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+ eda algo: same algo than eda-sa without sa, + plotting scripts and problem functions moved to application/common

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This commit is contained in:
Caner Candan 2010-09-22 14:38:15 +02:00
commit 65191e2212
16 changed files with 595 additions and 14 deletions
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1
CMakeLists.txt
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@ -83,6 +83,7 @@ ADD_SUBDIRECTORY(doc)
###################################################################################### ######################################################################################
###################################################################################### ######################################################################################
### 7) Create executable, link libraries and prepare target ### 7) Create executable, link libraries and prepare target
###################################################################################### ######################################################################################

6
application/CMakeLists.txt
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@ -2,6 +2,12 @@
### 1) Where do we go now ?!? ### 1) Where do we go now ?!?
###################################################################################### ######################################################################################
INCLUDE_DIRECTORIES(
${CMAKE_CURRENT_SOURCE_DIR}/common
)
ADD_SUBDIRECTORY(common)
ADD_SUBDIRECTORY(eda_sa) ADD_SUBDIRECTORY(eda_sa)
ADD_SUBDIRECTORY(eda)
###################################################################################### ######################################################################################

14
application/common/CMakeLists.txt Normal file
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@ -0,0 +1,14 @@
PROJECT(common)
SET(RESOURCES
gplot.py
ggobi.py
)
FOREACH(file ${RESOURCES})
EXECUTE_PROCESS(
COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_SOURCE_DIR}/${file}
${DO_BINARY_DIR}/${file}
)
ENDFOREACH(file)

42
application/common/Rosenbrock.h Normal file
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#ifndef _Rosenbrock_h
#define _Rosenbrock_h
#include <eo>
#include <es.h>
#include <es/eoRealInitBounded.h>
#include <es/eoRealOp.h>
#include <es/eoEsChromInit.h>
#include <es/eoRealOp.h>
#include <es/make_real.h>
#include <apply.h>
#include <eoProportionalCombinedOp.h>
template < typename EOT >
class Rosenbrock : public eoEvalFunc< EOT >
{
public:
typedef typename EOT::AtomType AtomType;
virtual void operator()( EOT& p )
{
if (!p.invalid())
return;
p.fitness( _evaluate( p ) );
}
private:
AtomType _evaluate( EOT& p )
{
AtomType r = 0.0;
for (unsigned int i = 0; i < p.size() - 1; ++i)
{
r += p[i] * p[i];
}
return r;
}
};
#endif // !_Rosenbrock_h

42
application/common/Sphere.h Normal file
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@ -0,0 +1,42 @@
#ifndef _Sphere_h
#define _Sphere_h
#include <eo>
#include <es.h>
#include <es/eoRealInitBounded.h>
#include <es/eoRealOp.h>
#include <es/eoEsChromInit.h>
#include <es/eoRealOp.h>
#include <es/make_real.h>
#include <apply.h>
#include <eoProportionalCombinedOp.h>
template < typename EOT >
class Sphere : public eoEvalFunc< EOT >
{
public:
typedef typename EOT::AtomType AtomType;
virtual void operator()( EOT& p )
{
if (!p.invalid())
return;
p.fitness( _evaluate( p ) );
}
private:
AtomType _evaluate( EOT& p )
{
AtomType r = 0.0;
for (unsigned int i = 0; i < p.size() - 1; ++i)
{
r += p[i] * p[i];
}
return r;
}
};
#endif // !_Sphere_h

68
application/common/ggobi.py Executable file
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@ -0,0 +1,68 @@
#!/usr/bin/env python
from pprint import *
import sys, os
if __name__ == '__main__':
# parameter phase
if len(sys.argv) < 2:
print 'Usage: %s [FILE]' % sys.argv[0]
sys.exit()
filename = sys.argv[1]
lines = open(filename).readlines()
# formatting phase
try:
results = [ x.split() for x in lines[1:-1] ]
except IOError, e:
print 'Error: %s' % e
sys.exit()
# dimension estimating phase
popsize = int(lines[0].split()[0])
dimsize = int(results[0][1])
# printing phase
print 'popsize: %d' % popsize
print 'dimsize: %d' % dimsize
print
pprint( results )
# cvs converting phase
i = 1
for x in results:
x.insert(0, '"%d"' % i)
i += 1
header = ['""', '"fitness"', '"dimsize"']
for i in range(0, dimsize):
header.append( '"dim%d"' % i )
results.insert(0, header)
# cvs printing phase
file_results = '\n'.join( [ ','.join( x ) for x in results ] )
print
print file_results
try:
open('%s.csv' % filename, 'w').write(file_results + '\n')
except IOError, e:
print 'Error: %s' % e
sys.exit()
# ggobi plotting phase
os.system('ggobi %s.csv' % filename)

399
application/common/gplot.py Executable file
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@ -0,0 +1,399 @@
#!/usr/bin/env python
"""plot.py -- Plot EDA-SA results file"""
import os, time, math, tempfile
import numpy
try:
import Gnuplot, Gnuplot.PlotItems, Gnuplot.funcutils
except ImportError:
# kludge in case Gnuplot hasn't been installed as a module yet:
import __init__
Gnuplot = __init__
import PlotItems
Gnuplot.PlotItems = PlotItems
import funcutils
Gnuplot.funcutils = funcutils
import optparse, logging, sys
LEVELS = {'debug': logging.DEBUG,
'info': logging.INFO,
'warning': logging.WARNING,
'error': logging.ERROR,
'critical': logging.CRITICAL}
def logger(level_name, filename='plot.log'):
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
filename=filename, filemode='a'
)
console = logging.StreamHandler()
console.setLevel(LEVELS.get(level_name, logging.NOTSET))
console.setFormatter(logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s'))
logging.getLogger('').addHandler(console)
def parser(parser=optparse.OptionParser()):
parser.add_option('-v', '--verbose', choices=LEVELS.keys(), default='warning', help='set a verbose level')
parser.add_option('-f', '--files', help='give some input sample files separated by comma (cf. gen1,gen2,...)', default='')
parser.add_option('-r', '--respop', help='define the population results containing folder', default='./ResPop')
parser.add_option('-o', '--output', help='give an output filename for logging', default='plot.log')
parser.add_option('-d', '--dimension', help='give a dimension size', default=2)
parser.add_option('-m', '--multiplot', action="store_true", help='plot all graphics in one window', dest="multiplot", default=True)
parser.add_option('-p', '--plot', action="store_false", help='plot graphics separetly, one by window', dest="multiplot")
parser.add_option('-w', '--windowid', help='give the window id you want to display, 0 means we display all ones, this option should be combined with -p', default=0)
parser.add_option('-G', '--graphicsdirectory', help='give a directory name for graphics, this option should be combined with -u', default='plot')
parser.add_option('-g', '--graphicsprefixname', help='give a prefix name for graphics, this option should be combined with -u', default='plot')
parser.add_option('-t', '--terminal', action="store_true", help='display graphics on gnuplot windows', dest="terminal", default=True)
parser.add_option('-u', '--png', action="store_false", help='display graphics on png files', dest="terminal")
options, args = parser.parse_args()
logger(options.verbose, options.output)
return options
options = parser()
def wait(str=None, prompt='Press return to show results...\n'):
if str is not None:
print str
raw_input(prompt)
def draw2DRect(min=(0,0), max=(1,1), color='black', state=None, g=None):
if g == None: g = Gnuplot.Gnuplot()
if state != None: state.append(g)
xmin, ymin = min
xmax, ymax = max
cmd = 'set arrow from %s,%s to %s,%s nohead lc rgb "%s"'
g(cmd % (xmin, ymin, xmin, ymax, color))
g(cmd % (xmin, ymax, xmax, ymax, color))
g(cmd % (xmax, ymax, xmax, ymin, color))
g(cmd % (xmax, ymin, xmin, ymin, color))
return g
def draw3DRect(min=(0,0,0), max=(1,1,1), state=None, g=None):
if g == None: g = Gnuplot.Gnuplot()
if state != None: state.append(g)
# TODO
return g
def getSortedFiles(path):
assert path != None
if options.files == '':
filelist = os.listdir(path)
filelist.sort()
else:
filelist = options.files.split(',')
checkFileErrors(path, filelist)
return filelist
def checkFileErrors(path, filelist):
for filename in filelist:
for line in open('%s/%s' % (path, filename)):
if '-nan' in line:
logging.warning("checkFileErrors: %s/%s file contains bad value, it is going to be skipped" % (path, filename))
filelist.remove(filename)
break
def plotXPointYFitness(path, fields='3:1', state=None, g=None):
if g == None:
g = Gnuplot.Gnuplot()
if not options.terminal:
g('set terminal png')
g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXPointYFitness'))
if state != None: state.append(g)
g.title('Fitness observation')
g.xlabel('Coordinates')
g.ylabel('Fitness (Quality)')
files=[]
for filename in getSortedFiles(path):
files.append(Gnuplot.File(path + '/' + filename, using=fields,
with_='points',
#title='distribution \'' + filename + '\''
title=""
)
)
if len(files) > 0:
g.plot(*files)
return g
def plotXYPointZFitness(path, fields='4:3:1', state=None, g=None):
if g == None:
g = Gnuplot.Gnuplot()
if not options.terminal:
g('set terminal png')
g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYPointZFitness'))
if state != None: state.append(g)
g.title('Fitness observation in 3-D')
g.xlabel('x-axes')
g.ylabel('y-axes')
g.zlabel('Fitness (Quality)')
files=[]
for filename in getSortedFiles(path):
files.append(Gnuplot.File(path + '/' + filename, using=fields,
with_='points',
#title='distribution \'' + filename + '\''
title=""
)
)
if len(files) > 0:
g.splot(*files)
return g
def plotXYPoint(path, fields='3:4', state=None, g=None):
if g == None:
g = Gnuplot.Gnuplot()
if not options.terminal:
g('set terminal png')
g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYPoint'))
if state != None: state.append(g)
g.title('Points observation in 2-D')
g.xlabel('x-axes')
g.ylabel('y-axes')
files=[]
for filename in getSortedFiles(path):
files.append(Gnuplot.File(path + '/' + filename, using=fields,
with_='points',
#title='distribution \'' + filename + '\''
title=""
)
)
if len(files) > 0:
g.plot(*files)
return g
def plotXYZPoint(path, fields='3:4:5', state=None, g=None):
if g == None:
g = Gnuplot.Gnuplot()
if not options.terminal:
g('set terminal png')
g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYZPoint'))
if state != None: state.append(g)
g.title('Points observation in 3-D')
g.xlabel('x-axes')
g.ylabel('y-axes')
g.zlabel('z-axes')
files=[]
for filename in getSortedFiles(path):
files.append(Gnuplot.File(path + '/' + filename, using=fields,
with_='points',
#title='distribution \'' + filename + '\''
title=""
)
)
if len(files) > 0:
g.splot(*files)
return g
def plotParams(path, field='1', state=None, g=None):
if g == None:
g = Gnuplot.Gnuplot()
if not options.terminal:
g('set terminal png')
g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYZPoint'))
if state != None: state.append(g)
g.title('Hyper-volume comparaison through all dimensions')
g.xlabel('Iterations')
g.ylabel('Hyper-volume')
g.plot(Gnuplot.File(path, with_='lines', using=field,
title='multivariate distribution narrowing'))
return g
def plot2DRectFromFiles(path, state=None, g=None, plot=True):
if g == None:
g = Gnuplot.Gnuplot()
if not options.terminal:
g('set terminal png')
g('set output \'%s_%s.png\'' % (options.graphicsprefixname, 'plot2DRectFromFiles'))
if state != None: state.append(g)
g.title('Rectangle drawing observation')
g.xlabel('x-axes')
g.ylabel('y-axes')
x1,x2,y1,y2 = 0,0,0,0
colors = ['red', 'orange', 'blue', 'green', 'gold', 'yellow', 'gray']
#colors = open('rgb.txt', 'r').readlines()
colors_size = len(colors)
i = 0 # for color
for filename in getSortedFiles(path):
line = open(path + '/' + filename, 'r').readline()
fields = line.split(' ')
if not fields[0] == '2':
print 'plot2DRectFromFiles: higher than 2 dimensions not possible to draw'
return
xmin,ymin,xmax,ymax = fields[1:5]
#print xmin,ymin,xmax,ymax
cur_color = colors[i % colors_size]
draw2DRect((xmin,ymin), (xmax,ymax), cur_color, g=g)
g('set obj rect from %s,%s to %s,%s back lw 1.0 fc rgb "%s" fillstyle solid 1.00 border -1'
% (xmin,ymin,xmax,ymax,cur_color)
)
if plot:
if float(xmin) < x1: x1 = float(xmin)
if float(ymin) < y1: y1 = float(ymin)
if float(xmax) > x2: x2 = float(xmax)
if float(ymax) > y2: y2 = float(ymax)
#print x1,y1,x2,y2
i += 1
#print x1,y1,x2,y2
if plot:
g.plot('[%s:%s][%s:%s] -9999 notitle' % (x1, x2, y1, y2))
return g
def main():
gstate = []
n = int(options.dimension)
w = int(options.windowid)
r = options.respop
if not options.terminal:
try:
os.mkdir(options.graphicsdirectory)
except OSError:
pass
if options.multiplot:
g = Gnuplot.Gnuplot()
if not options.terminal:
g('set terminal png')
g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'multiplot'))
g('set parametric')
g('set nokey')
g('set noxtic')
g('set noytic')
g('set noztic')
g('set size 1.0, 1.0')
g('set origin 0.0, 0.0')
g('set multiplot')
g('set size 0.5, 0.5')
g('set origin 0.0, 0.5')
if n >= 1:
plotXPointYFitness(r, state=gstate, g=g)
g('set size 0.5, 0.5')
g('set origin 0.0, 0.0')
if n >= 2:
plotXPointYFitness(r, '4:1', state=gstate, g=g)
g('set size 0.5, 0.5')
g('set origin 0.5, 0.5')
if n >= 2:
plotXYPointZFitness(r, state=gstate, g=g)
g('set size 0.5, 0.5')
g('set origin 0.5, 0.0')
if n >= 2:
plotXYPoint(r, state=gstate, g=g)
elif n >= 3:
plotXYZPoint(r, state=gstate, g=g)
g('set nomultiplot')
else:
if n >= 1 and w in [0, 1]:
plotXPointYFitness(r, state=gstate)
if n >= 2 and w in [0, 2]:
plotXPointYFitness(r, '4:1', state=gstate)
if n >= 2 and w in [0, 3]:
plotXYPointZFitness(r, state=gstate)
if n >= 3 and w in [0, 4]:
plotXYZPoint(r, state=gstate)
if n >= 2 and w in [0, 5]:
plotXYPoint(r, state=gstate)
# if n >= 1:
# plotParams('./ResParams.txt', state=gstate)
# if n >= 2:
# plot2DRectFromFiles('./ResBounds', state=gstate)
# plotXYPoint(r, state=gstate)
# g = plot2DRectFromFiles('./ResBounds', state=gstate, plot=False)
# plotXYPoint(r, g=g)
if options.terminal:
wait(prompt='Press return to end the plot.\n')
# when executed, just run main():
if __name__ == '__main__':
logging.debug('### plotting started ###')
main()
logging.debug('### plotting ended ###')

27
application/eda/CMakeLists.txt Normal file
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PROJECT(eda)
FIND_PACKAGE(Boost 1.33.0)
INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
SET(RESOURCES
${PROJECT_NAME}.param
)
FOREACH(file ${RESOURCES})
EXECUTE_PROCESS(
COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_SOURCE_DIR}/${file}
${DO_BINARY_DIR}/${file}
)
ENDFOREACH(file)
FILE(GLOB SOURCES *.cpp)
SET(EXECUTABLE_OUTPUT_PATH ${DO_BINARY_DIR})
ADD_EXECUTABLE(${PROJECT_NAME} ${SOURCES})
TARGET_LINK_LIBRARIES(${PROJECT_NAME} do doutils ${EO_LIBRARIES} ${MO_LIBRARIES} ${Boost_LIBRARIES})

7
application/eda/eda.param Normal file
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--rho=0 # -p : <etropolis sample size
--alpha=0 # -a : Temperature dicrease rate
--threshold=0.1 # -t : Temperature threshold stopping criteria
--sample-size=10 # -P : Sample size
--dimension-size=10 # -d : Dimension size
--temperature=100 # -T : Initial temperature
#--verbose # Enable verbose mode

267
application/eda/main.cpp Normal file
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#include <eo>
#include <mo>
#include <utils/eoLogger.h>
#include <utils/eoParserLogger.h>
#include <eoEvalFuncCounterBounder.h>
#include <do/make_pop.h>
#include <do/make_run.h>
#include <do/make_continue.h>
#include <do/make_checkpoint.h>
#include <do>
#include "Rosenbrock.h"
#include "Sphere.h"
typedef eoReal<eoMinimizingFitness> EOT;
typedef doNormalMulti< EOT > Distrib;
int main(int ac, char** av)
{
eoParserLogger parser(ac, av);
// Letters used by the following declarations:
// a d i p t
std::string section("Algorithm parameters");
// FIXME: default value to check
//double initial_temperature = parser.createParam((double)10e5, "temperature", "Initial temperature", 'i', section).value(); // i
eoState state;
//-----------------------------------------------------------------------------
// Instantiate all needed parameters for EDA algorithm
//-----------------------------------------------------------------------------
double selection_rate = parser.createParam((double)0.5, "selection_rate", "Selection Rate", 'R', section).value(); // R
eoSelect< EOT >* selector = new eoDetSelect< EOT >( selection_rate );
state.storeFunctor(selector);
doEstimator< Distrib >* estimator = new doEstimatorNormalMulti< EOT >();
state.storeFunctor(estimator);
eoSelectOne< EOT >* selectone = new eoDetTournamentSelect< EOT >( 2 );
state.storeFunctor(selectone);
doModifierMass< Distrib >* modifier = new doNormalMultiCenter< EOT >();
state.storeFunctor(modifier);
eoEvalFunc< EOT >* plainEval = new Rosenbrock< EOT >();
state.storeFunctor(plainEval);
unsigned long max_eval = parser.getORcreateParam((unsigned long)0, "maxEval", "Maximum number of evaluations (0 = none)", 'E', "Stopping criterion").value(); // E
eoEvalFuncCounterBounder< EOT > eval(*plainEval, max_eval);
eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5);
state.storeFunctor(gen);
unsigned int dimension_size = parser.createParam((unsigned int)10, "dimension-size", "Dimension size", 'd', section).value(); // d
eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( dimension_size, *gen );
state.storeFunctor(init);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// (1) Population init and sampler
//-----------------------------------------------------------------------------
// Generation of population from do_make_pop (creates parameters, manages persistance and so on...)
// ... and creates the parameters: L P r S
// this first sampler creates a uniform distribution independently from our distribution (it does not use doUniform).
eoPop< EOT >& pop = do_make_pop(parser, state, *init);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// (2) First evaluation before starting the research algorithm
//-----------------------------------------------------------------------------
apply(eval, pop);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Prepare bounder class to set bounds of sampling.
// This is used by doSampler.
//-----------------------------------------------------------------------------
doBounder< EOT >* bounder = new doBounderRng< EOT >(EOT(pop[0].size(), -5),
EOT(pop[0].size(), 5),
*gen);
state.storeFunctor(bounder);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Prepare sampler class with a specific distribution
//-----------------------------------------------------------------------------
doSampler< Distrib >* sampler = new doSamplerNormalMulti< EOT >( *bounder );
state.storeFunctor(sampler);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Metropolis sample parameters
//-----------------------------------------------------------------------------
//unsigned int popSize = parser.getORcreateParam((unsigned int)20, "popSize", "Population Size", 'P', "Evolution Engine").value();
//moContinuator< moDummyNeighbor<EOT> >* sa_continue = new moIterContinuator< moDummyNeighbor<EOT> >( popSize );
//state.storeFunctor(sa_continue);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// SA parameters
//-----------------------------------------------------------------------------
//double threshold_temperature = parser.createParam((double)0.1, "threshold", "Minimal temperature at which stop", 't', section).value(); // t
//double alpha = parser.createParam((double)0.1, "alpha", "Temperature decrease rate", 'a', section).value(); // a
//moCoolingSchedule<EOT>* cooling_schedule = new moSimpleCoolingSchedule<EOT>(initial_temperature, alpha, 0, threshold_temperature);
//state.storeFunctor(cooling_schedule);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// stopping criteria
// ... and creates the parameter letters: C E g G s T
//-----------------------------------------------------------------------------
eoContinue< EOT >& eo_continue = do_make_continue(parser, state, eval);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// population output
//-----------------------------------------------------------------------------
eoCheckPoint< EOT >& pop_continue = do_make_checkpoint(parser, state, eval, eo_continue);
doPopStat< EOT >* popStat = new doPopStat<EOT>;
state.storeFunctor(popStat);
pop_continue.add(*popStat);
doFileSnapshot* fileSnapshot = new doFileSnapshot("EDA_ResPop");
state.storeFunctor(fileSnapshot);
fileSnapshot->add(*popStat);
pop_continue.add(*fileSnapshot);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// distribution output
//-----------------------------------------------------------------------------
doDummyContinue< Distrib >* dummy_continue = new doDummyContinue< Distrib >();
state.storeFunctor(dummy_continue);
doCheckPoint< Distrib >* distribution_continue = new doCheckPoint< Distrib >( *dummy_continue );
state.storeFunctor(distribution_continue);
doDistribStat< Distrib >* distrib_stat = new doStatNormalMulti< EOT >();
state.storeFunctor(distrib_stat);
distribution_continue->add( *distrib_stat );
// eoMonitor* stdout_monitor = new eoStdoutMonitor();
// state.storeFunctor(stdout_monitor);
// stdout_monitor->add(*distrib_stat);
// distribution_continue->add( *stdout_monitor );
eoFileMonitor* file_monitor = new eoFileMonitor("eda_distribution_bounds.txt");
state.storeFunctor(file_monitor);
file_monitor->add(*distrib_stat);
distribution_continue->add( *file_monitor );
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// eoEPRemplacement causes the using of the current and previous
// sample for sampling.
//-----------------------------------------------------------------------------
eoReplacement< EOT >* replacor = new eoEPReplacement< EOT >(pop.size());
// Below, use eoGenerationalReplacement to sample only on the current sample
//eoReplacement< EOT >* replacor = new eoGenerationalReplacement< EOT >(); // FIXME: to define the size
state.storeFunctor(replacor);
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// EDA algorithm configuration
//-----------------------------------------------------------------------------
doAlgo< Distrib >* algo = new doEDA< Distrib >
(*selector, *estimator, *selectone, *modifier, *sampler,
pop_continue, *distribution_continue,
eval,
//*sa_continue, *cooling_schedule, initial_temperature,
*replacor);
//-----------------------------------------------------------------------------
// state.storeFunctor(algo);
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
exit(1);
}
// Help + Verbose routines
make_verbose(parser);
make_help(parser);
//-----------------------------------------------------------------------------
// Beginning of the algorithm call
//-----------------------------------------------------------------------------
try
{
do_run(*algo, pop);
}
catch (eoEvalFuncCounterBounderException& e)
{
eo::log << eo::warnings << "warning: " << e.what() << std::endl;
}
catch (std::exception& e)
{
eo::log << eo::errors << "error: " << e.what() << std::endl;
exit(EXIT_FAILURE);
}
//-----------------------------------------------------------------------------
return 0;
}

4
application/eda_sa/CMakeLists.txt
View file

@ -8,9 +8,7 @@ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
SET(RESOURCES SET(RESOURCES
eda_sa.param ${PROJECT_NAME}.param
gplot.py
ggobi.py
) )
FOREACH(file ${RESOURCES}) FOREACH(file ${RESOURCES})

4
application/eda_sa/main.cpp
View file

@ -163,7 +163,7 @@ int main(int ac, char** av)
state.storeFunctor(popStat); state.storeFunctor(popStat);
pop_continue.add(*popStat); pop_continue.add(*popStat);
doFileSnapshot* fileSnapshot = new doFileSnapshot("ResPop"); doFileSnapshot* fileSnapshot = new doFileSnapshot("EDASA_ResPop");
state.storeFunctor(fileSnapshot); state.storeFunctor(fileSnapshot);
fileSnapshot->add(*popStat); fileSnapshot->add(*popStat);
pop_continue.add(*fileSnapshot); pop_continue.add(*fileSnapshot);
@ -191,7 +191,7 @@ int main(int ac, char** av)
// stdout_monitor->add(*distrib_stat); // stdout_monitor->add(*distrib_stat);
// distribution_continue->add( *stdout_monitor ); // distribution_continue->add( *stdout_monitor );
eoFileMonitor* file_monitor = new eoFileMonitor("distribution_bounds.txt"); eoFileMonitor* file_monitor = new eoFileMonitor("eda_sa_distribution_bounds.txt");
state.storeFunctor(file_monitor); state.storeFunctor(file_monitor);
file_monitor->add(*distrib_stat); file_monitor->add(*distrib_stat);
distribution_continue->add( *file_monitor ); distribution_continue->add( *file_monitor );

1
src/do
View file

@ -10,6 +10,7 @@
#include "doAlgo.h" #include "doAlgo.h"
#include "doEDASA.h" #include "doEDASA.h"
#include "doEDA.h"
#include "doDistrib.h" #include "doDistrib.h"
#include "doUniform.h" #include "doUniform.h"

252
src/doEDA.h Normal file
View file

@ -0,0 +1,252 @@
// (c) Thales group, 2010
/*
Authors:
Johann Dreo <johann.dreo@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>
*/
#ifndef _doEDA_h
#define _doEDA_h
#include <eo>
#include <mo>
#include <utils/eoRNG.h>
#include "doAlgo.h"
#include "doEstimator.h"
#include "doModifierMass.h"
#include "doSampler.h"
#include "doContinue.h"
template < typename D >
class doEDA : public doAlgo< D >
{
public:
//! Alias for the type EOT
typedef typename D::EOType EOT;
//! Alias for the atom type
typedef typename EOT::AtomType AtomType;
//! Alias for the fitness
typedef typename EOT::Fitness Fitness;
public:
//! doEDA constructor
/*!
All the boxes used by a EDASA need to be given.
\param selector Population Selector
\param estimator Distribution Estimator
\param selectone SelectOne
\param modifier Distribution Modifier
\param sampler Distribution Sampler
\param pop_continue Population Continuator
\param distribution_continue Distribution Continuator
\param evaluation Evaluation function.
\param sa_continue Stopping criterion.
\param cooling_schedule Cooling schedule, describes how the temperature is modified.
\param initial_temperature The initial temperature.
\param replacor Population replacor
*/
doEDA (eoSelect< EOT > & selector,
doEstimator< D > & estimator,
eoSelectOne< EOT > & selectone,
doModifierMass< D > & modifier,
doSampler< D > & sampler,
eoContinue< EOT > & pop_continue,
doContinue< D > & distribution_continue,
eoEvalFunc < EOT > & evaluation,
//moContinuator< moDummyNeighbor<EOT> > & sa_continue,
//moCoolingSchedule<EOT> & cooling_schedule,
//double initial_temperature,
eoReplacement< EOT > & replacor
)
: _selector(selector),
_estimator(estimator),
_selectone(selectone),
_modifier(modifier),
_sampler(sampler),
_pop_continue(pop_continue),
_distribution_continue(distribution_continue),
_evaluation(evaluation),
//_sa_continue(sa_continue),
//_cooling_schedule(cooling_schedule),
//_initial_temperature(initial_temperature),
_replacor(replacor)
{}
//! function that launches the EDASA algorithm.
/*!
As a moTS or a moHC, the EDASA can be used for HYBRIDATION in an evolutionary algorithm.
\param pop A population to improve.
\return TRUE.
*/
void operator ()(eoPop< EOT > & pop)
{
assert(pop.size() > 0);
//double temperature = _initial_temperature;
eoPop< EOT > current_pop;
eoPop< EOT > selected_pop;
//-------------------------------------------------------------
// Estimating a first time the distribution parameter thanks
// to population.
//-------------------------------------------------------------
D distrib = _estimator(pop);
double size = distrib.size();
assert(size > 0);
//-------------------------------------------------------------
do
{
//-------------------------------------------------------------
// (3) Selection of the best points in the population
//-------------------------------------------------------------
selected_pop.clear();
_selector(pop, selected_pop);
assert( selected_pop.size() > 0 );
//-------------------------------------------------------------
//-------------------------------------------------------------
// (4) Estimation of the distribution parameters
//-------------------------------------------------------------
distrib = _estimator(selected_pop);
//-------------------------------------------------------------
// TODO: utiliser selected_pop ou pop ???
assert(selected_pop.size() > 0);
//-------------------------------------------------------------
// Init of a variable contening a point with the bestest fitnesses
//-------------------------------------------------------------
EOT current_solution = _selectone(selected_pop);
//-------------------------------------------------------------
//-------------------------------------------------------------
// Fit the current solution with the distribution parameters (bounds)
//-------------------------------------------------------------
// FIXME: si besoin de modifier la dispersion de la distribution
// _modifier_dispersion(distribution, selected_pop);
_modifier(distrib, current_solution);
//-------------------------------------------------------------
//-------------------------------------------------------------
// Evaluating a first time the current solution
//-------------------------------------------------------------
_evaluation( current_solution );
//-------------------------------------------------------------
//-------------------------------------------------------------
// Building of the sampler in current_pop
//-------------------------------------------------------------
//_sa_continue.init( current_solution );
current_pop.clear();
for ( unsigned int i = 0; i < pop.size(); ++i )
//do
{
EOT candidate_solution = _sampler(distrib);
_evaluation( candidate_solution );
// TODO: verifier le critere d'acceptation
if ( candidate_solution.fitness() < current_solution.fitness()
// || rng.uniform() < exp( ::fabs(candidate_solution.fitness() - current_solution.fitness()) / temperature )
)
{
current_pop.push_back(candidate_solution);
current_solution = candidate_solution;
}
}
//while ( _sa_continue( current_solution) );
//-------------------------------------------------------------
_replacor(pop, current_pop); // copy current_pop in pop
pop.sort();
//if ( ! _cooling_schedule( temperature ) ){ eo::log << eo::debug << "_cooling_schedule" << std::endl; break; }
if ( ! _distribution_continue( distrib ) ){ eo::log << eo::debug << "_distribution_continue" << std::endl; break; }
if ( ! _pop_continue( pop ) ){ eo::log << eo::debug << "_pop_continue" << std::endl; break; }
}
while ( 1 );
}
private:
//! A EOT selector
eoSelect < EOT > & _selector;
//! A EOT estimator. It is going to estimate distribution parameters.
doEstimator< D > & _estimator;
//! SelectOne
eoSelectOne< EOT > & _selectone;
//! A D modifier
doModifierMass< D > & _modifier;
//! A D sampler
doSampler< D > & _sampler;
//! A EOT population continuator
eoContinue < EOT > & _pop_continue;
//! A D continuator
doContinue < D > & _distribution_continue;
//! A full evaluation function.
eoEvalFunc < EOT > & _evaluation;
//! Stopping criterion before temperature update
//moContinuator< moDummyNeighbor<EOT> > & _sa_continue;
//! The cooling schedule
//moCoolingSchedule<EOT> & _cooling_schedule;
//! Initial temperature
//double _initial_temperature;
//! A EOT replacor
eoReplacement < EOT > & _replacor;
};
#endif // !_doEDA_h

24
src/doEDASA.h
View file

@ -159,6 +159,15 @@ public:
//------------------------------------------------------------- //-------------------------------------------------------------
//-------------------------------------------------------------
// Evaluating a first time the current solution
//-------------------------------------------------------------
_evaluation( current_solution );
//-------------------------------------------------------------
//------------------------------------------------------------- //-------------------------------------------------------------
// Building of the sampler in current_pop // Building of the sampler in current_pop
//------------------------------------------------------------- //-------------------------------------------------------------
@ -170,21 +179,20 @@ public:
do do
{ {
EOT candidate_solution = _sampler(distrib); EOT candidate_solution = _sampler(distrib);
_evaluation( candidate_solution );
EOT& e1 = candidate_solution;
_evaluation( e1 );
EOT& e2 = current_solution;
_evaluation( e2 );
// TODO: verifier le critere d'acceptation // TODO: verifier le critere d'acceptation
if ( e1.fitness() < e2.fitness() || if ( candidate_solution.fitness() < current_solution.fitness() ||
rng.uniform() < exp( ::fabs(e1.fitness() - e2.fitness()) / temperature ) ) rng.uniform() < exp( ::fabs(candidate_solution.fitness() - current_solution.fitness()) / temperature ) )
{ {
current_pop.push_back(candidate_solution); current_pop.push_back(candidate_solution);
current_solution = candidate_solution; current_solution = candidate_solution;
} }
} }
while ( _sa_continue( current_solution) ); while ( _sa_continue( current_solution ) );
//-------------------------------------------------------------
_replacor(pop, current_pop); // copy current_pop in pop _replacor(pop, current_pop); // copy current_pop in pop

2
test/CMakeLists.txt
View file

@ -30,7 +30,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/application/eda_sa) INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/application/common)
SET(SOURCES SET(SOURCES
t-doEstimatorNormalMulti t-doEstimatorNormalMulti