def pytest6(verbose=1):
""" Check generation of OA(32, t, 2^a) """
N = 32
k = 8
t = 3
l = [2] * 8
rr = []
gtrr = [3, 5, 10, 17, 33]
s = oalib.intVector(l)
adata = oalib.arraydata_t(s, N, t, k)
if verbose:
print('pytest6: run different algorithms on the same case')
algs = [oalib.MODE_ORIGINAL, oalib.MODE_J4]
for ii, alg in enumerate(algs):
algname = oalib.algnames(alg)
if verbose >= 2:
print('pytest6: running %s, alg %s' % (adata.fullidstr(), algname))
rr = []
tmp = oahelper.runExtend(N,
k,
t,
l,
verbose=verbose,
nums=rr,
algorithm=alg)
if not rr == gtrr:
print('pytest6: case %s' % adata.fullidstr())
print(
' algorithm %s: error: incorrect number of arrays! %s -> %s'
% (algname, rr, gtrr))
def pytest2level(verbose=1):
""" Check generation of OA(16,2, 4^2 2^a) """
N = 32
k = 10
t = 3
l = [2]
rr = []
t0 = time.time()
oahelper.runExtend(N,
k,
t,
l,
verbose=1,
nums=rr,
algorithm=oalib.MODE_ORIGINAL)
dt = time.time() - t0
t0 = time.time()
oahelper.runExtend(N,
k,
t,
l,
verbose=1,
nums=rr,
algorithm=oalib.MODE_LMC_2LEVEL)
dt2level = time.time() - t0
ll = l * k
s = oalib.intVector(ll)
adata = oalib.arraydata_t(s, N, t, k)
if verbose:
print('case %s: 2-level method %.2f [s] -> %.2f [s]' %
(adata.idstr(), dt, dt2level))
def runExtend(N,
k,
t=3,
l=2,
verbose=1,
initsols=None,
nums=[],
algorithm=None):
""" Run extension algorithm and return arrays
Args:
N (int): number of rows
k (int): number of columns to extend to
t (int): strength of the arrays
l (int): factors of the designs
initsols (None or list): list of arrays to extend, None to start with root
Returns:
list: list of generated designs
Example:
>>> import oapackage
>>> designs = oapackage.oahelper.runExtend(16, 5, 3, verbose=0)
"""
if verbose:
print('runExtend: N=%d, k=%d, t=%d' % (N, k, t))
if isinstance(l, list):
ll = l
else:
ll = [l]
ll = ll + [ll[-1]] * (k - len(ll))
s = oalib.intVector(ll)
adata = oalib.arraydata_t(s, N, t, k)
al = oalib.array_link(adata.N, adata.strength, 1)
al.create_root(adata)
if initsols is None:
sols0 = oalib.arraylist_t()
sols0.append(al)
tstart = t
else:
sols0 = initsols
tstart = sols0[0].n_columns
oaoptions = oalib.OAextend()
if algorithm is None:
oaoptions.setAlgorithmAuto(adata)
else:
oaoptions.setAlgorithm(algorithm, adata)
solsx = sols0
for ii in range(tstart, k):
solsx = oalib.arraylist_t()
oalib.extend_arraylist(sols0, adata, oaoptions, ii, solsx)
if verbose >= 2:
print(' ii %d: %d' % (ii, solsx.size()))
sols0 = solsx
nums.append(solsx.size())
sys.stdout.flush()
return solsx
def runExtend(N,
k,
t=3,
l=2,
verbose=1,
initsols=None,
nums=[],
algorithm=None):
""" Run extension algorithm and return arrays
Arguments
---------
N : integer
number of rows
k: integer
number of columns
t: integer
strength of the arrays
>>> r = runExtend(16, 5, 3, verbose=0)
"""
if verbose:
print('runExtend: N=%d, k=%d, t=%d' % (N, k, t))
if isinstance(l, list): # types.ListType):
ll = l
else:
ll = [l]
ll = ll + [ll[-1]] * (k - len(ll))
s = oalib.intVector(ll)
adata = oalib.arraydata_t(s, N, t, k)
al = oalib.array_link(adata.N, adata.strength, 1)
al.create_root(adata)
if initsols is None:
sols0 = oalib.arraylist_t()
sols0.append(al)
tstart = t
else:
sols0 = initsols
tstart = sols0[0].n_columns
oaoptions = oalib.OAextend()
if algorithm is None:
oaoptions.setAlgorithmAuto(adata)
else:
oaoptions.setAlgorithm(algorithm, adata)
solsx = sols0
for ii in range(tstart, k):
solsx = oalib.arraylist_t()
oalib.extend_arraylist(sols0, adata, oaoptions, ii, solsx)
if verbose >= 2:
print(' ii %d: %d' % (ii, solsx.size()))
sols0 = solsx
nums.append(solsx.size())
sys.stdout.flush()
return solsx
def runExtend(N, k, t=3, l=2, verbose=1, initsols=None, nums=[], algorithm=None):
""" Run extension algorithm and return arrays
Args:
N (int): number of rows
k (int): number of columns to extend to
t (int): strength of the arrays
l (int): factors of the designs
initsols (None or list): list of arrays to extend, None to start with root
Returns:
list: list of generated designs
Example:
>>> import oapackage
>>> designs = oapackage.oahelper.runExtend(16, 5, 3, verbose=0)
"""
if verbose:
print('runExtend: N=%d, k=%d, t=%d' % (N, k, t))
if isinstance(l, list):
ll = l
else:
ll = [l]
ll = ll + [ll[-1]] * (k - len(ll))
s = oalib.intVector(ll)
adata = oalib.arraydata_t(s, N, t, k)
al = oalib.array_link(adata.N, adata.strength, 1)
al.create_root(adata)
if initsols is None:
sols0 = oalib.arraylist_t()
sols0.append(al)
tstart = t
else:
sols0 = initsols
tstart = sols0[0].n_columns
oaoptions = oalib.OAextend()
if algorithm is None:
oaoptions.setAlgorithmAuto(adata)
else:
oaoptions.setAlgorithm(algorithm, adata)
solsx = sols0
for ii in range(tstart, k):
solsx = oalib.arraylist_t()
oalib.extend_arraylist(sols0, adata, oaoptions, ii, solsx)
if verbose >= 2:
print(' ii %d: %d' % (ii, solsx.size()))
sols0 = solsx
nums.append(solsx.size())
sys.stdout.flush()
return solsx
def _optimDeffhelper(classdata):
""" Helper function that is suitable for the multi-processing framework """
N = classdata[0]
k = classdata[1]
alpha = classdata[2]
method = classdata[3]
p = classdata[4]
nabort = p.get('nabort', 2500)
niter = p.get('nabort', 12000)
arrayclass = oalib.arraydata_t(2, N, 1, k)
al = arrayclass.randomarray(1)
vv = optimDeffPython(al,
niter=niter,
nabort=nabort,
verbose=0,
alpha=alpha,
method=method)
return vv[0], vv[1].getarray()
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
> pygmentize -f html example_python_testing.py
@author: Pieter Eendebak
"""
#%% Load packages
import sys, os
import numpy as np
print('Python OA Interface Check')
import oalib
import oapackage.oahelper as oahelper
#%%
print('-- Create design configuration --')
adata = oalib.arraydata_t(2, 32, 2, 7)
oaoptions = oalib.OAextend()
oaoptions.setAlgorithmAuto(adata)
adata.show()
print('-- Create root element --')
al = adata.create_root()
al.show()
al.showarray()
# Extend
print('-- Extend arrays --')
print('Extend to 3 columns')
newsols = oalib.extend_array(al, adata, oaoptions)
print(newsols)
