def arraystats(A, verbose=1):
""" Return statistics of an array """
Af = A.transpose().flatten()
al = oalib.array_link(A.shape[0], A.shape[1], 0)
alist = oalib.arraylist_t(1)
alist[0] = al
# al.array
ia = oalib.intArray.frompointer(al.array)
for x in range(0, A.size):
ia[x] = int(Af[x])
# al.showarray()
jresults = oalib.analyseArrays(alist, 0)
js = jresults[0]
vals = pointer2np(js.vals, js.nc)
jvals = getposjvals(A, 3, verbose=0)
jv = np.zeros(len(jvals))
c = Counter(abs(vals))
for ii, xx in enumerate(jvals):
if c.has_key(xx):
jv[ii] = c.get(xx)
if verbose:
print('Possible j-values: %s' % jvals, end="")
print(' values: %s' % jv.astype(int))
N = A.shape[0]
Ak = (1 / N ^ 2) * sum(vals**2)
print('Ak: %s' % Ak)
return Ak
def makearraylink(al):
""" Convert array to array_link object """
if isinstance(al, np.ndarray):
tmp = oalib.array_link()
tmp.setarray(al)
al = tmp
return al
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 makearraylink(array):
""" Convert array to array_link object
Args:
array (numpy array): array to convert
Returns:
array_link
"""
if isinstance(array, np.ndarray):
tmp = oalib.array_link()
tmp.setarray(array)
array = tmp
return array
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 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