+ eda algo: same algo than eda-sa without sa, + plotting scripts and problem functions moved to application/common
This commit is contained in:
Caner Candan
parent
ba6770df43
commit
65191e2212
16 changed files with 595 additions and 14 deletions
14
application/common/CMakeLists.txt
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14
application/common/CMakeLists.txt
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PROJECT(common)
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SET(RESOURCES
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gplot.py
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ggobi.py
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)
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FOREACH(file ${RESOURCES})
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EXECUTE_PROCESS(
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COMMAND ${CMAKE_COMMAND} -E copy_if_different
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${CMAKE_CURRENT_SOURCE_DIR}/${file}
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${DO_BINARY_DIR}/${file}
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)
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ENDFOREACH(file)
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42
application/common/Rosenbrock.h
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42
application/common/Rosenbrock.h
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#ifndef _Rosenbrock_h
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#define _Rosenbrock_h
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#include <eo>
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#include <es.h>
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#include <es/eoRealInitBounded.h>
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#include <es/eoRealOp.h>
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#include <es/eoEsChromInit.h>
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#include <es/eoRealOp.h>
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#include <es/make_real.h>
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#include <apply.h>
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#include <eoProportionalCombinedOp.h>
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template < typename EOT >
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class Rosenbrock : public eoEvalFunc< EOT >
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{
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public:
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typedef typename EOT::AtomType AtomType;
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virtual void operator()( EOT& p )
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{
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if (!p.invalid())
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return;
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p.fitness( _evaluate( p ) );
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}
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private:
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AtomType _evaluate( EOT& p )
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{
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AtomType r = 0.0;
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for (unsigned int i = 0; i < p.size() - 1; ++i)
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{
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r += p[i] * p[i];
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}
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return r;
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}
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};
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#endif // !_Rosenbrock_h
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42
application/common/Sphere.h
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42
application/common/Sphere.h
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#ifndef _Sphere_h
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#define _Sphere_h
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#include <eo>
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#include <es.h>
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#include <es/eoRealInitBounded.h>
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#include <es/eoRealOp.h>
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#include <es/eoEsChromInit.h>
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#include <es/eoRealOp.h>
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#include <es/make_real.h>
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#include <apply.h>
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#include <eoProportionalCombinedOp.h>
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template < typename EOT >
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class Sphere : public eoEvalFunc< EOT >
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{
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public:
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typedef typename EOT::AtomType AtomType;
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virtual void operator()( EOT& p )
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{
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if (!p.invalid())
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return;
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p.fitness( _evaluate( p ) );
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}
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private:
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AtomType _evaluate( EOT& p )
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{
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AtomType r = 0.0;
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for (unsigned int i = 0; i < p.size() - 1; ++i)
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{
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r += p[i] * p[i];
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}
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return r;
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}
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};
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#endif // !_Sphere_h
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68
application/common/ggobi.py
Executable file
68
application/common/ggobi.py
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#!/usr/bin/env python
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from pprint import *
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import sys, os
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if __name__ == '__main__':
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# parameter phase
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if len(sys.argv) < 2:
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print 'Usage: %s [FILE]' % sys.argv[0]
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sys.exit()
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filename = sys.argv[1]
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lines = open(filename).readlines()
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# formatting phase
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try:
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results = [ x.split() for x in lines[1:-1] ]
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except IOError, e:
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print 'Error: %s' % e
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sys.exit()
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# dimension estimating phase
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popsize = int(lines[0].split()[0])
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dimsize = int(results[0][1])
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# printing phase
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print 'popsize: %d' % popsize
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print 'dimsize: %d' % dimsize
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print
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pprint( results )
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# cvs converting phase
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i = 1
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for x in results:
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x.insert(0, '"%d"' % i)
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i += 1
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header = ['""', '"fitness"', '"dimsize"']
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for i in range(0, dimsize):
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header.append( '"dim%d"' % i )
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results.insert(0, header)
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# cvs printing phase
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file_results = '\n'.join( [ ','.join( x ) for x in results ] )
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print
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print file_results
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try:
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open('%s.csv' % filename, 'w').write(file_results + '\n')
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except IOError, e:
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print 'Error: %s' % e
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sys.exit()
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# ggobi plotting phase
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os.system('ggobi %s.csv' % filename)
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399
application/common/gplot.py
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399
application/common/gplot.py
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#!/usr/bin/env python
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"""plot.py -- Plot EDA-SA results file"""
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import os, time, math, tempfile
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import numpy
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try:
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import Gnuplot, Gnuplot.PlotItems, Gnuplot.funcutils
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except ImportError:
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# kludge in case Gnuplot hasn't been installed as a module yet:
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import __init__
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Gnuplot = __init__
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import PlotItems
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Gnuplot.PlotItems = PlotItems
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import funcutils
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Gnuplot.funcutils = funcutils
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import optparse, logging, sys
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LEVELS = {'debug': logging.DEBUG,
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'info': logging.INFO,
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'warning': logging.WARNING,
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'error': logging.ERROR,
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'critical': logging.CRITICAL}
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def logger(level_name, filename='plot.log'):
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logging.basicConfig(
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level=logging.DEBUG,
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format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
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filename=filename, filemode='a'
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)
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console = logging.StreamHandler()
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console.setLevel(LEVELS.get(level_name, logging.NOTSET))
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console.setFormatter(logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s'))
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logging.getLogger('').addHandler(console)
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def parser(parser=optparse.OptionParser()):
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parser.add_option('-v', '--verbose', choices=LEVELS.keys(), default='warning', help='set a verbose level')
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parser.add_option('-f', '--files', help='give some input sample files separated by comma (cf. gen1,gen2,...)', default='')
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parser.add_option('-r', '--respop', help='define the population results containing folder', default='./ResPop')
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parser.add_option('-o', '--output', help='give an output filename for logging', default='plot.log')
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parser.add_option('-d', '--dimension', help='give a dimension size', default=2)
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parser.add_option('-m', '--multiplot', action="store_true", help='plot all graphics in one window', dest="multiplot", default=True)
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parser.add_option('-p', '--plot', action="store_false", help='plot graphics separetly, one by window', dest="multiplot")
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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)
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parser.add_option('-G', '--graphicsdirectory', help='give a directory name for graphics, this option should be combined with -u', default='plot')
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parser.add_option('-g', '--graphicsprefixname', help='give a prefix name for graphics, this option should be combined with -u', default='plot')
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parser.add_option('-t', '--terminal', action="store_true", help='display graphics on gnuplot windows', dest="terminal", default=True)
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parser.add_option('-u', '--png', action="store_false", help='display graphics on png files', dest="terminal")
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options, args = parser.parse_args()
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logger(options.verbose, options.output)
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return options
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options = parser()
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def wait(str=None, prompt='Press return to show results...\n'):
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if str is not None:
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print str
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raw_input(prompt)
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def draw2DRect(min=(0,0), max=(1,1), color='black', state=None, g=None):
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if g == None: g = Gnuplot.Gnuplot()
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if state != None: state.append(g)
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xmin, ymin = min
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xmax, ymax = max
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cmd = 'set arrow from %s,%s to %s,%s nohead lc rgb "%s"'
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g(cmd % (xmin, ymin, xmin, ymax, color))
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g(cmd % (xmin, ymax, xmax, ymax, color))
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g(cmd % (xmax, ymax, xmax, ymin, color))
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g(cmd % (xmax, ymin, xmin, ymin, color))
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return g
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def draw3DRect(min=(0,0,0), max=(1,1,1), state=None, g=None):
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if g == None: g = Gnuplot.Gnuplot()
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if state != None: state.append(g)
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# TODO
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return g
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def getSortedFiles(path):
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assert path != None
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if options.files == '':
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filelist = os.listdir(path)
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filelist.sort()
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else:
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filelist = options.files.split(',')
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checkFileErrors(path, filelist)
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return filelist
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def checkFileErrors(path, filelist):
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for filename in filelist:
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for line in open('%s/%s' % (path, filename)):
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if '-nan' in line:
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logging.warning("checkFileErrors: %s/%s file contains bad value, it is going to be skipped" % (path, filename))
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filelist.remove(filename)
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break
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def plotXPointYFitness(path, fields='3:1', state=None, g=None):
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if g == None:
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g = Gnuplot.Gnuplot()
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if not options.terminal:
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g('set terminal png')
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g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXPointYFitness'))
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if state != None: state.append(g)
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g.title('Fitness observation')
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g.xlabel('Coordinates')
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g.ylabel('Fitness (Quality)')
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files=[]
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for filename in getSortedFiles(path):
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files.append(Gnuplot.File(path + '/' + filename, using=fields,
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with_='points',
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#title='distribution \'' + filename + '\''
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title=""
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)
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)
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if len(files) > 0:
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g.plot(*files)
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return g
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def plotXYPointZFitness(path, fields='4:3:1', state=None, g=None):
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if g == None:
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g = Gnuplot.Gnuplot()
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if not options.terminal:
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g('set terminal png')
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g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYPointZFitness'))
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if state != None: state.append(g)
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g.title('Fitness observation in 3-D')
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g.xlabel('x-axes')
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g.ylabel('y-axes')
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g.zlabel('Fitness (Quality)')
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files=[]
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for filename in getSortedFiles(path):
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files.append(Gnuplot.File(path + '/' + filename, using=fields,
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with_='points',
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#title='distribution \'' + filename + '\''
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title=""
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)
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)
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if len(files) > 0:
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g.splot(*files)
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return g
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def plotXYPoint(path, fields='3:4', state=None, g=None):
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if g == None:
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g = Gnuplot.Gnuplot()
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if not options.terminal:
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g('set terminal png')
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g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYPoint'))
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if state != None: state.append(g)
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g.title('Points observation in 2-D')
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g.xlabel('x-axes')
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g.ylabel('y-axes')
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files=[]
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for filename in getSortedFiles(path):
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files.append(Gnuplot.File(path + '/' + filename, using=fields,
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with_='points',
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#title='distribution \'' + filename + '\''
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title=""
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)
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)
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if len(files) > 0:
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g.plot(*files)
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return g
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def plotXYZPoint(path, fields='3:4:5', state=None, g=None):
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if g == None:
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g = Gnuplot.Gnuplot()
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if not options.terminal:
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g('set terminal png')
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g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYZPoint'))
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if state != None: state.append(g)
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g.title('Points observation in 3-D')
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g.xlabel('x-axes')
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g.ylabel('y-axes')
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g.zlabel('z-axes')
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files=[]
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for filename in getSortedFiles(path):
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files.append(Gnuplot.File(path + '/' + filename, using=fields,
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with_='points',
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#title='distribution \'' + filename + '\''
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title=""
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)
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)
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if len(files) > 0:
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g.splot(*files)
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return g
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def plotParams(path, field='1', state=None, g=None):
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if g == None:
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g = Gnuplot.Gnuplot()
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if not options.terminal:
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g('set terminal png')
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g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'plotXYZPoint'))
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if state != None: state.append(g)
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g.title('Hyper-volume comparaison through all dimensions')
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g.xlabel('Iterations')
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g.ylabel('Hyper-volume')
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g.plot(Gnuplot.File(path, with_='lines', using=field,
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title='multivariate distribution narrowing'))
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return g
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def plot2DRectFromFiles(path, state=None, g=None, plot=True):
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if g == None:
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g = Gnuplot.Gnuplot()
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if not options.terminal:
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g('set terminal png')
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g('set output \'%s_%s.png\'' % (options.graphicsprefixname, 'plot2DRectFromFiles'))
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if state != None: state.append(g)
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g.title('Rectangle drawing observation')
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g.xlabel('x-axes')
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g.ylabel('y-axes')
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x1,x2,y1,y2 = 0,0,0,0
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colors = ['red', 'orange', 'blue', 'green', 'gold', 'yellow', 'gray']
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#colors = open('rgb.txt', 'r').readlines()
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colors_size = len(colors)
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i = 0 # for color
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for filename in getSortedFiles(path):
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line = open(path + '/' + filename, 'r').readline()
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fields = line.split(' ')
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if not fields[0] == '2':
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print 'plot2DRectFromFiles: higher than 2 dimensions not possible to draw'
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return
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xmin,ymin,xmax,ymax = fields[1:5]
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#print xmin,ymin,xmax,ymax
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cur_color = colors[i % colors_size]
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draw2DRect((xmin,ymin), (xmax,ymax), cur_color, g=g)
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g('set obj rect from %s,%s to %s,%s back lw 1.0 fc rgb "%s" fillstyle solid 1.00 border -1'
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% (xmin,ymin,xmax,ymax,cur_color)
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)
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if plot:
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if float(xmin) < x1: x1 = float(xmin)
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if float(ymin) < y1: y1 = float(ymin)
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if float(xmax) > x2: x2 = float(xmax)
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if float(ymax) > y2: y2 = float(ymax)
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#print x1,y1,x2,y2
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i += 1
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#print x1,y1,x2,y2
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if plot:
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g.plot('[%s:%s][%s:%s] -9999 notitle' % (x1, x2, y1, y2))
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return g
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def main():
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gstate = []
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n = int(options.dimension)
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w = int(options.windowid)
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r = options.respop
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if not options.terminal:
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try:
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os.mkdir(options.graphicsdirectory)
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except OSError:
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pass
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if options.multiplot:
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g = Gnuplot.Gnuplot()
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if not options.terminal:
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g('set terminal png')
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g('set output \'%s/%s_%s.png\'' % (options.graphicsdirectory, options.graphicsprefixname, 'multiplot'))
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|
||||
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 ###')
|
||||
Reference in a new issue