def main(argv=None):
""" Main testing function """
print('OA performance testing')
ss = oalib.version()
print('OAlib: version %s' % ss)
ss = oalib.compile_information()
print(ss)
print('System:')
print(' Python: ' + ' '.join(sys.version.split('\n')))
print(' Machine: ' + ' '.join(['%s' % x for x in platform.uname()]))
if argv is None:
argv = sys.argv
try:
try:
opts, args = getopt.getopt(argv[1:], "h", ["help"])
except getopt.error as msg:
raise Usage(msg)
# more code, unchanged
except Usage as err:
print >> sys.stderr, err.msg
print >> sys.stderr, "for help use --help"
return 2
print('\nRunning tests:\n')
(dt, tt, cases, dt2) = pytest()
pytest2(oadir)
pytest3(verbose=0)
pytest4(verbose=1)
ta1 = pytest5(verbose=1)
pytest6(verbose=0)
pytest7(verbose=0)
pytest2level(verbose=1)
print('-----')
#tt=[];dt=0
dtx = ta1
print('\nResults:\n')
for ii, t in enumerate(tt):
print('%s: time %.2f [s]' % (cases[ii], t))
print('Total time: %.3f [s], %.3f [s], %.3f [s]' % (dt, dt2, dtx))
print(' should be of order 4.4 [s], 4.6 [s], 5.9 [s] (woelmuis)')
print(' should be of order 3.2 [s], 3.3 [s], 4.7 [s] (marmot) [v 2.0.0]')
print(
' should be of order 2.96 [s], 3.0 [s], 4.6 [s] (marmot) [v 2.0.24]')
def generateDpage(outputdir,
arrayclass,
dds,
allarrays,
fig=20,
optimfunc=[1, 0, 0],
nofig=False,
urlprefix='',
makeheader=True,
verbose=1,
lbls=None):
""" Helper function to generate web page with D-optimal design results """
if verbose:
print('generateDpage: dds %s' % str(dds.shape))
pp = oahelper.createPareto(dds)
narrays = dds.shape[0]
npareto = pp.number()
if verbose:
print('generateDpage: narrays %d' % narrays)
xstr = oahelper.series2htmlstr(arrayclass, case=1)
xstrplain = oahelper.series2htmlstr(arrayclass, html=0, case=1)
if verbose:
print('generateDpage: selectParetoArrays ')
paretoarrays = oahelper.selectParetoArrays(allarrays, pp)
at = array2Dtable(paretoarrays, verbose=1)
if verbose:
print('generateDpage: write file with Pareto arrays')
pfile0 = 'paretoarrays.oa'
pfile = os.path.join(outputdir, pfile0)
oalib.writearrayfile(pfile, paretoarrays)
istrlnk = markup.oneliner.a('paretoarrays.oa', href=urlprefix + pfile0)
if lbls is None:
lbls = ['Optimization of $D$']
hh = generateDscatter(dds, lbls=lbls, fig=fig, nofig=nofig)
oahelper.niceplot(hh.get('ax', None), despine=True, legend=hh['pltlegend'])
scatterfile = os.path.join(outputdir, 'scatterplot.png')
if verbose:
print('generateDpage: writen scatterplot to %s' % scatterfile)
plt.savefig(scatterfile, bbox_inches='tight', pad_inches=0.25, dpi=160)
#%% Create page
page = markup.page()
if makeheader:
page.init(
title="Class %s" % xstrplain,
css=('../oastyle.css'),
lang='en',
htmlattrs=dict({
'xmlns': 'http://www.w3.org/1999/xhtml',
'xml:lang': 'en'
}),
header="<!-- Start of page -->",
bodyattrs=dict({'style': 'padding-left: 3px;'}),
# doctype=markup.doctype.strict,
doctype=
'<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">',
metainfo=({
'text/html': 'charset=utf-8',
'keywords': 'orthogonal arrays designs',
'robots': 'index, follow',
'description': 'Even-Odd arrays'
}),
footer="<!-- End of page -->")
page.h1('Results for array class %s ' % xstr)
# mathjax is not updated properly...
ss = 'The Pareto optimaly was calculated according to the statistics \(D\), \(D1\) and \(Ds\).'
ss = 'The Pareto optimaly was calculated according to the statistics D, D<sub>1</sub> and D<sub>s</sub>.'
if npareto == 1:
page.p('Generated %d arrays, %d is Pareto optimal. %s' %
(narrays, npareto, ss))
else:
page.p('Generated %d arrays, %d are Pareto optimal. %s' %
(narrays, npareto, ss))
if narrays > 0:
scores = calcScore(dds, optimfunc)
tmp, dd, sols = selectDn(scores, dds, allarrays, nout=1)
A = sols[0]
bestdesignfile = os.path.join(outputdir, 'best-design.oa')
oalib.writearrayfile(bestdesignfile, A)
page.h2('Best design')
page.p('The best design: %s.' % e.a(
'best-design.oa', href=os.path.join(urlprefix, 'best-design.oa')))
page.p()
dd = dd[0]
page.span('D-efficiency: %.4f, ' % A.Defficiency()) # page.br()
page.span('D<sub>s</sub>-efficiency: %.4f, ' % dd[1]) # page.br()
page.span('D<sub>1</sub>-efficiency: %.4f' % dd[2])
page.br()
page.span('A-efficiency: %.3f' % A.Aefficiency())
page.br()
gwlp = A.GWLP()
# gwlp=','.join(['%.3f' % xq for xq in gwlp])
gwlp = oahelper.gwlp2str(gwlp, jstr=', ')
page.span('Generalized wordlength pattern: %s' % gwlp)
page.br()
# page.p('D-efficiency: %.3f' % A.Defficiency() )
pec = oalib.PECsequence(A)
pec = ','.join(['%.3f' % xq for xq in pec])
page.span('PEC-sequence: %s' % pec)
page.br()
page.h2('Table of Pareto optimal arrays ')
page.span(str(at))
page.p('All Pareto optimal arrays: %s' % istrlnk)
page.img(
src=urlprefix + 'scatterplot.png',
style=
"margin: 10px; width:95%; min-width: 300px; max-width:1100px; height: auto; "
)
citationstr = markup.oneliner.a(
'Complete Enumeration of Pure-Level and Mixed-Level Orthogonal Arrays',
href='http://dx.doi.org/10.1002/jcd.20236')
page.br(clear='both')
page.p(
'Citation notice: if you make use of the results on this page, please cite the following paper:'
)
page.p(
'%s, Journal of Combinatorial Designs, Volume 18, Issue 2, pages 123-140, 2010.'
% citationstr)
page.p('Generated with oapackage %s, date %s.' %
(oalib.version(), oahelper.timeString()))
outfile = os.path.join(outputdir, 'Dresults.html')
fid = open(outfile, 'wt')
fid.write(str(page))
fid.close()
print('written to file %s' % outfile)
return outfile
def miscunittest(verbose=1):
""" Perform some unit testing, return True if succesfull """
if verbose:
print('oapackage: unittest: oalib version %s' % oalib.version())
al = oalib.array_link()
ii = 0
al = oalib.exampleArray(ii, 0)
arrayclass = oalib.arraydata_t(2, 16, 2, 6) # fine
alist = [arrayclass.create_root()]
r = oalib.extend_arraylist(alist, arrayclass)
if len(r) != 3:
raise Exception('extension generation for %s failed' % (arrayclass, ))
if not isinstance(al.getarray(), np.ndarray):
print(
'oapackage: unittest: error: array interface not working properly')
else:
if not al[2, 0] == al.getarray()[2, 0]:
print(
'oapackage: unittest: error: array interface not working properly'
)
arrayclass = oalib.arraylink2arraydata(al)
if verbose >= 2:
print('unittest: calculate efficiencies')
Deff = al.Defficiency()
aa = oalib.Aefficiencies(al)
assert (aa[0] == 1.0)
assert (aa[1] == 1.0)
assert (aa[2] == 1.0)
if verbose >= 2:
print('## oapackage test: example array %d: Deff %.3f' % (ii, Deff))
# DOP reduction
if verbose >= 2:
print('unittest: test delete-one-factor GWLP reduction')
al = oalib.exampleArray(5, verbose)
al2 = al.randomperm()
alr = al.reduceDOP()
al2r = al2.reduceDOP()
if not alr == al2r:
print('error: DOP reduced arrays unequal!: %d' % (alr == al2r))
print('alr')
alr.showarraycompact()
print('al2r')
al2r.showarraycompact()
return False
transformation = oalib.reductionDOP(al)
check = transformation.apply(al) == al.reduceDOP()
if not check:
print('error: DOP reduction transformation is invalid')
# test graphtools
if verbose >= 2:
print('unittest: test graphtools')
from oapackage.graphtools import oa2graph
arrayclass = oalib.arraylink2arraydata(al)
_ = oa2graph(al, arrayclass)
test_numpy_interface()
test_nauty()
return True
def unittest(verbose=1):
""" Perform some unit testing, return True if succesfull """
if verbose:
print('oapackage: unittest: oalib version %s' % oalib.version())
al = oalib.array_link()
ii = 0
al = oalib.exampleArray(ii, 0)
#test_numpy_interface()
if not isinstance(al.getarray(), np.ndarray):
print(
'oapackage: unittest: error: array interface not working properly')
else:
if not al[2, 0] == al.getarray()[2, 0]:
print(
'oapackage: unittest: error: array interface not working properly'
)
arrayclass = oalib.arraylink2arraydata(al)
# print(arrayclass)
if verbose >= 2:
print('unittest: calculate efficiencies')
Deff = al.Defficiency()
aa = oalib.Aefficiencies(al)
if verbose >= 2:
print('## oapackage test: example array %d: Deff %.3f' % (ii, Deff))
# DOP reduction
if verbose >= 2:
print('unittest: test delete-one-factor GWLP reduction')
al = oalib.exampleArray(5, 1)
al2 = al.randomperm()
alr = al.reduceDOP()
al2r = al2.reduceDOP()
if not alr == al2r:
print('error: DOP reduced arrays unequal!: %d' % (alr == al2r))
print('alr')
alr.showarraycompact()
print('al2r')
al2r.showarraycompact()
return False
at = oalib.reductionDOP(al)
check = at.apply(al) == al.reduceDOP()
if not check:
print('error: DOP reduction transformation is invalid')
# test graphtools
if verbose >= 2:
print('unittest: test graphtools')
# import . graphtools
from .graphtools import oa2graph
arrayclass = oalib.arraylink2arraydata(al)
_ = oa2graph(al, arrayclass)
test_numpy_interface()
test_nauty()
return True
__uri__ = "http://www.pietereendebak.nl/oapackage/index.html"
__doc__ = __description__ + " <" + __uri__ + ">"
import oalib
oalib.setloglevel(oalib.SYSTEM)
oalib.log_print(-oalib.SYSTEM, '')
from oalib import *
# import .oahelper
from .oahelper import *
# import .Doptim
from .Doptim import *
from . import scanf
import numpy as np
__version__ = oalib.version()
#%%
def autodoctest():
""" Test the module using autodoc
Example:
>>> import oapackage
>>> arrayclass=oapackage.arraydata_t(2, 40, 0, 7)
>>> print(arrayclass)
arrayclass: N 40, k 7, strength 0, s {2,2,2,2,2,2,2}, order 0
"""
return
def generateDpage(outputdir, arrayclass, dds, allarrays, fig=20, optimfunc=[1, 0, 0],
nofig=False, urlprefix='', makeheader=True, verbose=1, lbls=None):
""" Helper function to generate web page with D-optimal design results """
if verbose:
print('generateDpage: dds %s' % str(dds.shape))
pp = oahelper.createPareto(dds)
narrays = dds.shape[0]
npareto = pp.number()
if verbose:
print('generateDpage: narrays %d' % narrays)
xstr = oahelper.series2htmlstr(arrayclass, case=1)
xstrplain = oahelper.series2htmlstr(arrayclass, html=0, case=1)
if verbose:
print('generateDpage: selectParetoArrays ')
paretoarrays = oahelper.selectParetoArrays(allarrays, pp)
at = array2Dtable(paretoarrays, verbose=1)
if verbose:
print('generateDpage: write file with Pareto arrays')
pfile0 = 'paretoarrays.oa'
pfile = os.path.join(outputdir, pfile0)
oalib.writearrayfile(pfile, paretoarrays)
istrlnk = markup.oneliner.a('paretoarrays.oa', href=urlprefix + pfile0)
if lbls is None:
lbls = ['Optimization of $D$']
if fig is not None:
hh = generateDscatter(dds, lbls=lbls, fig=fig, nofig=nofig)
oahelper.niceplot(hh.get('ax', None), despine=True, legend=hh['pltlegend'])
scatterfile = os.path.join(outputdir, 'scatterplot.png')
if verbose:
print('generateDpage: writen scatterplot to %s' % scatterfile)
plt.savefig(scatterfile, bbox_inches='tight', pad_inches=0.25, dpi=160)
page = markup.page()
if makeheader:
page.init(title="Class %s" % xstrplain,
css=('../oastyle.css'),
lang='en', htmlattrs=dict({'xmlns': 'http://www.w3.org/1999/xhtml', 'xml:lang': 'en'}),
header="<!-- Start of page -->",
bodyattrs=dict({'style': 'padding-left: 3px;'}),
doctype='<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">',
metainfo=({'text/html': 'charset=utf-8', 'keywords': 'orthogonal arrays designs',
'robots': 'index, follow', 'description': 'Even-Odd arrays'}),
footer="<!-- End of page -->")
page.h1('Results for array class %s ' % xstr)
ss = r'The Pareto optimaly was calculated according to the statistics D, D<sub>1</sub> and D<sub>s</sub>.'
if npareto == 1:
page.p('Generated %d arrays, %d is Pareto optimal. %s' %
(narrays, npareto, ss))
else:
page.p('Generated %d arrays, %d are Pareto optimal. %s' %
(narrays, npareto, ss))
if narrays > 0:
scores = calcScore(dds, optimfunc)
_, dd, sols = selectDn(scores, dds, allarrays, nout=1)
A = sols[0]
bestdesignfile = os.path.join(outputdir, 'best-design.oa')
oalib.writearrayfile(bestdesignfile, A)
page.h2('Best design')
page.p('The best design: %s.' %
e.a('best-design.oa', href=os.path.join(urlprefix, 'best-design.oa')))
page.p()
dd = dd[0]
page.span('D-efficiency: %.4f, ' % A.Defficiency()) # page.br()
page.span('D<sub>s</sub>-efficiency: %.4f, ' % dd[1]) # page.br()
page.span('D<sub>1</sub>-efficiency: %.4f' % dd[2])
page.br()
page.span('A-efficiency: %.3f' % A.Aefficiency())
page.br()
gwlp = A.GWLP()
# gwlp=','.join(['%.3f' % xq for xq in gwlp])
gwlp = oahelper.gwlp2str(gwlp, jstr=', ')
page.span('Generalized wordlength pattern: %s' % gwlp)
page.br()
# page.p('D-efficiency: %.3f' % A.Defficiency() )
pec = oalib.PECsequence(A)
pec = ','.join(['%.3f' % xq for xq in pec])
page.span('PEC-sequence: %s' % pec)
page.br()
page.h2('Table of Pareto optimal arrays ')
page.span(str(at))
page.p('All Pareto optimal arrays: %s' % istrlnk)
page.img(src=urlprefix + 'scatterplot.png',
style="margin: 10px; width:95%; min-width: 300px; max-width:1100px; height: auto; ")
citationstr = markup.oneliner.a(
'Complete Enumeration of Pure-Level and Mixed-Level Orthogonal Arrays', href='https://doi.org/10.1002/jcd.20236')
page.br(clear='both')
page.p(
'Citation notice: if you make use of the results on this page, please cite the following paper:')
page.p('%s, Journal of Combinatorial Designs, Volume 18, Issue 2, pages 123-140, 2010.' %
citationstr)
page.p('Generated with oapackage %s, date %s.' %
(oalib.version(), oahelper.timeString()))
outfile = os.path.join(outputdir, 'Dresults.html')
fid = open(outfile, 'wt')
fid.write(str(page))
fid.close()
print('written to file %s' % outfile)
return outfile