def test_modelmatrix(self):
al = oapackage.exampleArray(1, 0)
sizes = oapackage.array2modelmatrix_sizes(al)
k = al.n_columns
self.assertEqual(sizes, (1, 1 + k, int(1 + k + k * (k - 1) / 2),
int(1 + k + k * (k + 1) / 2)))
model_matrix = oapackage.array2modelmatrix(al, "main", verbose=0)
np.testing.assert_array_equal(2 * np.array(al) - 1, model_matrix[:,
1:])
conf_design = oapackage.exampleArray(41, 0)
sizes = oapackage.array2modelmatrix_sizes(conf_design)
k = conf_design.n_columns
self.assertEqual(sizes, (1, 1 + k, int(1 + k + k * (k - 1) / 2),
int(1 + k + k * (k + 1) / 2)))
model_matrix = oapackage.array2modelmatrix(conf_design, "i", 0)
self.assertTrue(model_matrix.shape[1] == sizes[2])
model_matrix = oapackage.array2modelmatrix(conf_design, "q", 0)
last_column = np.array(conf_design)[:, -1]
np.testing.assert_array_equal(model_matrix[:, -1],
last_column * last_column)
self.assertTrue(model_matrix.shape[1] == sizes[3])
def test_is_ortogonal_array(self):
al = oapackage.exampleArray(1, 0)
self.assertTrue(al.is_orthogonal_array())
al[1, 2] = -1
self.assertFalse(al.is_orthogonal_array())
al = oapackage.exampleArray(41, 0)
self.assertFalse(al.is_orthogonal_array())
def test_conference_model_statistics(self):
arrays = [
oapackage.exampleArray(idx, 0).selectFirstColumns(4)
for idx in [46, 47, 48]
]
dsds = [oapackage.conference2DSD(array) for array in arrays]
with mock.patch('sys.stdout', new_callable=io.StringIO) as mock_stdout:
statistics = [
oapackage.conference.modelStatistics(al, verbose=2)
for al in dsds
]
stdout = mock_stdout.getvalue()
self.assertIn('modelStatistics: condition number: ', stdout)
expected = [(0, 0, 0), (0, 0, 0),
(1, 17.081221494279234, 1.7610790263409104)]
_statistics_equal(statistics, expected)
arrays = [
oapackage.exampleArray(idx, 0).selectLastColumns(4)
for idx in [46, 47, 48]
]
dsds = [oapackage.conference2DSD(array) for array in arrays]
statistics = [
oapackage.conference.modelStatistics(al, verbose=0) for al in dsds
]
expected = [(1, 17.312358463836613, 1.8538666749267378),
(1, 17.312358463836613, 1.8538666749267378),
(1, 17.08122149427922, 1.7610790263409093)]
_statistics_equal(statistics, expected)
def test_array2eigenModelMatrixMixed(self):
array = oapackage.exampleArray(0, 0)
r = oapackage.array2eigenModelMatrixMixed(array.selectFirstColumns(1),
verbose=0)
main_effects = r[0]
np.testing.assert_array_equal(
main_effects,
np.array([[-1., -1., -1., -1., 1., 1., 1., 1.]]).T)
array = oapackage.exampleArray(10, 0).selectFirstColumns(2)
r = oapackage.array2eigenModelMatrixMixed(array, verbose=0)
main_effects = r[0]
interaction_model = r[1]
np.testing.assert_array_almost_equal(
main_effects,
np.array([[-1.22474487, -0.70710678, -1.22474487, -0.70710678],
[-1.22474487, -0.70710678, 1.22474487, -0.70710678],
[-1.22474487, -0.70710678, 0., 1.41421356],
[1.22474487, -0.70710678, 1.22474487, -0.70710678],
[1.22474487, -0.70710678, 1.22474487, -0.70710678],
[1.22474487, -0.70710678, 0., 1.41421356],
[0., 1.41421356, -1.22474487, -0.70710678],
[0., 1.41421356, -1.22474487, -0.70710678],
[0., 1.41421356, 0., 1.41421356]]))
np.testing.assert_array_almost_equal(
interaction_model,
np.array([[1.5, 0.8660254, 0.8660254, 0.5],
[-1.5, 0.8660254, -0.8660254, 0.5],
[-0., -1.73205081, -0., -1.],
[1.5, -0.8660254, -0.8660254, 0.5],
[1.5, -0.8660254, -0.8660254, 0.5],
[0., 1.73205081, -0., -1.], [-0., -0., -1.73205081, -1.],
[-0., -0., -1.73205081, -1.], [0., 0., 0., 2.]]))
def test_double_conference_foldover_permutation(self):
al = oapackage.exampleArray(37, 0)
expected = [
0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 11, 16, 19, 17, 18, 15, 14, 13,
12
]
permutation = oapackage.double_conference_foldover_permutation(al)
self.assertEqual(list(permutation), expected)
N = int(al.n_rows / 2)
folded = np.array(oapackage.array_link(np.array(al)[permutation, :]))
np.testing.assert_array_equal(folded[0:N, :], -folded[N:, :])
expected[5], expected[3] = expected[3], expected[5]
expected[-1], expected[4] = expected[4], expected[-1]
expected[-3], expected[7] = expected[7], expected[-3]
al = oapackage.array_link(np.array(al)[expected, :])
permutation = oapackage.double_conference_foldover_permutation(al)
folded = np.array(oapackage.array_link(np.array(al)[permutation, :]))
N = int(al.n_rows / 2)
np.testing.assert_array_equal(folded[0:N, :], -folded[N:, :])
al = oapackage.exampleArray(45, 0)
permutation = oapackage.double_conference_foldover_permutation(al)
self.assertEqual(permutation[0], -1)
al = oapackage.exampleArray(5, 0)
with self.assertRaises(RuntimeError):
permutation = oapackage.double_conference_foldover_permutation(al)
al = oapackage.array_link(3, 4, 0)
with self.assertRaises(RuntimeError):
permutation = oapackage.double_conference_foldover_permutation(al)
def test_generateDpage(self):
outputdir = tempfile.mkdtemp()
allarrays = [
oapackage.exampleArray(2, 0),
oapackage.exampleArray(2, 0)
]
dds = np.array([A.Defficiencies() for A in allarrays])
arrayclass = oapackage.arraylink2arraydata(allarrays[0])
with mock.patch('sys.stdout', new_callable=io.StringIO) as mock_stdout:
page = oapackage.Doptim.generateDpage(outputdir,
arrayclass,
dds,
allarrays,
fig=None,
optimfunc=[1, 0, 0],
nofig=True)
if self.guitest and 0:
print('test_generateDpage: run gui test')
page = oapackage.Doptim.generateDpage(outputdir,
arrayclass,
dds,
allarrays,
fig=100,
optimfunc=[1, 0, 0],
nofig=True)
self.assertIsInstance(page, oapackage.markup.page)
try:
import matplotlib
matplotlib.pyplot.close(100)
except ImportError:
pass
def test_exampleArray(self):
# test a selection of the example arrays
al = oapackage.exampleArray(5, 0)
self.assertTrue(al.md5() == '3885c883d3bee0c7546511255bb5c3ae')
al = oapackage.exampleArray(20, 0)
self.assertTrue(np.array(al).shape == (24, 3))
al = oapackage.exampleArray(40, 0)
self.assertTrue(np.array(al).shape == (14, 5))
def test_isConferenceFoldover(self):
al = oapackage.exampleArray(37, 0)
self.assertTrue(oapackage.isConferenceFoldover(al))
al[2, 0] = -1
self.assertFalse(oapackage.isConferenceFoldover(al))
al = oapackage.exampleArray(7, 0)
self.assertFalse(oapackage.isConferenceFoldover(al))
al = oapackage.exampleArray(45, 0)
self.assertFalse(oapackage.isConferenceFoldover(al))
def test_compareJ54(self):
al1 = oapackage.exampleArray(24, 0)
al2 = oapackage.exampleArray(25, 0)
al3 = oapackage.exampleArray(26, 0)
self.assertEqual(oapackage.compareJ54(al1, al2), -1)
self.assertEqual(oapackage.compareJ54(al2, al1), 1)
self.assertEqual(oapackage.compareJ54(al1, al3), 1)
self.assertEqual(oapackage.compareJ54(al2, al3), 1)
def test_Jcharacteristics(self):
al = oapackage.exampleArray(30, 0)
jx = al.Jcharacteristics(4)
self.assertEqual(jx, (0, ))
jx = al.Jcharacteristics(2)
self.assertEqual(jx, (0, 0, 0, 0, 0, 0))
al = oapackage.exampleArray(48, 0).selectFirstColumns(6)
jx = al.Jcharacteristics(4)
self.assertEqual(jx,
(4, 4, 4, 0, 8, -8, 8, 4, -4, -4, 8, 4, -4, 8, -4))
def test_misc_file_operations(self):
_, array_filename = tempfile.mkstemp(suffix='.oa')
lst = [oapackage.exampleArray(4, 0)]
oapackage.writearrayfile(array_filename, lst)
assert (oapackage.oahelper.oaIsBinary(array_filename) is False)
oapackage.writearrayfile(array_filename, oapackage.exampleArray(4, 0),
oapackage.ABINARY)
assert (oapackage.oahelper.oaIsBinary(array_filename))
oapackage.oahelper.oainfo(array_filename)
_ = oapackage.oahelper.compressOAfile(array_filename)
def test_designStandardError(self):
al = oapackage.exampleArray(14, 0)
v = oapackage.oahelper.designStandardError(al)
self.assertAlmostEqual(v[0], 0.3747931073686535)
al = oapackage.exampleArray(9, 0)
v = oapackage.oahelper.designStandardError(al)
np.testing.assert_array_almost_equal(
v[1],
np.array([
0.1679305, 0.17229075, 0.17286095, 0.17287786, 0.17303912,
0.17353519, 0.17548291
]))
def test_compareLMC(self):
al1 = oapackage.exampleArray(24, 0)
al2 = oapackage.exampleArray(25, 0)
al3 = oapackage.exampleArray(26, 0)
self.assertEqual(oapackage.compareLMC(al1, al2), -1)
self.assertEqual(oapackage.compareLMC(al2, al1), 1)
self.assertEqual(oapackage.compareLMC(al1, al3), 1)
al1 = oapackage.exampleArray(2, 0).selectFirstColumns(5)
al2 = oapackage.exampleArray(2, 0).selectLastColumns(5)
self.assertEqual(oapackage.compareLMC(al1, al2), -1)
def test_LMCcheckOriginal(self):
array = oapackage.exampleArray(1)
lmc_type = oapackage.LMCcheckOriginal(array)
self.assertEqual(lmc_type, oapackage.LMC_MORE)
array2 = array.selectColumns([0, 1, 2, 4, 3])
lmc_type = oapackage.LMCcheck(array2)
self.assertEqual(lmc_type, oapackage.LMC_LESS)
array = oapackage.exampleArray(5, 0)
with self.assertRaises(RuntimeError):
lmc_type = oapackage.LMCcheckOriginal(array)
def test_LMC(self):
al = oapackage.array_link(2, 2, 0)
al[1, 1] = -1
self.assertRaises(RuntimeError, oapackage.reduceLMCform, al)
al = oapackage.exampleArray(8, 0)
alr = oapackage.reduceLMCform(al)
self.assertTrue(alr == al)
array0 = oapackage.exampleArray(1, 0).selectFirstColumns(3)
array = array0.randomperm()
reduced_array = oapackage.reduceLMCform(array)
self.assertEqual(array0, reduced_array)
def test_array_class_functions(self):
al = oapackage.exampleArray(1, 0)
self.assertTrue(al.is2level())
self.assertFalse(al.is_mixed_level())
al = oapackage.exampleArray(11, 0)
self.assertTrue(al.is2level())
self.assertFalse(al.is_mixed_level())
al = oapackage.array_link(2, 2, 0)
al[1, 1] = -1
self.assertFalse(al.is2level())
self.assertFalse(al.is_mixed_level())
def test_array_link_dimensions(self):
for example_idx in [0, 2, 6, 10]:
al = oapackage.exampleArray(example_idx, 0)
self.assertEqual(al.size, al.n_rows * al.n_columns)
self.assertEqual(al.shape, (al.n_rows, al.n_columns))
with self.assertRaises(AttributeError):
al.shape = 1
def test_arraylink2arraydata(self):
al = oapackage.exampleArray(0, 0)
adata = oapackage.arraylink2arraydata(al)
self.assertEqual(
str(adata), r'arrayclass: N 8, k 2, strength 2, s {2,2}, order 0')
al = oapackage.array_link(4, 4, 0)
al.setconstant(0)
adata = oapackage.arraylink2arraydata(al)
al.setconstant(-1)
with self.assertRaises(RuntimeError):
_ = oapackage.arraylink2arraydata(al)
for ii in [0, 4, 8, 10]:
al = oapackage.exampleArray(ii, 0)
arrayclass = oapackage.arraylink2arraydata(al, strength=-1)
self.assertEqual(arrayclass.strength, al.strength())
def test_modelmatrix_verbosity(self):
conf_design = oapackage.exampleArray(41, 0)
with mock.patch('sys.stdout', new_callable=io.StringIO) as mock_stdout:
oapackage.array2modelmatrix(conf_design, "i", 1)
stdout = mock_stdout.getvalue()
self.assertIn(
'array2modelmatrix: type conference, model_type_idx 2', stdout)
def test_rankStructure(self):
array = oapackage.exampleArray(45, 0)
array2 = oapackage.exampleArray(46, 0)
rank_structure = oapackage.rankStructure(array)
rank_structure.verbose = 2
if python3:
with patch('sys.stdout', new_callable=io.StringIO) as mock_stdout:
rank_structure.info()
rank_structure.verbose = 0
rank_direct = rank_structure.rankxf(array)
rank = rank_structure.rankxf(array)
rank2 = rank_structure.rankxf(array2)
self.assertEqual(rank_direct, 20)
self.assertEqual(rank, 20)
self.assertEqual(rank2, 20)
def test_nArrayFile(self):
_, array_filename = tempfile.mkstemp(suffix='.oa',
dir=tempfile.tempdir)
oapackage.writearrayfile(array_filename,
[oapackage.exampleArray(4, 0)])
self.assertEqual(oapackage.oahelper.nArrayFile(array_filename), 1)
self.assertEqual(oapackage.oahelper.nArrayFile('notavalidfile.oa'), -1)
def test_findfiles(self):
_, array_filename = tempfile.mkstemp(suffix='.oa',
dir=tempfile.tempdir)
lst = [oapackage.exampleArray(4, 0)]
oapackage.writearrayfile(array_filename, lst)
lst = oapackage.oahelper.findfiles(tempfile.tempdir, '.*oa')
self.assertIn(os.path.split(array_filename)[-1], lst)
def test_extendSingleArray():
A = oapackage.exampleArray(4, 1)
adata = oapackage.arraylink2arraydata(A, extracols=2)
B = A.selectFirstColumns(5)
ee = extendSingleArray(B, adata, t=2, verbose=1)
assert (ee[0].n_columns == B.n_columns + 1)
assert (ee[1] == A.selectFirstColumns(6))
def test_write_arrayfile_with_comment(self):
designs = [oapackage.exampleArray(3)]
filename = tempfile.mktemp(suffix='.oa')
write_text_arrayfile(filename, designs, comment='Test comment')
arrays = oapackage.readarrayfile(filename, 0)
self.assertEqual(len(designs), len(arrays))
self.assertEqual(designs[0], arrays[0])
def test_extendSingleArray():
A = oapackage.exampleArray(4, 1)
adata = oapackage.arraylink2arraydata(A, extracols=2)
B = A.selectFirstColumns(5)
ee = extendSingleArray(B, adata, t=2, verbose=1)
assert(ee[0].n_columns == B.n_columns + 1)
assert(ee[1] == A.selectFirstColumns(6))
def test_optimDeffPython(self):
al = oapackage.exampleArray(2, 0)
with mock.patch('sys.stdout', new_callable=io.StringIO) as mock_stdout:
_, al = oapackage.Doptim.optimDeffPython(al,
arrayclass=None,
niter=1000,
nabort=1500,
verbose=1,
alpha=[1, 0, 0],
method=0)
stdout = mock_stdout.getvalue()
self.assertTrue(
stdout.startswith('optimDeff: initial Deff 0.0000'))
for method in [
oapackage.oalib.DOPTIM_SWAP, oapackage.oalib.DOPTIM_FLIP,
oapackage.oalib.DOPTIM_UPDATE
]:
r, al = oapackage.Doptim.optimDeffPython(al,
arrayclass=None,
niter=100,
nabort=200,
verbose=0,
alpha=[1, 0, 0],
method=method)
def test_nauty(verbose=0):
if verbose:
print('test_nauty: test reduction to normal form')
al = oapackage.exampleArray(0, verbose)
alr = al.randomperm()
tr = oapackage.reduceOAnauty(alr)
alx = tr.apply(alr)
assert (alx == al)
def test_selectFirstColumns(self):
al = oapackage.exampleArray(41, 0)
al = al.selectFirstColumns(3)
self.assertEqual(al.n_columns, 3)
al = oapackage.array_link()
with self.assertRaises(RuntimeError):
al = al.selectFirstColumns(1)
def test_write_latex_format(self):
lst = [oapackage.exampleArray(2, 0)]
filename = tempfile.mktemp(suffix='.tex')
oapackage.writearrayfile(filename, oapackage.arraylist_t(lst),
oapackage.ALATEX)
with open(filename, 'rt') as fid:
latex = fid.read()
self.assertIsInstance(latex, str)
def test_array2eigenModelMatrixMixed(self):
array = oapackage.exampleArray(5, 0)
model = oapackage.array2eigenModelMatrixMixed(array)
expected_main_effects = np.frombuffer(
b'\xcc;\x7ff\x9e\xa0\xf6\xbf=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf.!\t\x14\x8e\x98\xf3\xbf\xcc;\x7ff\x9e\xa0\xe6\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\xcc;\x7ff\x9e\xa0\xf6\xbf=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf.!\t\x14\x8e\x98\xf3\xbf\xcc;\x7ff\x9e\xa0\xe6\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\xcc;\x7ff\x9e\xa0\xf6\xbf=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf.!\t\x14\x8e\x98\xf3?\xcc;\x7ff\x9e\xa0\xe6\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\xcc;\x7ff\x9e\xa0\xf6\xbf=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf.!\t\x14\x8e\x98\xf3?\xcc;\x7ff\x9e\xa0\xe6\xbf\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\xcc;\x7ff\x9e\xa0\xf6\xbf=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf\x00\x00\x00\x00\x00\x00\x00\x00\xcc;\x7ff\x9e\xa0\xf6?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\xcc;\x7ff\x9e\xa0\xf6\xbf=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf\x00\x00\x00\x00\x00\x00\x00\x00\xcc;\x7ff\x9e\xa0\xf6?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\xcc;\x7ff\x9e\xa0\xf6?=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf.!\t\x14\x8e\x98\xf3\xbf\xcc;\x7ff\x9e\xa0\xe6\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\xcc;\x7ff\x9e\xa0\xf6?=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf.!\t\x14\x8e\x98\xf3\xbf\xcc;\x7ff\x9e\xa0\xe6\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\xcc;\x7ff\x9e\xa0\xf6?=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf.!\t\x14\x8e\x98\xf3?\xcc;\x7ff\x9e\xa0\xe6\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0?\xcc;\x7ff\x9e\xa0\xf6?=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf.!\t\x14\x8e\x98\xf3?\xcc;\x7ff\x9e\xa0\xe6\xbf\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0\xbf\xcc;\x7ff\x9e\xa0\xf6?=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf\x00\x00\x00\x00\x00\x00\x00\x00\xcc;\x7ff\x9e\xa0\xf6?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\xcc;\x7ff\x9e\xa0\xf6?=,\x0cp\xbd \xea\xbf\x1c3\x90E\xa7y\xe2\xbf\x00\x00\x00\x00\x00\x00\x00\x00\xcc;\x7ff\x9e\xa0\xf6?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\xf0\xbf\x00\x00\x00\x00\x00\x00\x00\x00=,\x0cp\xbd 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).reshape(24, 8)
main_effects, interaction_effects = model[0], model[1]
np.testing.assert_array_equal(main_effects, expected_main_effects)
self.assertEqual(interaction_effects.shape, (24, 24))
def test_generateDpage(self):
outputdir = tempfile.mkdtemp()
allarrays = [oapackage.exampleArray(2, 0), oapackage.exampleArray(2, 0)]
dds = np.array([A.Defficiencies() for A in allarrays])
arrayclass = oapackage.arraylink2arraydata(allarrays[0])
with mock.patch('sys.stdout', new_callable=io.StringIO) as mock_stdout:
page = oapackage.Doptim.generateDpage(outputdir, arrayclass, dds, allarrays,
fig=None, optimfunc=[1, 0, 0], nofig=True)
if self.guitest and 0:
print('test_generateDpage: run gui test')
page = oapackage.Doptim.generateDpage(outputdir, arrayclass, dds, allarrays,
fig=100, optimfunc=[1, 0, 0], nofig=True)
try:
import matplotlib
matplotlib.pyplot.close(100)
except Exception:
pass
def test_selectArrays(self):
_, array_filename = tempfile.mkstemp(suffix='.oa',
dir=tempfile.tempdir)
_, array_filename_out = tempfile.mkstemp(suffix='.oa',
dir=tempfile.tempdir)
oapackage.writearrayfile(
array_filename,
[oapackage.exampleArray(4, 0),
oapackage.exampleArray(4, 0)])
oapackage.oahelper.selectArraysInFile(array_filename,
array_filename_out, [1],
afmode=oalib.ABINARY,
verbose=1,
cache=0)
oapackage.oahelper.selectArraysInFile(array_filename,
array_filename_out, [-1],
afmode=oalib.ABINARY,
verbose=1,
cache=0)
def test_optimDeffPython(self):
al = oapackage.exampleArray(2, 0)
with mock.patch('sys.stdout', new_callable=io.StringIO) as mock_stdout:
_, al = oapackage.Doptim.optimDeffPython(
al, arrayclass=None, niter=1000, nabort=1500, verbose=1, alpha=[1, 0, 0], method=0)
stdout = mock_stdout.getvalue()
self.assertTrue(stdout.startswith('optimDeff: initial Deff 0.0000'))
for method in [oapackage.oalib.DOPTIM_SWAP, oapackage.oalib.DOPTIM_FLIP, oapackage.oalib.DOPTIM_UPDATE]:
r, al = oapackage.Doptim.optimDeffPython(
al, arrayclass=None, niter=100, nabort=200, verbose=0, alpha=[1, 0, 0], method=method)
def test_array2Dtable(self):
sols = [oapackage.exampleArray(9, 0)]
_ = oapackage.Doptim.array2Dtable(sols, verbose=1, titlestr=None)
def test_selectJ():
al = oapackage.exampleArray(12, 1)
sols0 = [al]
r = selectJ(sols0)
assert(len(r) == 0)
# -*- coding: utf-8 -*-
"""
Example script for Python interface to Orthogonal Array code.
mathescape, numbersep=5pt, label=Python session, gobble=0, frame=lines, framesep=1.5mm, bgcolor=bg
> pygmentize -P "bgcolor=.95,.95,.95" -P "style=colorful" -f html example_python_testing.py
> pygmentize -S colorful -f html > style.css; cp style.css ~/misc/homepage/oapage/
@author: Pieter Eendebak
"""
#import oalib
import oapackage
print('oalib version: %s' % oapackage.version() )
al=oapackage.exampleArray(0)
al.showarray()
print('D-efficiency %f, rank %d' % (al.Defficiency(), al.rank()) )
print('Generalized wordlength pattern: %s' % str(al.GWLP()))
al=oapackage.exampleArray(1)
print('Generalized wordlength pattern: %s' % str(al.GWLP()))
def test_select_isomorphism():
ll = [oapackage.exampleArray(0), oapackage.exampleArray(0)]
indices, mm = selectIsomorphismClasses(ll, verbose=3)
assert(indices[0] == indices[1])
assert(len(mm) == 2)
assert(np.all(mm[0] == mm[1]))
import oapackage
def addData(data, extra_data, index=0, arrays=None, extra_arrays=None):
""" Vertically stack data together """
nn = extra_data.shape[1]
ww = np.vstack((extra_data, index * np.ones(nn,)))
data = np.hstack((data, ww))
if arrays is None:
return data
else:
allarrays = oapackage.joinArrayLists([arrays, extra_arrays])
return data, allarrays
#%% Load a strength 3 orthogonal array that is D-optimal
strength3_pareto = oapackage.exampleArray(44)
arrayclass = oapackage.arraylink2arraydata(strength3_pareto)
#%% Optimize with alpha variations
def optimize_arrays(sols, alpha=None, verbose=1, niter=400):
""" Optimize set of designs """
vv2 = []
ll = oapackage.arraylist_t()
for ii, A in enumerate(sols):
Dinit = A.Defficiency()
Df, Ax = oapackage.optimDeffPython(
A, niter=niter, verbose=0, alpha=alpha)
D, Ds, D1 = Ax.Defficiencies()
ll.push_back(Ax)
