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 extendSingleArray(A, adata, t=3, verbose=1):
""" Extend a single array """
oaoptions = oalib.OAextend()
sols0 = oalib.arraylist_t()
solsx = oalib.arraylist_t()
sols0.push_back(A)
#N = A.n_rows
k = A.n_columns
n = oalib.extend_arraylist(sols0, adata, oaoptions, k, solsx)
sys.stdout.flush()
return solsx
def extendSingleArray(A, adata, t=3, verbose=1):
""" Extend a single orthogonal array """
oaoptions = oalib.OAextend()
oaoptions.setAlgorithmAuto(adata)
sols0 = oalib.arraylist_t()
solsx = oalib.arraylist_t()
sols0.push_back(A)
k = A.n_columns
n = oalib.extend_arraylist(sols0, adata, oaoptions, k, solsx)
assert(n >= len(solsx))
sys.stdout.flush()
return solsx
def extendSingleArray(A, adata, t=3, verbose=1):
""" Extend a single orthogonal array """
oaoptions = oalib.OAextend()
oaoptions.setAlgorithmAuto(adata)
sols0 = oalib.arraylist_t()
solsx = oalib.arraylist_t()
sols0.push_back(A)
k = A.n_columns
n = oalib.extend_arraylist(sols0, adata, oaoptions, k, solsx)
assert (n >= len(solsx))
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 selectArraysInFile(infile,
outfile,
idx,
afmode=oalib.ATEXT,
verbose=1,
cache=1):
""" Select arrays in a file by indices
Args:
infile (str): file with designs
outfile (str): output file with designs
inx (list of indices)
Returns:
None
"""
if not checkFiles(outfile, cache=cache):
gidxint = oalib.intVector([int(x) for x in idx])
sols = oalib.arraylist_t()
oalib.selectArrays(infile, gidxint, sols, 0)
af = oalib.arrayfile_t(infile, 1)
_ = oalib.writearrayfile(outfile, sols, afmode, af.nrows, af.ncols)
if verbose >= 2:
print('selectArrays: write array file %s in mode %d' %
(outfile, afmode))
else:
if verbose >= 2:
print('output file %s already exists' % outfile)
def joinArrayLists(ww):
""" Concetenate a list of array lists into a single list """
ll = oalib.arraylist_t()
for w in ww:
for al in w:
ll.push_back(al)
return ll
def selectArrays(infile, outfile, idx, afmode=oalib.ATEXT, verbose=1, cache=1):
""" Select arrays in a file by indices
Input:
- infile (string)
- outfile (string)
- inx (list of indices)
Output:
- None
"""
if not checkFiles(outfile, cache=cache):
gidxint = oalib.intVector([int(x) for x in idx])
# print(' xx select: %s' % str(gidxint))
# print(' xx select: %s' % str([v for v in gidxint]))
sols = oalib.arraylist_t()
oalib.selectArrays(infile, gidxint, sols, 0)
af = oalib.arrayfile_t(infile, 1)
af.nrows
r = oalib.writearrayfile(outfile, sols, afmode, af.nrows, af.ncols)
if verbose >= 2:
print('selectArrays: write array file %s in mode %d' %
(outfile, afmode))
else:
if verbose >= 2:
print('output file %s already exists' % outfile)
def selectParetoArrays(allarrays, pp):
""" Select arrays using a Pareto object """
paretoarrays = oalib.arraylist_t()
paretoidx = np.array(pp.allindices())
ww = oalib.longVector(tuple(paretoidx.tolist()))
oalib.selectArrays(allarrays, ww, paretoarrays)
return paretoarrays
def joinArrayLists(ww):
""" Concetenate a list of array lists into a single list """
ll = oalib.arraylist_t()
for w in ww:
for al in w:
ll.push_back(al)
return ll
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 selectParetoArrays(array_list, pareto_object):
""" Select arrays using a Pareto object
Args:
array_list (list): list of arrays
pareto (object): oapackage Pareto object
Returns:
list: list with all Pareto optimal designs
"""
paretoarrays = oalib.arraylist_t()
paretoidx = np.array(pareto_object.allindices())
ww = oalib.longVector(tuple(paretoidx.tolist()))
oalib.selectArrays(array_list, ww, paretoarrays)
return paretoarrays
def selectParetoArrays(array_list, pareto_object):
""" Select arrays using a Pareto object
Args:
array_list (list): list of arrays
pareto (object): oapackage Pareto object
Returns:
list: list with all Pareto optimal designs
"""
paretoarrays = oalib.arraylist_t()
paretoidx = np.array(pareto_object.allindices())
ww = oalib.longVector(tuple(paretoidx.tolist()))
oalib.selectArrays(array_list, ww, paretoarrays)
return paretoarrays
def selectJ(sols0, jj=5, jresults=None, verbose=1):
""" Select only arrays with J-characteristics non-zero """
if jresults is None:
jresults = oalib.analyseArrays(sols0, verbose, jj)
solseo = oalib.arraylist_t()
v = []
for ii, js in enumerate(jresults):
# js.show()
# if not np.array(js.vals)[0]==0:
# solseo.append(sols0[ii])
v.append(js.vals[0])
si = [i for (i, j) in sorted(enumerate(v), key=operator.itemgetter(1))]
for jj in si:
if v[jj] > 0:
solseo.append(sols0[jj])
if verbose:
print('selectJ: kept %d/%d solutions' % (solseo.size(), sols0.size()))
return solseo
def selectJ(sols0, jj=5, jresults=None, verbose=1):
""" Select only arrays with J-characteristics non-zero
We asssume the designs are in even-odd ordering (i.e. only check the J value of first columns)
"""
if jresults is None:
jresults = oalib.analyseArrays(sols0, verbose, jj)
solseo = oalib.arraylist_t()
v = []
for ii, js in enumerate(jresults):
v.append(js.values[0])
si = [i for (i, j) in sorted(enumerate(v), key=operator.itemgetter(1))]
for jj in si:
if v[jj] > 0:
solseo.append(sols0[jj])
if verbose:
print('selectJ: kept %d/%d solutions' % (solseo.size(), len(sols0)))
return solseo
def selectJ(sols0, jj=5, jresults=None, verbose=1):
""" Select only arrays with J-characteristics non-zero
We asssume the designs are in even-odd ordering (i.e. only check the J value of first columns)
"""
if jresults is None:
jresults = oalib.analyseArrays(sols0, verbose, jj)
solseo = oalib.arraylist_t()
v = []
for ii, js in enumerate(jresults):
v.append(js.values[0])
si = [i for (i, j) in sorted(enumerate(v), key=operator.itemgetter(1))]
for jj in si:
if v[jj] > 0:
solseo.append(sols0[jj])
if verbose:
print('selectJ: kept %d/%d solutions' % (solseo.size(), len(sols0)))
return solseo
def selectArraysInFile(infile, outfile, idx, afmode=oalib.ATEXT, verbose=1, cache=1):
""" Select arrays in a file by indices
Args:
infile (str): file with designs
outfile (str): output file with designs
inx (list of indices)
Returns:
None
"""
if not checkFiles(outfile, cache=cache):
gidxint = oalib.intVector([int(x) for x in idx])
sols = oalib.arraylist_t()
oalib.selectArrays(infile, gidxint, sols, 0)
af = oalib.arrayfile_t(infile, 1)
_ = oalib.writearrayfile(outfile, sols, afmode, af.nrows, af.ncols)
if verbose >= 2:
print('selectArrays: write array file %s in mode %d' %
(outfile, afmode))
else:
if verbose >= 2:
print('output file %s already exists' % outfile)