------------------------------------
class eoChromMutation: public eoMonOp<Chrom>
{
public:
bool operator()(Chrom& chrom)
{
mse::net tmp(chrom);
tmp.train(*trn_set, 10, 0, 0.001);
return true;
}
};
//-----------------------------------------------------------------------------
// eoChromXover
//-----------------------------------------------------------------------------
class eoChromXover: public eoQuadOp<Chrom>
{
public:
bool operator()(Chrom& chrom1, Chrom& chrom2)
{
chrom1.normalize();
chrom2.desaturate();
mse::net tmp1(chrom1), tmp2(chrom2);
ensure_datasets_initialized();
tmp1.train(*trn_set, 100, 0, 0.001);
tmp2.train(*trn_set, 100, 0, 0.001);
return true;
}
};
//-----------------------------------------------------------------------------
// eoChromEvaluator
//-----------------------------------------------------------------------------
int correct(const mlp::net& net, const mlp::set& set)
{
int sum = 0;
for (mlp::set::const_iterator s = set.begin(); s != set.end(); ++s)
{
unsigned partial = 0;
for (unsigned i = 0; i < s->output.size(); ++i)
if ((s->output[i] < 0.5 && net(s->input)[i] < 0.5) ||
(s->output[i] > 0.5 && net(s->input)[i] > 0.5))
++partial;
if (partial == s->output.size())
++sum;
}
return sum;
}
phenotype eoChromEvaluator(const Chrom& chrom)
{
phenotype p;
ensure_datasets_initialized();
p.trn_ok = correct(chrom, *trn_set);
p.val_ok = correct(chrom, *val_set);
p.tst_ok = correct(chrom, *tst_set);
p.mse_error = mse::error(chrom, *val_set);
return p;
}
//-----------------------------------------------------------------------------
#endif // gprop_h
// Local Variables:
// mode:C++
// End:

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//-----------------------------------------------------------------------------
// l2.h
//-----------------------------------------------------------------------------
#ifndef l2_h
#define l2_h
//-----------------------------------------------------------------------------
#include <math.h> // log
#include <qp.h> // neuron layer net set
//-----------------------------------------------------------------------------
namespace l2
{
//---------------------------------------------------------------------------
// useful typedefs
//---------------------------------------------------------------------------
using qp::real;
using qp::vector;
using qp::max_real;
using qp::min_real;
using qp::set;
using qp::neuron;
using qp::layer;
//---------------------------------------------------------------------------
// error
//---------------------------------------------------------------------------
real error(const mlp::net& net, const set& ts)
{
real error_ = 0.0;
for (set::const_iterator s = ts.begin(); s != ts.end(); ++s)
{
vector out = net(s->input);
for (unsigned i = 0; i < out.size(); ++i)
{
real target = s->output[i];
real value = out[i];
error_ -= target * log(value + min_real) +
(1.0 - target) * log(1.0 - value + min_real);
}
}
return error_;
}
//-------------------------------------------------------------------------
// l2
//-------------------------------------------------------------------------
class net: public qp::net
{
public:
net(mlp::net& n): qp::net(n) {}
real error(const set& ts)
{
real error_ = 0;
for (set::const_iterator s = ts.begin(); s != ts.end(); ++s)
{
forward(s->input);
error_ -= backward(s->input, s->output);
}
return error_;
}
private:
real backward(const vector& input, const vector& output)
{
reverse_iterator current_layer = rbegin();
reverse_iterator backward_layer = current_layer + 1;
real error_ = 0;
// output layer
for (unsigned j = 0; j < current_layer->size(); ++j)
{
neuron& n = (*current_layer)[j];
real out = output[j];
n.ndelta += n.delta = (out - n.out) /
(n.out * (1.0 - n.out) + min_real) * n.out * (1.0 - n.out);
if (size() == 1) // monolayer
n.dxo += n.delta * input;
else // multilayer
for (unsigned k = 0; k < n.dxo.size(); ++k)
n.dxo[k] += n.delta * (*backward_layer)[k].out;
error_ += out * log(n.out + min_real) +
(1.0 - out) * log(1.0 - n.out + min_real);
}
// hidden layers
while (++current_layer != rend())
{
reverse_iterator forward_layer = current_layer - 1;
reverse_iterator backward_layer = current_layer + 1;
for (unsigned j = 0; j < current_layer->size(); ++j)
{
neuron& n = (*current_layer)[j];
real sum = 0;
for (unsigned k = 0; k < forward_layer->size(); ++k)
{
neuron& nf = (*forward_layer)[k];
sum += nf.delta * (nf.n->weight[j] + nf.dweight1[j]);
}
n.delta = n.out * (1.0 - n.out) * sum;
n.ndelta += n.delta;
if (backward_layer == rend()) // first hidden layer
n.dxo += n.delta * input;
else // rest of hidden layers
for (unsigned k = 0; k < n.dxo.size(); ++k)
n.dxo[k] += n.delta * (*backward_layer)[k].out;
}
}
return error_;
}
};
//---------------------------------------------------------------------------
} // namespace l2
//-----------------------------------------------------------------------------
#endif // l2_h
// Local Variables:
// mode:C++
// End:

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