def test_intercept_flag(rows=10, columns=9):
inout = get_random_array(rows, columns)
x = inout[0]
y = inout[1]
ntX = HomogenNumericTable(x)
ntY = HomogenNumericTable(y)
ridge_training_algorithm = ridge_training.Batch()
ridge_training_algorithm.input.set(ridge_training.data, ntX)
ridge_training_algorithm.input.set(ridge_training.dependentVariables, ntY)
# set parameter
alpha = 1.0
alpha_nt = HomogenNumericTable(np.array([alpha], ndmin=2))
ridge_training_algorithm.parameter.ridgeParameters = alpha_nt
result = ridge_training_algorithm.compute()
model = result.get(ridge_training.model)
beta_coeff = model.getBeta()
np_beta = getNumpyArray(beta_coeff)
daal_intercept = np_beta[0,0]
regression = ScikitRidgeRegression(alpha=1.0, fit_intercept=True)
regression.fit(x, y)
scikit_intercept = regression.intercept_
assert_array_almost_equal(scikit_intercept, [daal_intercept])
def check_chisquare(f_obs, f_exp, ddof, axis, expected_chi2):
# Use this only for arrays that have no masked values.
f_obs = np.asarray(f_obs)
if axis is None:
num_obs = f_obs.size
else:
if axis == 'no':
use_axis = 0
else:
use_axis = axis
b = np.broadcast(f_obs, f_exp)
num_obs = b.shape[use_axis]
if axis == 'no':
chi2, p = mstats.chisquare(f_obs, f_exp=f_exp, ddof=ddof)
else:
chi2, p = mstats.chisquare(f_obs, f_exp=f_exp, ddof=ddof, axis=axis)
assert_array_equal(chi2, expected_chi2)
ddof = np.asarray(ddof)
expected_p = stats.chisqprob(expected_chi2, num_obs - 1 - ddof)
assert_array_equal(p, expected_p)
# Also compare to stats.chisquare
if axis == 'no':
stats_chisq, stats_p = stats.chisquare(f_obs, f_exp=f_exp, ddof=ddof)
else:
stats_chisq, stats_p = stats.chisquare(f_obs,
f_exp=f_exp,
ddof=ddof,
axis=axis)
assert_array_almost_equal(chi2, stats_chisq)
assert_array_almost_equal(p, stats_p)
def get_daal_prediction(x=np.arange(10).reshape(10,1), y=np.arange(10).reshape(10,1)):
ntX = HomogenNumericTable(x)
ntY = HomogenNumericTable(y)
ridge_training_algorithm = ridge_training.Batch()
ridge_training_algorithm.input.set(ridge_training.data, ntX)
ridge_training_algorithm.input.set(ridge_training.dependentVariables, ntY)
# set parameter
alpha = 0.0
alpha_nt = HomogenNumericTable(np.array([alpha], ndmin=2))
ridge_training_algorithm.parameter.ridgeParameters = alpha_nt
result = ridge_training_algorithm.compute()
model = result.get(ridge_training.model)
ridge_prediction_algorithm = ridge_prediction.Batch()
ridge_prediction_algorithm.input.setModel(ridge_prediction.model, model)
ridge_prediction_algorithm.input.setTable(ridge_prediction.data, ntX)
result = ridge_prediction_algorithm.compute()
np_predicted = getNumpyArray(result.get(ridge_prediction.prediction))
# assert the same as the initial dependent variable
assert_array_almost_equal(y, np_predicted)
return np_predicted
def test_svd_daal_vs_sklearn(rows=1000, columns=1000):
indata = get_random_array(rows, columns)
daal_input = HomogenNumericTable(indata)
algorithm = svd.Batch()
algorithm.input.set(svd.data, daal_input)
start_sklearn = time.time()
_U, s, _Vh = np.linalg.svd(indata, full_matrices=False)
end_sklearn = time.time()
start_daal = time.time()
result = algorithm.compute()
end_daal = time.time()
if os.getenv("CHECKPERFORMANCE") is not None:
assert (end_daal - start_daal <= end_sklearn - start_sklearn)
sigma = getNumpyArray(result.get(svd.singularValues))
_rows, cols = sigma.shape
d_sigma = sigma.reshape(cols, )
assert_array_almost_equal(d_sigma, s)
print("SVD for matrix[{}][{}]".format(rows, columns))
print("+ Sklearn SVD: {}".format(end_sklearn - start_sklearn))
print("+ Sklearn Daal: {}".format(end_daal - start_daal))
def check_chisquare(f_obs, f_exp, ddof, axis, expected_chi2):
# Use this only for arrays that have no masked values.
f_obs = np.asarray(f_obs)
if axis is None:
num_obs = f_obs.size
else:
if axis == 'no':
use_axis = 0
else:
use_axis = axis
b = np.broadcast(f_obs, f_exp)
num_obs = b.shape[use_axis]
if axis == 'no':
chi2, p = mstats.chisquare(f_obs, f_exp=f_exp, ddof=ddof)
else:
chi2, p = mstats.chisquare(f_obs, f_exp=f_exp, ddof=ddof, axis=axis)
assert_array_equal(chi2, expected_chi2)
ddof = np.asarray(ddof)
expected_p = stats.chisqprob(expected_chi2, num_obs - 1 - ddof)
assert_array_equal(p, expected_p)
# Also compare to stats.chisquare
if axis == 'no':
stats_chisq, stats_p = stats.chisquare(f_obs, f_exp=f_exp, ddof=ddof)
else:
stats_chisq, stats_p = stats.chisquare(f_obs, f_exp=f_exp, ddof=ddof,
axis=axis)
assert_array_almost_equal(chi2, stats_chisq)
assert_array_almost_equal(p, stats_p)
def test_kalman(self):
# V0 = 12
h = np.atleast_2d(1) # voltimeter measure the voltage itself
q = 1e-9 # variance of process noise as the car operates
r = 0.05 ** 2 # variance of measurement error
b = 0 # no system input
u = 0 # no system input
filt = Kalman(R=r, A=1, Q=q, H=h, B=b)
# Generate random voltages and watch the filter operate.
n = 50
# truth = np.random.randn(n) * np.sqrt(q) + V0
truth = np.array([12.0000146639, 12.0000065349, 12.0000032619, 11.9999884321, 11.9999738705, 11.9999717554, 12.000012208, 12.0000269596, 12.0000235391, 12.0000420788, 11.9999763588, 12.0000272251, 11.9999278487, 11.9999775611, 12.0000280208, 11.9999788802, 11.9999531533, 11.9999963402, 11.9999318055, 11.9999537065, 12.0000011098, 11.9999750291, 12.000012755, 11.9999355349, 11.9999960117, 12.0000033276, 12.0000100317, 11.9999962376, 12.0000527124, 12.000019087, 12.0000273276, 11.9999461331, 12.0000527385, 11.9999990413, 11.9999850764, 12.0000031025, 11.9999868222, 11.9999830042, 11.9999881952, 12.0000064122, 12.0000343455, 11.9999779108, 12.0000134648, 12.0000329604, 12.0000536949, 11.999990415, 11.9999935299, 11.9999850717, 12.0000048284, 12.000060395]) # @IgnorePep8
# print(', '.join(['{0}'.format(y) for y in truth]))
# noise = np.random.randn(n) * np.sqrt(r)
noise = np.array([0.0621366489443, 0.0247330994998, 0.109271521369, -0.0567657373852, -0.0315244553453, -0.0025701462034, 0.00181288937042, 0.109022849782, 0.0241169949603, -0.0543790728855, 0.0380117839575, 0.0582078684346, -0.0734606815139, -0.0665977120387, 0.0270631615171, 0.0369150024436, 0.0788445252483, 0.0111006834355, 0.0169567513801, 0.057081645789, -0.0293106512335, 0.0120282068494, 0.0211769283138, -0.0703228625119, -0.0222740803259, 0.0636500853308, 0.0302268639638, 0.0823316446844, 0.0504871636818, -0.0295402185417, 0.0780534199429, -0.0275453184976, -0.0613567940452, -0.0416930336494, -0.0972202720552, 0.0367572628693, 0.0150242119742, -0.0269063072041, 0.0654834111234, 0.0281867030757, -0.0978716452136, -0.0209143055692, -0.0236015624104, 0.0215804707908, -0.0525669442916, -0.00999304544556, -0.120029281573, -0.0255283929591, -0.00426938028504, -0.0487170747831]) # @IgnorePep8
# print('noise')
# print(', '.join(['{0}'.format(y) for y in noise]))
z = truth + noise # measurement
x = np.zeros(n)
for i, zi in enumerate(z):
x[i] = filt(zi, u) # perform a Kalman filter iteration
print(', '.join(['{0}'.format(y) for y in x]))
assert_array_almost_equal(x, [12.0621513128, 12.0434454699, 12.065388589, 12.0348470726, 12.0215675093, 12.0175398445, 12.0152948689, 12.0270143185, 12.0266950063, 12.0185917138, 12.0203550503, 12.0235117738, 12.0160466547, 12.0101417447, 12.0112717378, 12.0128731715, 12.0167512202, 12.0164370857, 12.0164608484, 12.0184896738, 12.0162133963, 12.0160220138, 12.0162467099, 12.0126366982, 12.0112399981, 12.01325607, 12.0138850472, 12.0163296762, 12.0175094638, 12.0159415984, 12.0179463317, 12.0165228489, 12.0141641309, 12.0125210028, 12.0093846209, 12.0101451843, 12.0102767167, 12.0092975878, 12.0107382282, 12.01117469, 12.0085152867, 12.0078138971, 12.0070834443, 12.0074137537, 12.0060816948, 12.0057319401, 12.0030552687, 12.0024592874, 12.0023220236, 12.0013021198]) # @IgnorePep8
def test_case(self):
model = clone(estimator)
model.fit(**fit_data)
for method in methods:
try:
code = sklearn2code(model, method, javascript)
except ExpressionTypeNotSupportedError:
continue
js = execjs.get('Node')
context = js.compile(code)
exported_pred = []
try:
for _, row in export_predict_data['X'].iterrows():
val = context.eval('%s(%s)' % (method, ', '.join(
[str(x) if x == x else 'NaN' for x in row])))
exported_pred.append(val)
exported_pred = np.array(exported_pred)
pred = DataFrame(getattr(model, method)(**predict_data))
assert_array_almost_equal(np.ravel(pred),
np.ravel(exported_pred), 3)
except:
# print(code)
import clipboard
clipboard.copy(code)
raise
def test_kurtosis(self):
# Set flags for axis = 0 and fisher=0 (Pearson's definition of kurtosis
# for compatibility with Matlab)
y = mstats.kurtosis(self.testmathworks, 0, fisher=0, bias=1)
assert_almost_equal(y, 2.1658856802973, 10)
# Note that MATLAB has confusing docs for the following case
# kurtosis(x,0) gives an unbiased estimate of Pearson's skewness
# kurtosis(x) gives a biased estimate of Fisher's skewness (Pearson-3)
# The MATLAB docs imply that both should give Fisher's
y = mstats.kurtosis(self.testmathworks, fisher=0, bias=0)
assert_almost_equal(y, 3.663542721189047, 10)
y = mstats.kurtosis(self.testcase, 0, 0)
assert_almost_equal(y, 1.64)
# test that kurtosis works on multidimensional masked arrays
correct_2d = ma.array(
np.array([-1.5, -3.0, -1.47247052385, 0.0, -1.26979517952]),
mask=np.array([False, False, False, True, False], dtype=np.bool),
)
assert_array_almost_equal(mstats.kurtosis(self.testcase_2d, 1), correct_2d)
for i, row in enumerate(self.testcase_2d):
assert_almost_equal(mstats.kurtosis(row), correct_2d[i])
correct_2d_bias_corrected = ma.array(
np.array([-1.5, -3.0, -1.88988209538, 0.0, -0.5234638463918877]),
mask=np.array([False, False, False, True, False], dtype=np.bool),
)
assert_array_almost_equal(mstats.kurtosis(self.testcase_2d, 1, bias=False), correct_2d_bias_corrected)
for i, row in enumerate(self.testcase_2d):
assert_almost_equal(mstats.kurtosis(row, bias=False), correct_2d_bias_corrected[i])
# Check consistency between stats and mstats implementations
assert_array_almost_equal_nulp(mstats.kurtosis(self.testcase_2d[2, :]), stats.kurtosis(self.testcase_2d[2, :]))
def test_linear_regression_simple():
# calculate beta coefficients
x = np.array([0., 2., 3.]).reshape(3, 1)
nt_x = nt_y = HomogenNumericTable(x)
lr_alg = linear_training.Batch(method=linear_training.qrDense)
lr_alg.input.set(linear_training.data, nt_x)
lr_alg.input.set(linear_training.dependentVariables, nt_y)
result = lr_alg.compute()
model = result.get(linear_training.model)
beta_coeff = model.getBeta()
np_beta_coeff = getNumpyArray(beta_coeff)
res_beta_coeff = np.array([0, 1]).reshape(1, 2)
assert_almost_equal(res_beta_coeff, np_beta_coeff)
# predict
lr_alg_predict = linear_prediction.Batch()
lr_alg_predict.input.setModel(linear_prediction.model, model)
lr_alg_predict.input.setTable(linear_prediction.data, nt_x)
result = lr_alg_predict.compute()
np_predict = getNumpyArray(result.get(linear_prediction.prediction))
assert_array_almost_equal(x, np_predict)
def test_chisquare_masked_arrays():
# The other tests were taken from the tests for stats.chisquare, so
# they don't test the function with masked arrays. Here masked arrays
# are tested.
obs = np.array([[8, 8, 16, 32, -1], [-1, -1, 3, 4, 5]]).T
mask = np.array([[0, 0, 0, 0, 1], [1, 1, 0, 0, 0]]).T
mobs = ma.masked_array(obs, mask)
expected_chisq = np.array([24.0, 0.5])
chisq, p = mstats.chisquare(mobs)
assert_array_equal(chisq, expected_chisq)
assert_array_almost_equal(
p, stats.chisqprob(expected_chisq,
mobs.count(axis=0) - 1))
chisq, p = mstats.chisquare(mobs.T, axis=1)
assert_array_equal(chisq, expected_chisq)
assert_array_almost_equal(
p, stats.chisqprob(expected_chisq,
mobs.T.count(axis=1) - 1))
# When axis=None, the two values should have type np.float64.
chisq, p = mstats.chisquare([1, 2, 3], axis=None)
assert_(isinstance(chisq, np.float64))
assert_(isinstance(p, np.float64))
assert_equal(chisq, 1.0)
assert_almost_equal(p, stats.chisqprob(1.0, 2))
def test_tile_array(self):
a = np.array([[1, 2], [3, 4], [5, 6]])
a_tiled = hm.linalg.tile_array(a, 2)
a_tiled_expected = np.array([[1, 2, 0, 0], [3, 4, 0, 0], [5, 6, 0, 0],
[0, 0, 1, 2], [0, 0, 3, 4], [0, 0, 5, 6]])
assert_array_almost_equal(a_tiled.toarray(), a_tiled_expected)
def test_golden_section():
data = mlclass.ex4()
x = add_bias(data['x'])
y = data['y']
theta = array((.01, .01, .01))
p = -grad(x, y, theta, 0.)
c = lambda alpha: nan_guard(cost(x, y, theta + alpha*p, 0.))
assert_array_almost_equal((0.000739624, 0.685489), golden_section((-1.61803, 0, 1, 880.894, 0.778512, 651.614), c))
def test_zmap(self):
# This is not in R, so tested by using:
# (testcase[i]-mean(testcase,axis=0)) / sqrt(var(testcase)*3/4)
y = mstats.zmap(self.testcase, self.testcase)
desired_unmaskedvals = ([-1.3416407864999, -0.44721359549996,
0.44721359549996, 1.3416407864999])
assert_array_almost_equal(desired_unmaskedvals,
y.data[y.mask == False], decimal=12)
def test_zmap(self):
# This is not in R, so tested by using:
# (testcase[i]-mean(testcase,axis=0)) / sqrt(var(testcase)*3/4)
y = mstats.zmap(self.testcase, self.testcase)
desired_unmaskedvals = ([-1.3416407864999, -0.44721359549996,
0.44721359549996, 1.3416407864999])
assert_array_almost_equal(desired_unmaskedvals,
y.data[y.mask == False], decimal=12)
def test_line_search():
data = mlclass.ex4()
x = add_bias(data['x'])
y = data['y']
theta = array((.01, .01, .01))
p = -grad(x, y, theta, 0.)
c = lambda alpha: cost(x, y, theta + alpha*p, 0.)
assert_array_almost_equal((0.000739624, 0.685489), line_search(0., 1., c))
def test_create_interpolation_least_squares_domain_repetitive_extrapolation(
self):
""
n = 16
kh = 1.0
max_conv_factor = 0.3
a = hm.linalg.helmholtz_1d_operator(kh, n)
location = np.arange(n)
level = hm.setup.hierarchy.create_finest_level(a)
# Generate relaxed test matrix.
x = _get_test_matrix(a, n, 10, num_examples=8)
coarsener = hm.setup.coarsening_uniform.UniformCoarsener(
level, x, 4, repetitive=True)
r, aggregate_size, num_components = coarsener.get_optimal_coarsening(
max_conv_factor)[:3]
assert aggregate_size == 6
assert num_components == 2
p = hm.setup.interpolation.create_interpolation_least_squares_domain(
x,
a,
r,
location,
n,
aggregate_size=aggregate_size,
num_components=num_components,
repetitive=True)
num_test_examples = 5
x_test = x[:, -num_test_examples:]
error_a = np.mean(
norm(a.dot(x_test - p.dot(r.dot(x_test))), axis=0) /
norm(x_test, axis=0))
assert p[0].nnz == 4
assert error_a == pytest.approx(0.492, 1e-2)
assert p.shape == (16, 6)
# To print p:
#print(','.join(np.array2string(y, separator=",", formatter={'float_kind':lambda x: "%.2f" % x}) for y in np.array(p.todense())))
assert_array_almost_equal(p.todense(), [
[-0.26, 0.17, 0.00, 0.00, -0.20, 0.14],
[0.07, 0.56, 0.00, 0.00, -0.08, 0.20],
[0.27, 0.11, 0.00, 0.00, 0.16, 0.02],
[0.34, -0.25, 0.01, -0.02, 0.00, 0.00],
[-0.03, -0.40, -0.13, -0.05, 0.00, 0.00],
[-0.30, -0.16, -0.11, -0.01, 0.00, 0.00],
[-0.20, 0.14, -0.26, 0.17, 0.00, 0.00],
[-0.08, 0.20, 0.07, 0.56, 0.00, 0.00],
[0.16, 0.02, 0.27, 0.11, 0.00, 0.00],
[0.00, 0.00, 0.34, -0.25, 0.01, -0.02],
[0.00, 0.00, -0.22, -0.26, -0.39, 0.12],
[0.00, 0.00, -0.38, 0.04, -0.04, 0.55],
[0.00, 0.00, 0.16, 0.02, 0.27, 0.11],
[0.01, -0.02, 0.00, 0.00, 0.34, -0.25],
[-0.13, -0.05, 0.00, 0.00, -0.03, -0.40],
[-0.11, -0.01, 0.00, 0.00, -0.30, -0.16],
],
decimal=2)
def test_2D(self):
a = ma.array(((1, 2, 3, 4), (1, 2, 3, 4), (1, 2, 3, 4)), mask=((0, 0, 0, 0), (1, 0, 0, 1), (0, 1, 1, 0)))
actual = mstats.hmean(a)
desired = ma.array((1, 2, 3, 4))
assert_array_almost_equal(actual, desired, decimal=14)
actual1 = mstats.hmean(a, axis=-1)
desired = (4.0 / (1 / 1.0 + 1 / 2.0 + 1 / 3.0 + 1 / 4.0), 2.0 / (1 / 2.0 + 1 / 3.0), 2.0 / (1 / 1.0 + 1 / 4.0))
assert_array_almost_equal(actual1, desired, decimal=14)
def test_savitzky_golay(self):
t = np.linspace(-4, 4, 100)
# noise = np.random.normal(0, 0.05, t.shape)
noise = np.array([-0.0100738410948, 0.0434144660993, -0.00378151879776, 0.0113356386249, 0.00435077505515, -0.0477602072563, 0.0373494077292, -0.0133865881648, -0.058259106898, 0.0661995082581, -0.0302004598725, 0.0251073570423, 0.0504480752083, 0.00591197638959, -0.0936100824835, -0.0475801028574, 0.164260739963, 0.000309393717298, 0.0145265378376, 0.0451974209359, -0.0296464887607, 0.00113264461646, 0.0203243951278, 0.0250086489045, 0.0286663554031, 0.0162585459204, -0.0285237485127, 0.0841528003829, -0.0449728982279, 0.0549796633406, -0.0968901623365, 0.0306727572312, -0.06950957371, 0.00598396964893, 0.0583904237732, 0.0271856795988, 0.0503237614252, 0.179978222833, 0.0909965842309, -0.037723727536, 0.0766788834896, -0.135152061379, -0.0275445486266, 0.00437867535899, -0.0272885999582, -0.0167170993005, 0.0522077667657, -0.044618733434, -0.0323362657615, 0.0122726298648, 0.0311304227245, -0.106361849439, 0.0526578516171, 0.0600674983294, 0.0745276212563, -0.0488453979797, -0.000833273665862, 0.0232768529385, 0.0138869047145, -0.0581069396022, 0.0321001340163, -0.023975724861, -0.0281919023447, 0.0341550408589, -0.0128104984676, -0.0214928514613, -0.0930630211028, -0.086094936458, 0.0169055851217, -0.0106085935018, 0.0114499301052, 0.120823119533, 0.0401375561218, 0.0979979215035, -0.015930504967, 0.0730359376807, -0.0369380623571, 0.0628171477772, -0.0271592027456, -0.0805267873905, -0.047314352792, -0.00693573205681, -0.0276294819462, -0.00896110691771, 0.0248482543453, 0.0877066047642, -0.0325533337143, -0.0638923240986, 0.0512523528302, 0.0720952473332, 0.00555629231342, 0.0562912258368, 0.0518574742355, -0.0599288505845, 0.0129657160415, -0.0025435076237, -0.0136966498082, 0.0260013064028, 0.0315561663839, -0.0293194006299]) # @IgnorePep8
# print(', '.join(['{0}'.format(y) for y in noise]))
y = np.exp(-t**2) + noise
ysg = SavitzkyGolay(n=20, degree=2).smooth(y)
# print(', '.join(['{0}'.format(y) for y in ysg]))
assert_array_almost_equal(ysg,[0.08136940307, 0.0628995512206, 0.0459066440291, 0.0303906814954, 0.0163516636196, 0.00378959040169, -0.00729553815838, -0.0169037220606, -0.0250349613049, -0.0316892558914, -0.03686660582, -0.0405670110908, -0.0427904717036, -0.0435369876586, -0.0428065589558, -0.0405991855951, -0.0369148675765, -0.0317536049001, -0.0251153975657, -0.0170002455736, -0.00740814892354, 0.00138883298422, 0.00903982318392, 0.0156981288342, 0.0262571138525, 0.038712235996, 0.0497401536595, 0.0708145615737, 0.0930139468092, 0.115399487253, 0.145859174356, 0.181612636791, 0.217133614374, 0.257717904903, 0.300137304571, 0.345750694351, 0.392370647909, 0.447698806473, 0.498669071812, 0.552242388661, 0.602481962016, 0.649961345551, 0.695325299394, 0.735374047294, 0.773010811455, 0.805919165272, 0.834865852047, 0.854796400219, 0.86842923705, 0.871717227059, 0.870973756546, 0.854091989437, 0.838398655214, 0.810673923439, 0.783634317013, 0.749908334726, 0.714315301461, 0.67175727743, 0.634614314389, 0.593943523363, 0.54497174327, 0.497539947485, 0.442464744684, 0.39039262486, 0.339641566641, 0.287962531039, 0.243889096129, 0.20650960823, 0.165038163827, 0.127423305227, 0.098217909507, 0.0723906956301, 0.0457840790019, 0.0325691800506, 0.0207065223098, 0.0137400799931, 0.00547944733578, -0.000268557810876, -0.00301934919753, -0.00213643706217, -0.0101846106787, -0.0170002602175, -0.0225833856784, -0.0269339870616, -0.030052064367, -0.0319376175946, -0.0325906467444, -0.0320111518164, -0.0301991328106, -0.0271545897271, -0.0228775225657, -0.0173679313266, -0.0106258160097, -0.00265117661497, 0.00655598685753, 0.0169956744078, 0.0286678860359, 0.0415726217417, 0.0557098815254, 0.0710796653868]) # @IgnorePep8
def test_gram_schmidt(self):
a = np.random.random((10, 4))
q = hm.linalg.gram_schmidt(a)
q_expected = _gram_schmidt_explicit(a)
assert_array_almost_equal(
hm.linalg.normalize_signs(q, axis=1),
hm.linalg.normalize_signs(q_expected, axis=1))
def test_ctm_adjoint():
scen, control = small_scenario()
state = CTMSimulator().simulate(scen, control)
hx = CTMAdjoint(scen).hx(state, control)
hu = CTMAdjoint(scen).hu(state, control)
assert_array_equal(hx, np.tril(hx))
u = np.ones(control.flatten().shape) * 0.01
adjoint = CTMAdjoint(scen)
assert_array_almost_equal(adjoint.grad(u), adjoint.grad_fd(u), 3)
def test_bracket():
data = mlclass.ex4()
x = add_bias(data['x'])
y = data['y']
theta = array((.01, .01, .01))
p = -grad(x, y, theta, 0.)
c = lambda alpha: nan_guard(cost(x, y, theta + alpha*p, 0.))
assert_array_almost_equal((-1.61803, 0, 1, 880.894, 0.778512, 651.614), bracket(0., 1., c), decimal=3)
def test_min_sample_size_axis(self):
data = [[40.0, 0.0, 40.0, 0.0],
[40.0, 0.0, 40.0, 0.0]]
self.assertAlmostEqual(2236.5791393864079,
min_sample_size(data, 0.95, 0.05))
x = 4051.185794406982
assert_array_almost_equal([x, x],
min_sample_size(data, .95, .05, 1))
def test_zscore_multicolumns():
input_ = np.random.rand(10, 3)
sc_zscore = stats.zscore(input_, axis=0, ddof=1)
da_input = HomogenNumericTable(input_)
da_zscore = z_score(da_input)
np_da_zscore = getNumpyArray(da_zscore)
assert_array_almost_equal(sc_zscore, np_da_zscore)
def test_2D(self):
a = ma.array(((1, 2, 3, 4), (1, 2, 3, 4), (1, 2, 3, 4)),
mask=((0, 0, 0, 0), (1, 0, 0, 1), (0, 1, 1, 0)))
actual = mstats.hmean(a)
desired = ma.array((1, 2, 3, 4))
assert_array_almost_equal(actual, desired, decimal=14)
actual1 = mstats.hmean(a, axis=-1)
desired = (4. / (1 / 1. + 1 / 2. + 1 / 3. + 1 / 4.),
2. / (1 / 2. + 1 / 3.), 2. / (1 / 1. + 1 / 4.))
assert_array_almost_equal(actual1, desired, decimal=14)
def test_scaled_norm_of_matrix_3d(self):
num_functions = 4
x = 2 * np.random.random((10, 2, num_functions)) - 1
actual = hm.linalg.scaled_norm_of_matrix(x)
y = x.reshape(20, num_functions)
factor = 1 / np.prod(x.shape[:-1])**0.5
expected = factor * np.array(
[norm(y[:, i]) for i in range(y.shape[1])])
assert_array_almost_equal(actual, expected, 10)
def test_gauss_seidel_sweep_same_as_loop_implementation(self):
n = 16
kh = 0.5
a = hm.linalg.helmholtz_1d_operator(kh, n)
relaxer = hm.solve.relax.GsRelaxer(a)
x = np.random.random((n, 5))
b = np.zeros_like(x)
for i in range(10):
y = gs_relax_with_loop(kh, x)
x = relaxer.step(x, b)
assert_array_almost_equal(x - x.mean(), y - y.mean())
def test_penalize_nothing_var():
adj1, _ = dumb_admm_system()
old_ju1 = adj1.ju
alpha = 0.0
def new_ju1(x, u):
ju = old_ju1(x, u)
ju[1] = alpha * 2 * (u[1] - 3.0)
return ju
adj1.ju = new_ju1
assert_array_almost_equal(AcceleratedGradient().solve(adj1, numpy.zeros(2)), [1.0, 0.0], 3)
alpha = 1.0
assert_array_almost_equal(AcceleratedGradient().solve(adj1, numpy.zeros(2)), [1.0, 3.0], 3)
def test_ridge_regression_against_scikit(rows=10, columns=9):
'''
Test prediction daal against scikit
:param rows:
:param columns:
'''
inout = get_random_array(rows, columns)
x = inout[0]
y = inout[1]
daal_predicted = get_daal_prediction(x, y)
scik_predicted = get_scikit_prediction(x, y)
assert_array_almost_equal(daal_predicted, scik_predicted)
def test_td_target():
trials = 10
time_steps = 100
rewards = np.random.normal(size=(trials, time_steps, 1))
values = np.random.normal(size=(trials, time_steps, 1))
gamma = .9
expected_result = rewards.copy()
expected_result[:, :-1, :] += gamma * values[:, 1:, :]
assert_array_almost_equal(expected_result,
td_target(gamma, rewards, values))
def test_spaceGroupQuery(self):
sg = self.stru2.sg
assert sg.number is 225
assert sg.num_sym_equiv is 192
assert sg.num_primitive_sym_equiv is 48
assert sg.short_name=='Fm-3m'
assert sg.alt_name=='F M 3 M'
assert sg.point_group_name=='PGm3barm'
assert sg.crystal_system=='CUBIC'
assert sg.pdb_name=='F 4/m -3 2/m'
assert_array_almost_equal(sg.symop_list[1].R, numpy.identity(3))
assert_array_almost_equal(sg.symop_list[1].t, numpy.array([ 0. , 0.5, 0.5]))
def test_spaceGroupQuery(self):
sg = self.stru2.sg
assert sg.number is 225
assert sg.num_sym_equiv is 192
assert sg.num_primitive_sym_equiv is 48
assert sg.short_name=='Fm-3m'
assert sg.alt_name=='F M 3 M'
assert sg.point_group_name=='PGm3barm'
assert sg.crystal_system=='CUBIC'
assert sg.pdb_name=='F 4/m -3 2/m'
assert_array_almost_equal(sg.symop_list[1].R, numpy.identity(3))
assert_array_almost_equal(sg.symop_list[1].t, numpy.array([ 0. , 0.5, 0.5]))
def test_discount():
trials = 10
time_steps = 100
rewards = np.random.normal(size=(trials, time_steps))
gamma = .9
expected_result = np.empty(shape=(trials, time_steps))
for i in range(time_steps):
discount_vec = gamma**np.arange(time_steps - i)
expected_result[:, i] = np.dot(rewards[:, i:], discount_vec)
assert_array_almost_equal(expected_result, discount(gamma, rewards))
def test_pairwise_cos_similarity(self):
# Compare with explicit summation.
x = 2 * np.random.random((10, 4)) - 1
y = 2 * np.random.random((10, 3)) - 1
x[:, 0] = 0
actual = hm.linalg.pairwise_cos_similarity(x, y)
expected = np.array([[
sum(x[:, i] * y[:, j]) / np.clip(
(sum(x[:, i]**2) * sum(y[:, j]**2))**0.5, 1e-15, None)
for j in range(y.shape[1])
] for i in range(x.shape[1])])
assert_array_almost_equal(actual, expected, 10)
def test_confidence_interval_axis(self):
data = [[8.0, 7.0, 5.0, 9.0, 9.5, 11.3, 5.2, 8.5],
[8.0, 7.0, 5.0, 9.0, 9.5, 11.3, 5.2, 8.5]]
assert_array_almost_equal([1.67722628, 1.67722628],
half_confidence_interval_size(data, .95,
axis=1))
assert_array_almost_equal([ 0., 0., 0., 0., 0., 0., 0., 0.],
half_confidence_interval_size(data, .95,
axis=0))
self.assertAlmostEqual(1.06902922476,
half_confidence_interval_size(data, .95))
def test_helmholtz_1d_operator(self):
kh = 1.5
n = 8
a = hm.linalg.helmholtz_1d_operator(kh, n)
a_expected = \
[[0.25, 1., 0., 0., 0., 0., 0., 1.],
[1., 0.25, 1., 0., 0., 0., 0., 0.],
[0., 1., 0.25, 1., 0., 0., 0., 0.],
[0., 0., 1., 0.25, 1., 0., 0., 0.],
[0., 0., 0., 1., 0.25, 1., 0., 0.],
[0., 0., 0., 0., 1., 0.25, 1., 0.],
[0., 0., 0., 0., 0., 1., 0.25, 1.],
[1., 0., 0., 0., 0., 0., 1., 0.25]]
assert_array_almost_equal(a.toarray(), a_expected)
def test_create_uniform_coarsening_domain_indivisible_size(self):
n = 17
kh = 0.5
aggregate_size = 4
a = hm.linalg.helmholtz_1d_operator(kh, n)
# Generate relaxed test matrix.
x = _get_test_matrix(a, n, 10)
# Generate coarse variables (R) on the non-repetitive domain.
coarsener = hm.setup.coarsening_uniform.FixedAggSizeUniformCoarsener(x, aggregate_size, repetitive=True)
result = coarsener.all_candidate_coarsening()
# For a cycle index of 1, the max coarsening ratio is 0.7, and aggregate_size * 0.7 = 2.8, so we can have at
# most # 2 PCs per aggregate.
assert len(result) == 2
r_values = np.array([item[1][0] for item in result])
mean_energy_error = np.array([item[1][1] for item in result])
assert_array_almost_equal(mean_energy_error, [0.477069, 0.175552], decimal=5)
assert r_values[0].shape == (5, 17)
r = r_values[1]
assert r.shape == (10, 17)
# To print r:
# print(','.join(np.array2string(y, separator=",", formatter={'float_kind':lambda x: "%.2f" % x})
# for y in np.array(r.todense())))
assert_array_almost_equal(
r.todense(), [
[-0.27, -0.53, -0.62, -0.52, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
0.00],
[0.70, 0.38, -0.12, -0.59, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
0.00],
[0.00, 0.00, 0.00, 0.00, -0.27, -0.53, -0.62, -0.52, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
0.00],
[0.00, 0.00, 0.00, 0.00, 0.70, 0.38, -0.12, -0.59, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
0.00],
[0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, -0.27, -0.53, -0.62, -0.52, 0.00, 0.00, 0.00, 0.00,
0.00],
[0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.70, 0.38, -0.12, -0.59, 0.00, 0.00, 0.00, 0.00,
0.00],
[0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, -0.27, -0.53, -0.62, -0.52,
0.00],
[0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.70, 0.38, -0.12, -0.59,
0.00],
[0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, -0.27, -0.53, -0.62,
-0.52],
[0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.70, 0.38, -0.12, -0.59]
], decimal=2)
def test_linear_regression_daal_vs_sklearn(rows=10,
columns=9,
verbose=False):
inout = get_random_array(rows, columns)
x = inout[0]
y = inout[1]
start_sklearn = time.time()
lin_solver_sklearn = h2o4gpu.LinearRegression(verbose=True,
backend='sklearn')
lin_solver_sklearn.fit(x, y)
sklearn_predicted = lin_solver_sklearn.predict(x)
end_sklearn = time.time()
print(("Sklearn prediction: ", sklearn_predicted) if verbose else "",
end="")
start_daal = time.time()
lin_solver_daal = h2o4gpu.LinearRegression(
fit_intercept=True,
verbose=True,
backend='daal',
method=LinearMethod.normal_equation)
lin_solver_daal.fit(x, y)
daal_predicted = lin_solver_daal.predict(x)
end_daal = time.time()
print(("Daal prediction: ", daal_predicted) if verbose else "", end="")
print("Prediction calculated:")
print("+ Sklearn: {}".format(end_sklearn - start_sklearn))
print("+ Daal: {}".format(end_daal - start_daal))
assert_array_almost_equal(daal_predicted, sklearn_predicted, decimal=4)
assert_array_almost_equal(daal_predicted, y, decimal=4)
if os.getenv("CHECKPERFORMANCE") is not None:
assert end_daal - start_daal <= end_sklearn - start_sklearn
sklearn_score = lin_solver_sklearn.score(x, y)
daal_score = lin_solver_daal.score(x, y)
print("Score calculated: ")
print("+ Sklearn: {}".format(sklearn_score))
print("+ Daal: {}".format(daal_score))
assert daal_score == sklearn_score
def check_equal(cdfmapping, mapping):
assert_array_equal(cdfmapping.img.shape, mapping.img.shape)
assert_array_equal(cdfmapping.lats.shape, mapping.lats.shape)
assert_array_equal(cdfmapping.img, mapping.img)
assert_array_equal(cdfmapping.lats, mapping.lats)
assert_array_equal(cdfmapping.lons, mapping.lons)
assert_array_equal(cdfmapping.latsCenter, mapping.latsCenter)
assert_array_equal(cdfmapping.lonsCenter, mapping.lonsCenter)
assert_equal(cdfmapping.boundingBox, mapping.boundingBox)
# elevation is stored as float32, so there is some loss of accuracy
assert_array_almost_equal(cdfmapping.elevation, mapping.elevation, decimal=5)
assert_equal(cdfmapping.photoTime, mapping.photoTime)
assert_equal(cdfmapping.cameraPosGCRS, mapping.cameraPosGCRS)
def test_sparse_circulant(self):
vals = np.array([1, 2, 3, 5, 4])
offsets = np.array([-2, -1, 0, 2, 1])
n = 8
a = hm.linalg.sparse_circulant(vals, offsets, n)
a_expected = \
[[3., 4., 5., 0., 0., 0., 1., 2.],
[2., 3., 4., 5., 0., 0., 0., 1.],
[1., 2., 3., 4., 5., 0., 0., 0.],
[0., 1., 2., 3., 4., 5., 0., 0.],
[0., 0., 1., 2., 3., 4., 5., 0.],
[0., 0., 0., 1., 2., 3., 4., 5.],
[5., 0., 0., 0., 1., 2., 3., 4.],
[4., 5., 0., 0., 0., 1., 2., 3.]]
assert_array_almost_equal(a.toarray(), a_expected)
def test_gauss_seidel_sweep_reduces_energy_for_spd(self):
n = 16
kh = 0
# Make a positive definite (= -Laplacian).
a = -hm.linalg.helmholtz_1d_operator(kh, n)
relaxer = hm.solve.relax.GsRelaxer(a)
x = np.random.random((n, 1))
b = np.zeros_like(x)
energy = x.T.dot(a.dot(x))[0, 0]
for i in range(10):
y = gs_relax_with_loop(kh, x)
x = relaxer.step(x, b)
assert_array_almost_equal(x - x.mean(), y - y.mean())
energy_new = x.T.dot(a.dot(x))[0, 0]
assert energy_new < energy
energy = energy_new
def test_case(self):
model = clone(estimator)
model.fit(**fit_data)
for method in methods:
pred = getattr(model, method)(**predict_data)
code = sklearn2code(model, method, numpy_flat)
try:
module = exec_module('test_module', code)
exported_pred = getattr(module,
method)(**export_predict_data['X'])
if isinstance(exported_pred, tuple):
exported_pred = DataFrame(dict(enumerate(exported_pred)))
assert_array_almost_equal(pred, exported_pred, 3)
except:
# print(code)
# import clipboard
# clipboard.copy(code)
raise
def test_svd_simple_check():
indata = np.array([[1, 3, 4], [5, 6, 9], [1, 2, 3], [7, 6, 8]])
dataSource = HomogenNumericTable(indata)
algorithm = svd.Batch()
algorithm.input.set(svd.data, dataSource)
result = algorithm.compute()
sigma = getNumpyArray(result.get(svd.singularValues))
U = getNumpyArray(result.get(svd.leftSingularMatrix))
V = getNumpyArray(result.get(svd.rightSingularMatrix))
# create diagonal matrix of Singular values
_rows, cols = sigma.shape
d_sigma = sigma.reshape(cols, )
outdata = np.dot(U, np.dot(np.diag(d_sigma), V))
assert_array_almost_equal(outdata, indata)
def test_ritz(self):
n = 16
kh = 0
a = hm.linalg.helmholtz_1d_operator(kh, n)
x = np.random.random((n, 4))
action = lambda x: a.dot(x)
y, lam_y = hm.linalg.ritz(x, action)
lam_y_expected = np.array(
[_rq(y[:, k], action) for k in range(y.shape[1])])
assert_array_almost_equal(lam_y, lam_y_expected)
assert y.shape == x.shape
r = action(y)
r = np.array([r[:, k] - lam_y[k] * y[:, k] for k in range(y.shape[1])])
assert norm(r.dot(x)) < 1e-14
def test_tile_csr_matrix(self):
n = 4
kh = 0.5
a = hm.linalg.helmholtz_1d_operator(kh, n)
a_expected = \
[[-1.75, 1., 0., 1.],
[1., -1.75, 1., 0.],
[0., 1., -1.75, 1.],
[1., 0., 1., -1.75]]
assert_array_almost_equal(a.toarray(), a_expected)
for growth_factor in range(2, 5):
a_tiled = hm.linalg.tile_csr_matrix(a, growth_factor)
a_tiled_expected = hm.linalg.helmholtz_1d_operator(
kh, growth_factor * n).tocsr()
assert_array_almost_equal(a_tiled.toarray(),
a_tiled_expected.toarray())
def test_all(self):
for i, node in enumerate(self.nodes):
assert_array_almost_equal(AcceleratedGradient(50).solve(node.f, numpy.ones(2) * 10), [i] * 2)
graph = Graph(self.nodes, self.edges)
problem = MultiAgentProblem(graph, 100)
problem.solve()
for edge in self.edges:
assert_array_almost_equal(edge.x_values(edge.l_node), edge.x_values(edge.r_node) * -1.0, 2)
for i, node in enumerate(self.nodes):
x = node.x
if i is 0:
self.assertAlmostEqual(x[0], 0.0, 2)
else:
self.assertAlmostEqual(x[0], i - 0.5, 2)
if i is self.n - 1:
self.assertAlmostEqual(x[1], i, 2)
else:
self.assertAlmostEqual(x[1], i + 0.5, 2)
def test_tile_csr_matrix_level2_operator(self):
a = np.array([[-0.16, 0.05, 0.18, 0.35, 0., 0., 0.18, -0.21],
[0.05, -1.22, -0.21, -0.42, 0., 0., 0.35, -0.42],
[0.18, -0.21, -0.16, 0.05, 0.18, 0.35, 0., 0.],
[0.35, -0.42, 0.05, -1.22, -0.21, -0.42, 0., 0.],
[0., 0., 0.18, -0.21, -0.16, 0.05, 0.18, 0.35],
[0., 0., 0.35, -0.42, 0.05, -1.22, -0.21, -0.42],
[0.18, 0.35, 0., 0., 0.18, -0.21, -0.16, 0.05],
[-0.21, -0.42, 0., 0., 0.35, -0.42, 0.05, -1.22]])
a_tiled = hm.linalg.tile_csr_matrix(scipy.sparse.csr_matrix(a), 2)
# The tiled operator should have blocks of of 2 6-point stencils that are periodic on 16 points.
wrapped_around = np.zeros_like(a)
wrapped_around[-2:, :2] = a[-2:, :2]
wrapped_around[:2, -2:] = a[:2, -2:]
a_tiled_expected = np.block([[a - wrapped_around, wrapped_around],
[wrapped_around, a - wrapped_around]])
assert_array_almost_equal(a_tiled.toarray(), a_tiled_expected)
def test_admm_on_dumb():
adj1, adj2 = dumb_admm_system()
xymap1 = []
xymap2 = []
uymap1 = [0, 1]
uymap2 = [0, 1]
yzmap1 = [0, 1]
yzmap2 = [1, 0]
data1 = AdjointAdmmData(adj1, xymap1, uymap1, yzmap1, numpy.zeros(2), rho=.5)
data2 = AdjointAdmmData(adj2, xymap2, uymap2, yzmap2, numpy.zeros(2), rho=.5)
sp1 = AdjointAdmmSubProblem(data1, solver=AcceleratedGradient())
sp2 = AdjointAdmmSubProblem(data2, solver=AcceleratedGradient())
def objective(problem):
return (problem.z[0] - 1) ** 2 + (problem.z[1] - 2) ** 2 + sum(
[sp.data.admm_cost() for sp in problem.sub_problems])
problem = Admm([sp2, sp1], n_iters=40, objective=objective)
problem.solve()
assert_array_almost_equal(problem.z, [1.0, 2.0])
def test_dataset_to_instances(self, default_rank = [1, 2, 3, 4, 5]):
#create the final numpy array manually and see if the conversion happens ok
newdata = []
default_rank = Ranking(default_rank).inverse().integers()
for i in range(1, 101):
for rank_strings in range(5):
vector = sorted([(str(k),k+rank_strings) for k in range(20)])
vector = np.array([float(v) for _, v in vector])
#newdata.append([vector, int(rank_strings)+1, i])
newdata.append([vector, default_rank[rank_strings], i])
newdata = np.array(newdata)
newmetadata = {'input_size' : 20, #size of feature vector
'scores' : set([1, 2, 3, 4, 5])}
data, metadata = dataset_to_instances(self.train_filename).raw_source()
for i in range(np.shape(data)[0]):
vector1, rank1, query1 = data[i]
vector2, rank2, query2 = newdata[i]
assert_array_almost_equal(vector1, vector2, err_msg="MLPython: error in the conversion of batch data")
assert_equal(rank1, rank2, err_msg="MLPython: error in the conversion of rank_strings value")
assert_equal(query1, query2)
assert_equal(metadata, newmetadata, err_msg="MLPython: error in the conversion of metadata")
def test_chisquare_masked_arrays():
# The other tests were taken from the tests for stats.chisquare, so
# they don't test the function with masked arrays. Here masked arrays
# are tested.
obs = np.array([[8, 8, 16, 32, -1], [-1, -1, 3, 4, 5]]).T
mask = np.array([[0, 0, 0, 0, 1], [1, 1, 0, 0, 0]]).T
mobs = ma.masked_array(obs, mask)
expected_chisq = np.array([24.0, 0.5])
chisq, p = mstats.chisquare(mobs)
assert_array_equal(chisq, expected_chisq)
assert_array_almost_equal(p, stats.chisqprob(expected_chisq, mobs.count(axis=0) - 1))
chisq, p = mstats.chisquare(mobs.T, axis=1)
assert_array_equal(chisq, expected_chisq)
assert_array_almost_equal(p, stats.chisqprob(expected_chisq, mobs.T.count(axis=1) - 1))
# When axis=None, the two values should have type np.float64.
chisq, p = mstats.chisquare([1,2,3], axis=None)
assert_(isinstance(chisq, np.float64))
assert_(isinstance(p, np.float64))
assert_equal(chisq, 1.0)
assert_almost_equal(p, stats.chisqprob(1.0, 2))
def test_both():
t = 3
nl = 2
nr = 2
zl = numpy.zeros(t)
zr = numpy.zeros(t)
p = numpy.zeros(t)
beta = .5
cl = LeftAdmm(zl, p, beta, t, nl).no_control()
cr = RightAdmm(zl, p, beta, t, nl).no_control()
for i in range(100):
l = LeftAdmm(zl, p, beta, t, nl)
cl = l.optimal_control()
xl = l.fs(cl)[nl - 1, :]
cr = RightAdmm(zr, p, beta, t, nr).optimal_control()
xr = cr[[0] + range(nr, len(cr))]
v = -p + beta / 2.0 * (xl - xr)
zl = 1.0 / beta * (-p - v) + xl
zr = 1.0 / beta * (-p - v) - xr
p = -v
fsl = LeftAdmm(zl, p, beta, t, nl).solve()
fsr = RightAdmm(zr, p, beta, t, nl).solve()
assert_array_almost_equal(fsl[-1, :], fsr[0, :], 7)
assert_array_almost_equal(numpy.concatenate((fsl[:-1, :], fsr), 0), numpy.eye(3) / 3.0, 3)
def test_2D(self):
a = ma.array(((1, 2, 3, 4), (1, 2, 3, 4), (1, 2, 3, 4)), mask=((0, 0, 0, 0), (1, 0, 0, 1), (0, 1, 1, 0)))
actual = mstats.gmean(a)
desired = np.array((1, 2, 3, 4))
assert_array_almost_equal(actual, desired, decimal=14)
desired1 = mstats.gmean(a, axis=0)
assert_array_almost_equal(actual, desired1, decimal=14)
actual = mstats.gmean(a, -1)
desired = ma.array((np.power(1 * 2 * 3 * 4, 1.0 / 4.0), np.power(2 * 3, 1.0 / 2.0), np.power(1 * 4, 1.0 / 2.0)))
assert_array_almost_equal(actual, desired, decimal=14)
def test_vs_nonmasked(self):
x = np.array((-2, -1, 0, 1, 2, 3) * 4) ** 2
assert_array_almost_equal(mstats.normaltest(x), stats.normaltest(x))
assert_array_almost_equal(mstats.skewtest(x), stats.skewtest(x))
assert_array_almost_equal(mstats.kurtosistest(x), stats.kurtosistest(x))
funcs = [stats.normaltest, stats.skewtest, stats.kurtosistest]
mfuncs = [mstats.normaltest, mstats.skewtest, mstats.kurtosistest]
x = [1, 2, 3, 4]
for func, mfunc in zip(funcs, mfuncs):
assert_raises(ValueError, func, x)
assert_raises(ValueError, mfunc, x)
def test_hampelfilter(self):
Y = np.array([4979, 5002, 5004, 5000, 4987, 4989, 5008, 5013, 5000, 4996, 5026, 5000, 5003, 4988, 4991, 5017, 5013, 5004, 4990, 4997, 5010, 5007, 5001, 4970, 5002, 4986, 5032, 5003, 4994, 5001, 4988, 4998, 5002, 4996, 4988, 5009, 5003, 4986, 4996, 4994, 4997, 5003, 5012, 5002, 5001, 5006, 5006, 4986, 4998, 4978, 4995, 4999, 4987, 5015, 5009, 5016, 4995, 5007, 5013, 4996, 5018, 4992, 4989, 4994, 4991, 4995, 5018, 5007, 5008, 4990, 5010, 4986, 5009, 4999, 5008, 5000, 5001, 5000, 5004, 5032, 5009, 5005, 5014, 5000, 4992, 4994, 4991, 4993, 5000, 5005, 4993, 5003, 4995, 4980, 4995, 4999, 5007, 5000, 4988, 4982, 5030, 4997, 4993, 5009, 4993, 5020, 5010, 4997, 4987, 4999, 5006, 4984, 5000, 4987, 4986, 5006, 5002, 5001, 5003, 4996, 4994, 5002, 4989, 4998, 4996, 5007, 4993, 4998, 5001, 4989, 5012, 5001, 5010, 4996, 5004, 5008, 5002, 5024, 4997, 5001, 5010, 5023, 4996, 5018, 5002, 4990, 5009, 4997, 5016, 5000, 5013, 5008, 4990, 5011, 4996, 5010, 5004, 5023, 4999, 5004, 4996, 5011, 4998, 5000, 4988, 5000, 4993, 4998, 5000, 5006, 5010, 4988, 5000, 4997, 4995, 4996, 5005, 5003, 5009, 5009, 4997, 5010, 5014, 4990, 5013, 5015, 5011, 4987, 5004, 4999, 5030, 5000, 5000, 4999, 5013, 5012, 5001, 5012, 4995, 4997, 4995, 4985, 4989, 5007, 5010, 4997, 5011, 4995, 5000, 5011, 4998, 4991, 5021, 5003, 4985, 4991, 4995, 5018, 4979, 5003, 5011, 5009, 5001, 4998, 5008, 4994, 5016, 4992, 5008, 4993, 4983, 5010, 5023, 4975, 4987, 4994, 5002, 4984, 5005, 5006, 5005, 5000, 4996, 5000, 4999, 5004, 4994, 5000, 4981, 5001, 4994, 4993, 5000, 5004, 5001, 4992, 5002, 5006, 4997, 4987, 5001, 5008, 5011, 4995, 5006, 4976, 4999, 4989, 5008, 4996, 4997, 5006, 5005, 5007, 4990, 5010, 4996, 4998, 5000, 5014, 5002, 5001, 4996, 4997, 5000, 5003, 5000, 4986, 5013, 5001, 4990, 4990, 5010, 5000, 5021, 5000, 5006, 4995, 5012, 5019, 5000, 5006, 4999, 5007, 5014, 5000, 4994, 4991, 5010, 4985, 4988, 5007, 5005, 5000, 5005, 4997, 4995, 4987, 5000, 5000, 5009, 5000, 4999, 5011, 5018, 4994, 5000, 4995, 5000, 5008, 4994, 4992, 5000, 4998, 4992, 5006, 4996, 5000, 5018, 5000, 5022, 5002, 5007, 5000, 5012, 5014, 5010, 4997, 4996, 5014, 4995, 4991, 5006, 4992, 5008, 5004, 4995, 5016, 4974, 5005, 5000, 4985, 5002, 5000, 5009, 4991, 4995, 5004, 4987, 5014, 4986, 5008, 4985, 4995, 5010, 5000, 5001, 5013, 4988, 5001, 5002, 4986, 4985, 5001, 4995, 5004, 4998, 4998, 4992, 5003, 5000, 4991, 4998, 5002, 5011, 4986, 5013, 4997, 5000, 4997, 5003, 5014, 4998, 5002, 5006, 5015, 4992, 4992, 4995, 4998, 4994, 5007, 4977, 5004, 5005, 4990, 4991, 5001, 5010, 4991, 4990, 5006, 5004, 5004, 4997, 5001, 4992, 5000, 5000, 4996, 4987, 4993, 5001, 5006, 4999, 4993, 4999, 5001, 5001, 5014, 4985, 5010, 5006, 4989, 5002, 5011, 4999, 5010, 5005, 5002, 5010, 4990, 4994, 5000, 4985, 5010, 5000, 4999, 5000, 4977, 5007, 5005, 4990, 5000, 4985, 5003, 5009, 5012, 5012, 5000, 5018, 4997, 5002, 4992, 4999, 4997, 5005, 5009, 4989, 5005, 4988, 5001, 5000, 5018, 4999, 5005, 4997, 5015, 5001, 4988, 4983, 5013, 4992, 5002, 5012, 4999, 5013, 5000, 4988, 4989, 4996, 5000, 5002, 4999, 5021, 4991, 5009, 5005, 4994, 5000, 4994, 4985, 4999, 4980, 5013, 5014, 5000, 4996, 5008, 5028, 5002, 5004, 4999, 5012, 4992, 5002, 4987, 5004, 5009, 5004, 5013, 4989, 5027, 4992, 5016, 5007, 5003, 5013, 5003, 4983, 5000, 4987, 5001, 4998, 4994, 4998, 4997, 5023, 4971, 5001, 4990, 5025, 5003, 4996, 5006, 5005, 4995, 4994, 5023, 5003, 5005, 4991, 5001, 5028, 4996, 5001, 5005, 5001, 5001, 5028, 4983, 5000, 5005, 5001, 4999, 5003, 4982, 5000, 5012, 5011, 5008, 5000, 4998, 4994, 4988, 5013, 4998, 5017, 4991, 5007, 5016, 5007, 4997, 4974, 4997, 5006, 5003, 5010, 5003, 4997, 4997, 4994, 4998, 4987, 5004, 4974, 5009, 5006, 5009, 4984, 5010, 5023, 5000, 5008, 4992, 5008, 4993, 5010, 5012, 4989, 5002, 4993, 5007, 4985, 4990, 4988, 4997, 5000, 4994, 5004, 4981, 5000, 4999, 5003, 4988, 5006, 5019, 5003, 4992, 4977, 4998, 4987, 4995, 4987, 5000, 4986, 4998, 4996, 5008, 5011, 5009, 5000, 4999, 5010, 4999, 5009, 5010, 4992, 4998, 4994, 5009, 4998, 5013, 5011, 4997, 5016, 4995, 5003, 4986, 5010, 4995, 4986, 5025, 4990, 5010, 4990, 4996, 5000, 5002, 4994, 5002, 5000, 5020, 4995, 5003, 5006, 5000, 4997, 4996, 5010, 4992, 5013, 4998, 4988, 4999, 5004, 5004, 5002, 5002, 5001, 4986, 5011, 5012, 4988, 5000, 5000, 5012, 5004, 5004, 4984, 5012, 4998, 5005, 5005, 5005, 4995, 4971, 5006, 5000, 5008, 5015, 4999, 4999, 4996, 5000, 4992, 5019, 5020, 4999, 4991, 5020, 5000, 5002, 5000, 5003, 4985, 4990, 5011, 5012, 4997, 4989, 4999, 5006, 4997, 4992, 4999, 4985, 4999, 5012, 5003, 4989, 5010, 5010, 5012, 4990, 4986, 5014, 5000, 4994, 5017, 4995, 5005, 5003, 5000, 5000, 4988, 5018, 5007, 5009, 5002, 5004, 4999, 5026, 4987, 4986, 5000, 4994, 5012, 5022, 4996, 5002, 4986, 4990, 4989, 5030, 4997, 5002, 5004, 4999, 5000, 4992, 4977, 4997, 4998, 5000, 4987, 5032, 4998, 5014, 4978, 5001, 4988, 5006, 5003, 5005, 5021, 5005, 5000, 5003, 4990, 4991, 4990, 5016, 5006, 4981, 5002, 4998, 4989, 4995, 5007, 5004, 5019, 5001, 5004, 5000, 4996, 4988, 5022, 5003, 5009, 4998, 5003, 4991, 5000, 4988, 5004, 5002, 4991, 4998, 4996, 4991, 5013, 5007, 5010, 5004, 5006, 5007, 4993, 5000, 5002, 4992, 4999, 4992, 5001, 4989, 4992, 5015, 5011, 5008, 5004, 4990, 4995, 4993, 5004, 4995, 4982, 5008, 5000, 4993, 5000, 5000, 4991, 5005, 5008, 5003, 4994, 4997, 5012, 4995, 5009, 5020, 5010, 5019, 4979, 5013, 4990, 5002, 5000, 5015, 4989, 5009, 4998, 5004, 5010, 4988, 4994, 5004, 4985, 4998, 4991, 4985, 4994, 4986, 5010, 4990, 5002, 5005, 5008, 5004, 4988, 4980, 5005, 4994, 5004, 4998, 4990, 5010, 5003, 5011, 4992, 5009, 5003, 5013, 4996, 4997, 4989, 4992, 5002, 4992, 4996, 4999, 5000, 5009, 4990, 4992, 5020, 4981, 5011, 5000, 5008, 4997, 4994, 4982, 5014, 5013, 4996, 5002, 5011, 5003, 5000, 5015, 4999, 5001, 5002, 5018, 4984, 5022, 5009, 5006, 5009, 5000, 4974, 4991, 5020, 5000, 4987, 5003, 4987, 5003, 5002, 5016, 4997, 5022, 5005, 4998, 4999, 5001, 5000, 5008, 5000, 5001, 4994, 4991, 4997, 4990, 4991, 4995, 5008, 5007, 4994, 5000, 5007, 4988, 5014, 5003, 4998, 4995, 5000, 5000, 5004], dtype=float) # @IgnorePep8
# randint = np.random.randint
# Y = 5000 + np.int_(10*np.random.randn(1000))
# outliers = randint(0, 1000, size=(10,))
outliers = np.array([470, 795, 399, 614, 864, 37, 815, 112, 69, 16])
# noise = randint(1000, size=(10,))
noise = np.array([932, 286, 736, 427, 858, 63, 243, 264, 668, 844])
# print(', '.join(['{0:d}'.format(y) for y in Y]))
Y[outliers] = Y[outliers] + noise
YY, _res = HampelFilter(fulloutput=True)(Y)
assert_array_almost_equal(YY[outliers], [5002, 5000, 5003, 5008, 5000,
4997, 4998, 4999, 5009, 4997])
assert_array_almost_equal(np.int_(YY), [5001, 5002, 5004, 5000, 4987, 4989, 5008, 5013, 5000, 4996, 5000, 5000, 5003, 4988, 4991, 5017, 4997, 5004, 4990, 4997, 5010, 5007, 5001, 4970, 5002, 4986, 5032, 5003, 4994, 5001, 4988, 4998, 5002, 4996, 4988, 5009, 5003, 4997, 4996, 4994, 4997, 5003, 5012, 5002, 5001, 5006, 5006, 4986, 4998, 4978, 4995, 4999, 4987, 5015, 5009, 5016, 4995, 5007, 5013, 4996, 5018, 4992, 4989, 4994, 4991, 4995, 5018, 5007, 5008, 5009, 5010, 5008, 5009, 4999, 5000, 5000, 5001, 5000, 5004, 5005, 5009, 5005, 5014, 5000, 4992, 4994, 4991, 4993, 5000, 5005, 4993, 5003, 4995, 4980, 4995, 4999, 5007, 5000, 4988, 4982, 5030, 4997, 4993, 5009, 4993, 5020, 5010, 4997, 4987, 4999, 5006, 4984, 4999, 4987, 4986, 5006, 5002, 5001, 5003, 4996, 4994, 5002, 4989, 4998, 4996, 5007, 4993, 4998, 5001, 4989, 5012, 5001, 5010, 4996, 5004, 5008, 5002, 5004, 4997, 5001, 5010, 5023, 4996, 5018, 5002, 4990, 5009, 4997, 5016, 5000, 5013, 5008, 4990, 5011, 4996, 5010, 5004, 5023, 4999, 5004, 4996, 5011, 4998, 5000, 4998, 5000, 4993, 4998, 5000, 5006, 5010, 4988, 5000, 4997, 4995, 4996, 5005, 5003, 5009, 5009, 4997, 5010, 5014, 5011, 5013, 5015, 5011, 4987, 5004, 4999, 5000, 5000, 5000, 4999, 5001, 5012, 5001, 5012, 4995, 4997, 4995, 4985, 4989, 5007, 5010, 4997, 5011, 4995, 5000, 5011, 4998, 4991, 5021, 5003, 4985, 4991, 4995, 5018, 4979, 5003, 5011, 5009, 5001, 4998, 5008, 4994, 5016, 4992, 5008, 4993, 4983, 5010, 5023, 4975, 4987, 4994, 5002, 5002, 5005, 5006, 5005, 5000, 4996, 5000, 4999, 5004, 5000, 5000, 4981, 5001, 4994, 4993, 5000, 5004, 5001, 4992, 5002, 5006, 4997, 4987, 5001, 5008, 5011, 4995, 5006, 4976, 4999, 4989, 5008, 4996, 4997, 5006, 5005, 5007, 4990, 5010, 4996, 4998, 5000, 5000, 5002, 5001, 4996, 4997, 5000, 5003, 5000, 5000, 5013, 5001, 4990, 4990, 5010, 5000, 5021, 5000, 5006, 4995, 5012, 5019, 5000, 5006, 4999, 5007, 5014, 5000, 4994, 4991, 5010, 4985, 4988, 5007, 5005, 5000, 5005, 4997, 4995, 4987, 5000, 5000, 5000, 5000, 4999, 5011, 5018, 4994, 5000, 4995, 5000, 5008, 4994, 4992, 5000, 4998, 4992, 5006, 4996, 5000, 5018, 5000, 5002, 5002, 5007, 5000, 5012, 5014, 5010, 4997, 4996, 5014, 4995, 4991, 5006, 4992, 5008, 5004, 4995, 5016, 5000, 5005, 5000, 4985, 5002, 5000, 5009, 4991, 4995, 5004, 4987, 5014, 4986, 5008, 4985, 4995, 5010, 5000, 5001, 5001, 5001, 5001, 5002, 4986, 5001, 5001, 4995, 5004, 4998, 4998, 4992, 5003, 5000, 4991, 4998, 5002, 5011, 5000, 5013, 4997, 5000, 5003, 5003, 5014, 4998, 5002, 5006, 5015, 4992, 4992, 4995, 4998, 4994, 5007, 4977, 5004, 5005, 4990, 4991, 4991, 4991, 4991, 5004, 5006, 5004, 5004, 4997, 5001, 4992, 5000, 5000, 4996, 4987, 4993, 5001, 5006, 4999, 4993, 4999, 5001, 5001, 5014, 4985, 5010, 5006, 4989, 5002, 5011, 4999, 5010, 5005, 5002, 5010, 4990, 4994, 5000, 4985, 5000, 5000, 4999, 5000, 5000, 5007, 5005, 4990, 5000, 4985, 5003, 5009, 5012, 5012, 5000, 5002, 4997, 5002, 4992, 4999, 4997, 5005, 5009, 4989, 5005, 4988, 5001, 5000, 5000, 4999, 5005, 4997, 5015, 5001, 4988, 4983, 5013, 4992, 5002, 5012, 4999, 5013, 5000, 4988, 4989, 4996, 5000, 5002, 4999, 5002, 4991, 5009, 5005, 4994, 5000, 4994, 4985, 4999, 4980, 5013, 5014, 5000, 4996, 5008, 5002, 5002, 5004, 4999, 5012, 4992, 5002, 4987, 5004, 5009, 5004, 5013, 4989, 5027, 4992, 5016, 5007, 5003, 5013, 5003, 5001, 5000, 4987, 5001, 4998, 4994, 4998, 4997, 4997, 4971, 5001, 4990, 5001, 5003, 4996, 5006, 5005, 4995, 5005, 5023, 5003, 5005, 4991, 5001, 5001, 4996, 5001, 5005, 5001, 5001, 5001, 5001, 5000, 5005, 5001, 4999, 5003, 5001, 5000, 5012, 5011, 5008, 5000, 4998, 4994, 4988, 5013, 4998, 5017, 4991, 5007, 5016, 5007, 4997, 5003, 4997, 5006, 5003, 5010, 5003, 4997, 4997, 4994, 4998, 4987, 5004, 5004, 5009, 5006, 5009, 5009, 5010, 5023, 5000, 5008, 5008, 5008, 4993, 5010, 5012, 4989, 5002, 4993, 4990, 4985, 4990, 4988, 4997, 5000, 4994, 5004, 5000, 5000, 4999, 5003, 5003, 5006, 5019, 5003, 4992, 4977, 4998, 4987, 4995, 4987, 5000, 4986, 4998, 4996, 5008, 5011, 5009, 5000, 5009, 5010, 4999, 5009, 5010, 4992, 4998, 4994, 5009, 4998, 5013, 5011, 4997, 5016, 4995, 5003, 4986, 5010, 4995, 4986, 5025, 4990, 5010, 4990, 4996, 5000, 5002, 4994, 5002, 5000, 5002, 4995, 5003, 5006, 5000, 4997, 4996, 4998, 4992, 5013, 4998, 4988, 4999, 5004, 5004, 5002, 5002, 5001, 4986, 5011, 5012, 4988, 5000, 5000, 5012, 5004, 5004, 4984, 5004, 5005, 5005, 5005, 5005, 5005, 5005, 5006, 5000, 5008, 5015, 4999, 4999, 4996, 5000, 4992, 5019, 5020, 4999, 4991, 5000, 5000, 5002, 5000, 5003, 4985, 4990, 5011, 5012, 4997, 4989, 4999, 4997, 4997, 4992, 4999, 4985, 4999, 5012, 5003, 5010, 5010, 5010, 5012, 5010, 4986, 5014, 5000, 4994, 5017, 4995, 5005, 5003, 5000, 5000, 4988, 5018, 5007, 5009, 5002, 5004, 4999, 5000, 4987, 4986, 5000, 4994, 5012, 5022, 4996, 5002, 4986, 4990, 4989, 4997, 4997, 5002, 5004, 4999, 5000, 4992, 4998, 4997, 4998, 5000, 5000, 5032, 4998, 5014, 4978, 5001, 5003, 5006, 5003, 5005, 5005, 5005, 5000, 5003, 4990, 4991, 4990, 5016, 5006, 4981, 4998, 4998, 4989, 4995, 5007, 5004, 5004, 5001, 5004, 5000, 4996, 4988, 5000, 5003, 5009, 4998, 5003, 4991, 5000, 4988, 5004, 5002, 4991, 4998, 4996, 4991, 5013, 5007, 5010, 5004, 5006, 5007, 4993, 5000, 5002, 4992, 4999, 4992, 5001, 4989, 4992, 5015, 5011, 5008, 5004, 4990, 4995, 4993, 5004, 5000, 4982, 5008, 5000, 4993, 5000, 5000, 4991, 5005, 5008, 5003, 4994, 4997, 5012, 4995, 5009, 5020, 5010, 5019, 4979, 5013, 4990, 5002, 5000, 5015, 4989, 5009, 4998, 5004, 5010, 4988, 4994, 5004, 4985, 4998, 4991, 4985, 4994, 4986, 5010, 4990, 5002, 5005, 5008, 5004, 4988, 5004, 5005, 4994, 5004, 4998, 4990, 5010, 5003, 5011, 4992, 5009, 5003, 5013, 4996, 4997, 4989, 4992, 5002, 4992, 4996, 4999, 5000, 5009, 4990, 4992, 5020, 4981, 5011, 5000, 5008, 4997, 4994, 4982, 5014, 5013, 4996, 5002, 5011, 5003, 5000, 5002, 4999, 5001, 5002, 5018, 4984, 5022, 5009, 5006, 5009, 5000, 4974, 4991, 5020, 5000, 4987, 5003, 5002, 5003, 5002, 5016, 4997, 5002, 5005, 4998, 4999, 5001, 5000, 5000, 5000, 5001, 4994, 4991, 4997, 4990, 4991, 4995, 5008, 5007, 4994, 5000, 5007, 4988, 5014, 5003, 4998, 4995, 5000, 5000, 5004]) # @IgnorePep8
YY1, _res1 = HampelFilter(dx=1, t=3, adaptive=0.1, fulloutput=True)(Y)
assert_array_almost_equal(np.int_(YY1), [4999, 5002, 5004, 5000, 4987, 4989, 5008, 5013, 5000, 4996, 5026, 5000, 5003, 4988, 4991, 5017, 5003, 5004, 4990, 4997, 5010, 5007, 5001, 4970, 5002, 4986, 5032, 5003, 4994, 5001, 4988, 4998, 5002, 4996, 4988, 5009, 5003, 5001, 4996, 4994, 4997, 5003, 5012, 5002, 5001, 5006, 5006, 4986, 4998, 4978, 4995, 4999, 4987, 5015, 5009, 5016, 4995, 5007, 5013, 4996, 5018, 4992, 4989, 4994, 4991, 4995, 5018, 5007, 5008, 5006, 5010, 4986, 5009, 4999, 5008, 5000, 5001, 5000, 5004, 5004, 5009, 5005, 5014, 5000, 4992, 4994, 4991, 4993, 5000, 5005, 4993, 5003, 4995, 4980, 4995, 4999, 5007, 5000, 4988, 4982, 5030, 4997, 4993, 5009, 4993, 5020, 5010, 4997, 4987, 4999, 5006, 4984, 4998, 4987, 4986, 5006, 5002, 5001, 5003, 4996, 4994, 5002, 4989, 4998, 4996, 5007, 4993, 4998, 5001, 4989, 5012, 5001, 5010, 4996, 5004, 5008, 5002, 5024, 4997, 5001, 5010, 5023, 4996, 5018, 5002, 4990, 5009, 4997, 5016, 5000, 5013, 5008, 4990, 5011, 4996, 5010, 5004, 5023, 4999, 5004, 4996, 5011, 4998, 5000, 4988, 5000, 4993, 4998, 5000, 5006, 5010, 4988, 5000, 4997, 4995, 4996, 5005, 5003, 5009, 5009, 4997, 5010, 5014, 5009, 5013, 5015, 5011, 5005, 5004, 4999, 5002, 5000, 5000, 4999, 5013, 5012, 5001, 5012, 4995, 4997, 4995, 4985, 4989, 5007, 5010, 4997, 5011, 4995, 5000, 5011, 4998, 4991, 5021, 5003, 4985, 4991, 4995, 5018, 4979, 5003, 5011, 5009, 5001, 4998, 5008, 4994, 5016, 4992, 5008, 4993, 4983, 5010, 5023, 4975, 4987, 4994, 5002, 4984, 5005, 5006, 5005, 5000, 4996, 5000, 4999, 5004, 4994, 5000, 4981, 5001, 4994, 4993, 5000, 5004, 5001, 4992, 5002, 5006, 4997, 4987, 5001, 5008, 5011, 4995, 5006, 4976, 4999, 4989, 5008, 4996, 4997, 5006, 5005, 5007, 4990, 5010, 4996, 4998, 5000, 5000, 5002, 5001, 4996, 4997, 5000, 5003, 5000, 4986, 5013, 5001, 4990, 4990, 5010, 5000, 5021, 5000, 5006, 4995, 5012, 5019, 5000, 5006, 4999, 5007, 5014, 5000, 4994, 4991, 5010, 4985, 4988, 5007, 5005, 5000, 5005, 4997, 4995, 4999, 5000, 5000, 5009, 5000, 4999, 5011, 5018, 4994, 5000, 4995, 5000, 5008, 4994, 4992, 5000, 4998, 4992, 5006, 4996, 5000, 5018, 5000, 5022, 5002, 5007, 5000, 5012, 5014, 5010, 4997, 4996, 5014, 4995, 4991, 5006, 4992, 5008, 5004, 4995, 5016, 5000, 5005, 5000, 4985, 5002, 5000, 5009, 4991, 4995, 5004, 4987, 5014, 4986, 5008, 4985, 4995, 5010, 5000, 5001, 5013, 4988, 5001, 5002, 4986, 4985, 5001, 4995, 5004, 4998, 4998, 4992, 5003, 5000, 4991, 4998, 5002, 5011, 4986, 5013, 4997, 5000, 5002, 5003, 5014, 4998, 5002, 5006, 5015, 4992, 4992, 4995, 4998, 4994, 5007, 4977, 5004, 5005, 4990, 4991, 5001, 5010, 4991, 4990, 5006, 5004, 5004, 4997, 5001, 4992, 5000, 5000, 4996, 4987, 4993, 5001, 5006, 4999, 4993, 4999, 5001, 5001, 5014, 4985, 5010, 5006, 4989, 5002, 5011, 4999, 5010, 5005, 5002, 5010, 4990, 4994, 5000, 4985, 5010, 5000, 4999, 5000, 4977, 5007, 5005, 4990, 5000, 4985, 5003, 5009, 5012, 5012, 5000, 5003, 4997, 5002, 4992, 4999, 4997, 5005, 5009, 4989, 5005, 4988, 5001, 5000, 5000, 4999, 5005, 4997, 5015, 5001, 4988, 4983, 5013, 4992, 5002, 5012, 4999, 5013, 5000, 4988, 4989, 4996, 5000, 5002, 4999, 5021, 4991, 5009, 5005, 4994, 5000, 4994, 4985, 4999, 4980, 5013, 5014, 5000, 4996, 5008, 5028, 5002, 5004, 4999, 5012, 4992, 5002, 4987, 5004, 5009, 5004, 5013, 4989, 5027, 4992, 5016, 5007, 5003, 5013, 5003, 4999, 5000, 4987, 5001, 4998, 4994, 4998, 4997, 4998, 4998, 5001, 4990, 5025, 5003, 4996, 5006, 5005, 4995, 4994, 5023, 5003, 5005, 4991, 5001, 5001, 4996, 5001, 5005, 5001, 5001, 5000, 5000, 5000, 5005, 5001, 4999, 5003, 4982, 5000, 5012, 5011, 5008, 5000, 4998, 4994, 4988, 5013, 4998, 5017, 4991, 5007, 5016, 5007, 4997, 4974, 4997, 5006, 5003, 5010, 5003, 4997, 4997, 4994, 4998, 4987, 5004, 5001, 5009, 5006, 5009, 4984, 5010, 5023, 5000, 5008, 5007, 5008, 4993, 5010, 5012, 4989, 5002, 4993, 5007, 4985, 4990, 4988, 4997, 5000, 4994, 5004, 4981, 5000, 4999, 5003, 4988, 5006, 5019, 5003, 4992, 4977, 4998, 4987, 4995, 4987, 5000, 4986, 4998, 4996, 5008, 5011, 5009, 5000, 4999, 5010, 4999, 5009, 5010, 4992, 4998, 4994, 5009, 4998, 5013, 5011, 4997, 5016, 4995, 5003, 4986, 5010, 4995, 4986, 5025, 4990, 5010, 4990, 4996, 5000, 5002, 4994, 5002, 5000, 5001, 4995, 5003, 5006, 5000, 4997, 4996, 5010, 4992, 5013, 4998, 4988, 4999, 5004, 5004, 5002, 5002, 5001, 4986, 5011, 5012, 4988, 5000, 5000, 5012, 5004, 5004, 4984, 5012, 4998, 5005, 5005, 5005, 4995, 5004, 5006, 5000, 5008, 5015, 4999, 4999, 4996, 5000, 4992, 5019, 5020, 4999, 4991, 5020, 5000, 5002, 5000, 5003, 4985, 4990, 5011, 5012, 4997, 4989, 4999, 5006, 4997, 4992, 4999, 4985, 4999, 5012, 5003, 4989, 5010, 5010, 5012, 4990, 4986, 5014, 5000, 4994, 5017, 4995, 5005, 5003, 5000, 5000, 4988, 5018, 5007, 5009, 5002, 5004, 4999, 5026, 4987, 4986, 5000, 4994, 5012, 5022, 4996, 5002, 4986, 4990, 4989, 4997, 4997, 5002, 5004, 4999, 5000, 4992, 4999, 4997, 4998, 5000, 5002, 5032, 4998, 5014, 4978, 5001, 4988, 5006, 5003, 5005, 5002, 5005, 5000, 5003, 4990, 4991, 4990, 5016, 5006, 4981, 4999, 4998, 4989, 4995, 5007, 5004, 5019, 5001, 5004, 5000, 4996, 4988, 5001, 5003, 5009, 4998, 5003, 4991, 5000, 4988, 5004, 5002, 4991, 4998, 4996, 4991, 5013, 5007, 5010, 5004, 5006, 5007, 4993, 5000, 5002, 4992, 4999, 4992, 5001, 4989, 4992, 5015, 5011, 5008, 5004, 4990, 4995, 4993, 5004, 5000, 4982, 5008, 5000, 4993, 5000, 5000, 4991, 5005, 5008, 5003, 4994, 4997, 5012, 4995, 5009, 5020, 5010, 5019, 4979, 5013, 4990, 5002, 5000, 5015, 4989, 5009, 4998, 5004, 5010, 4988, 4994, 5004, 4985, 4998, 4991, 4985, 4994, 4986, 5010, 4990, 5002, 5005, 5008, 5004, 4988, 4980, 5005, 4994, 5004, 4998, 4990, 5010, 5003, 5011, 4992, 5009, 5003, 5013, 4996, 4997, 4989, 4992, 5002, 4992, 4996, 4999, 5000, 5009, 4990, 4992, 5020, 4981, 5011, 5000, 5008, 4997, 4994, 4982, 5014, 5013, 4996, 5002, 5011, 5003, 5000, 5015, 4999, 5001, 5002, 5018, 4984, 5022, 5009, 5006, 5009, 5000, 4974, 4991, 5020, 5000, 4987, 5003, 4987, 5003, 5002, 5016, 4997, 5022, 5005, 4998, 4999, 5001, 5000, 4999, 5000, 5001, 4994, 4991, 4997, 4990, 4991, 4995, 5008, 5007, 4994, 5000, 5007, 4988, 5014, 5003, 4998, 4995, 5000, 5000, 5004]) # @IgnorePep8
YY2, _res2 = HampelFilter(dx=3, t=0, fulloutput=True)(Y) # Y0 =
assert_array_almost_equal(np.int_(YY2), [5001, 5000, 4994, 5000, 5002, 5000, 5000, 5000, 5000, 5003, 5000, 5000, 5000, 5003, 5003, 5003, 4997, 5004, 5007, 5004, 5001, 5001, 5001, 5002, 5002, 5001, 5001, 5001, 4998, 5001, 4998, 4996, 4998, 4998, 5002, 5002, 4996, 4997, 5003, 5003, 5002, 5001, 5002, 5003, 5003, 5002, 5001, 4998, 4998, 4995, 4995, 4998, 4999, 4999, 5007, 5009, 5009, 5009, 5007, 4996, 4996, 4994, 4994, 4994, 4994, 4995, 5007, 5008, 5008, 5009, 5008, 5008, 5008, 5001, 5000, 5001, 5001, 5004, 5004, 5005, 5005, 5005, 5005, 5000, 4994, 4994, 4994, 4993, 4994, 4995, 4995, 4995, 4995, 4995, 4999, 4995, 4995, 4999, 4999, 4997, 4997, 4993, 4997, 5009, 4997, 4997, 4999, 4999, 4999, 4999, 4997, 4987, 4999, 5002, 5001, 5002, 5001, 5001, 5002, 5001, 4998, 4996, 4996, 4996, 4998, 4998, 4998, 4998, 5001, 5001, 5001, 5001, 5004, 5004, 5004, 5004, 5002, 5004, 5008, 5002, 5010, 5002, 5002, 5009, 5002, 5002, 5002, 5002, 5008, 5008, 5008, 5008, 5008, 5008, 5008, 5004, 5004, 5004, 5004, 5004, 5000, 4999, 5000, 4998, 4998, 4998, 5000, 5000, 5000, 5000, 5000, 5000, 4997, 4997, 4997, 5000, 5003, 5003, 5005, 5009, 5009, 5009, 5010, 5011, 5011, 5011, 5004, 5011, 5004, 5000, 5000, 5000, 5000, 5001, 5001, 5001, 5001, 5001, 4997, 4995, 4995, 4995, 4997, 4997, 4997, 5000, 5007, 5000, 4998, 5000, 5000, 5000, 4998, 4995, 4995, 4995, 4995, 4995, 5003, 5003, 5003, 5003, 5003, 5008, 5001, 5001, 4998, 4994, 4994, 5008, 4993, 4993, 4993, 4994, 4994, 4994, 4994, 5002, 5002, 5002, 5000, 5000, 5000, 5000, 5000, 4999, 5000, 4999, 4994, 4994, 5000, 5000, 5000, 5000, 5001, 5001, 5001, 5001, 5001, 5002, 5001, 5001, 5001, 5001, 4999, 4999, 4996, 4997, 4997, 4999, 5005, 5005, 5005, 5005, 5005, 5000, 5000, 5000, 5001, 5000, 5000, 5000, 5001, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5001, 5000, 5000, 5000, 5006, 5006, 5006, 5006, 5006, 5006, 5007, 5006, 5000, 5000, 5000, 5000, 4994, 4994, 4994, 5000, 5005, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 4995, 5000, 4998, 4998, 4998, 4996, 4998, 5000, 5000, 5000, 5002, 5002, 5002, 5007, 5007, 5010, 5007, 5007, 5010, 5010, 4997, 4997, 4996, 4996, 5004, 4995, 5004, 5004, 5004, 5004, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 4995, 4995, 4995, 4995, 4995, 5000, 5000, 5001, 5000, 5001, 5001, 5001, 5001, 5001, 4995, 5001, 4998, 4998, 4998, 4998, 4998, 4998, 4998, 4998, 5000, 5000, 5000, 4998, 5000, 5002, 5003, 5003, 5003, 5002, 5003, 5006, 5003, 5002, 4998, 4998, 4995, 4995, 4994, 4995, 4998, 4998, 4994, 5001, 5001, 5001, 4991, 4991, 5001, 5004, 5004, 5001, 5001, 5001, 5000, 5000, 4997, 4996, 4996, 5000, 4999, 4996, 4999, 4999, 5001, 5001, 4999, 5001, 5001, 5001, 5002, 5006, 5002, 5006, 5005, 5002, 5005, 5005, 5002, 5002, 5000, 5000, 5000, 4999, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5003, 5003, 5003, 5003, 5009, 5009, 5009, 5002, 5000, 4999, 4999, 4999, 4999, 4999, 4999, 5001, 5001, 5001, 5000, 5001, 5000, 5001, 5001, 5001, 4999, 5001, 4997, 5001, 5001, 4999, 5002, 5002, 5000, 5000, 4999, 4999, 5000, 4999, 4999, 4999, 5000, 5002, 5002, 5000, 5000, 4994, 4999, 4994, 4994, 4999, 4999, 4999, 5000, 5008, 5008, 5004, 5002, 5004, 5004, 5002, 5002, 5002, 5002, 5004, 5004, 5004, 5004, 5004, 5009, 5007, 5007, 5007, 5007, 5003, 5003, 5003, 5001, 5000, 4998, 4998, 4998, 4998, 4998, 4998, 4997, 4998, 5001, 5001, 5001, 5003, 5003, 5003, 5003, 5003, 5005, 5003, 5001, 5003, 5003, 5001, 5001, 5001, 5001, 5001, 5001, 5001, 5001, 5001, 5001, 5001, 5000, 5000, 5001, 5001, 5003, 5003, 5000, 5000, 5000, 5000, 4998, 4998, 4998, 4998, 5007, 5007, 5007, 5007, 4997, 5006, 5003, 5003, 5003, 5003, 5003, 5003, 4998, 4997, 4997, 4997, 4997, 4998, 5004, 5004, 5006, 5009, 5009, 5008, 5009, 5008, 5008, 5008, 5008, 5008, 5008, 5002, 5002, 5002, 4993, 4990, 4993, 4993, 4994, 4994, 4994, 4997, 4999, 5000, 4999, 5000, 5000, 5003, 5003, 5003, 4998, 4998, 4995, 4992, 4992, 4987, 4995, 4995, 4996, 4998, 5000, 5000, 5000, 5008, 5008, 5009, 5009, 5000, 4999, 4999, 4999, 4998, 4998, 4998, 4998, 5009, 5009, 5003, 5003, 5003, 4997, 4995, 4995, 4995, 4995, 4995, 4995, 4996, 5000, 4996, 5000, 5000, 5000, 5000, 5002, 5002, 5002, 5000, 5000, 5000, 5000, 5000, 4998, 4997, 4998, 4999, 4999, 5002, 5002, 5002, 5002, 5002, 5002, 5002, 5001, 5000, 5000, 5004, 5004, 5000, 5004, 5004, 5004, 5004, 5005, 5005, 5005, 5005, 5005, 5005, 5005, 5000, 5000, 5000, 5000, 4999, 4999, 4999, 4999, 4999, 5000, 5000, 5002, 5000, 5000, 5000, 5000, 5000, 5002, 5000, 4997, 4997, 4999, 4999, 4997, 4997, 4997, 4999, 4999, 4999, 4999, 4999, 5003, 5010, 5010, 5003, 5010, 5010, 5000, 5000, 4995, 5000, 5003, 5000, 5000, 5000, 5000, 5003, 5003, 5002, 5004, 5004, 5007, 5004, 5002, 5000, 4999, 4999, 5000, 4996, 5000, 5000, 4996, 4996, 4996, 4996, 4997, 4997, 4999, 5000, 5000, 4999, 4999, 4998, 4998, 4998, 4998, 4998, 5000, 5000, 5001, 5001, 5001, 5001, 5003, 5003, 5005, 5005, 5005, 5003, 5003, 5000, 5000, 5000, 4991, 4991, 4998, 4998, 4998, 4998, 4998, 5004, 5001, 5004, 5004, 5004, 5001, 5001, 5001, 5003, 5000, 5003, 5003, 5003, 5000, 5000, 5000, 5000, 4998, 4998, 4996, 4998, 4998, 4998, 5004, 5006, 5007, 5007, 5006, 5004, 5002, 5000, 4999, 4999, 4999, 4992, 4992, 4999, 5001, 5004, 5004, 5004, 5004, 5004, 5004, 4995, 4995, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5003, 5003, 5003, 5003, 5009, 5010, 5010, 5010, 5010, 5010, 5002, 5002, 5000, 5002, 5000, 5002, 5004, 5004, 4998, 5004, 4998, 4998, 4994, 4991, 4994, 4991, 4991, 4991, 4991, 4994, 5002, 5004, 5004, 5002, 5004, 5004, 5004, 4998, 4994, 4998, 5003, 5003, 5003, 5003, 5003, 5009, 5003, 5003, 4997, 4997, 4997, 4996, 4996, 4996, 4996, 4999, 4999, 4996, 4999, 4999, 5000, 5000, 5000, 5000, 5000, 4997, 5000, 5000, 4997, 4997, 5002, 5003, 5003, 5003, 5002, 5002, 5002, 5002, 5001, 5002, 5002, 5006, 5009, 5009, 5006, 5006, 5006, 5000, 5000, 5000, 4991, 5000, 5002, 5002, 5002, 5003, 5003, 5003, 5002, 5001, 5000, 5001, 5000, 5000, 5000, 5000, 5000, 4997, 4994, 4994, 4994, 4995, 4995, 4995, 5000, 5000, 5007, 5003, 5000, 5000, 5000, 5000, 5000, 5000, 5000, 5000]) # @IgnorePep8
def test_pass_info():
beta_op.beta = 1.0
beta_op.factor = 1.02
beta_op.factor = 1.000
beta_op.beta_admm_factor = 1.000
n, t = 10, 10
scen_full = Scenario.blank(n, t)
scen_full.ic.mainline[0] = 0.5
admm = CtmAdjointAdmm.from_full_scenario(scen_full, 5, beta=30.0, n_iters=400)
d1 = admm.l_scen.simulate(admm.l_scen.no_control()).density
d2 = admm.r_scen.simulate(admm.r_scen.no_control()).density
sln = admm.solve()
d3 = sln.l.fs(sln.l.construct_control(sln.cl)).density
d4 = sln.r.fs(sln.r.construct_control(sln.cr)).density
subplot(2, 2, 1)
pcolor(d1, cmap="binary", vmin=0.0, vmax=1.0)
xlabel("Time")
ylabel("Space")
title("Initial Upstream Subnetwork")
colorbar()
subplot(2, 2, 2)
pcolor(d2, cmap="binary", vmin=0.0, vmax=1.0)
xlabel("Time")
ylabel("Space")
title("Initial Downstream Subnetwork")
colorbar()
subplot(2, 2, 3)
pcolor(d3, cmap="binary", vmin=0.0, vmax=1.0)
xlabel("Time")
ylabel("Space")
title("Final Upstream Subnetwork")
colorbar()
subplot(2, 2, 4)
pcolor(d4, cmap="binary", vmin=0.0, vmax=1.0)
xlabel("Time")
ylabel("Space")
title("Final Downstream Subnetwork")
colorbar()
savefig("init-final.pdf")
sln.density_summary()
cl = sln.l.construct_control(sln.cl)
cr = sln.r.construct_control(sln.cr)
assert_array_almost_equal(cl[0][-2:, :], cr[0][:2, :])
assert_array_almost_equal(cl[1], [0, 0, 0.5, 0], 2)
assert_array_almost_equal(cr[1], [0, 0.5, 0, 0], 2)
assert_almost_equals(sln.history.x[-1], 0.0, 2)
assert_almost_equals(sln.history.y[-1], 0.0, 2)
def test_fs_controlled():
beta_op.beta = 1.0
scen, control = small_scenario()
ca = CTMAdjoint(scen)
for _ in range(5):
c = rand(scen.N * scen.T, 1).flatten()
assert_array_almost_equal(ca.grad(c), ca.grad_fd(c))
# fs = CTMSimulator().simulate(scen, control)
ca = ControlledCtmAdjoint(True, scen)
control = ca.construct_control(ca.no_control())
fs = ca.fs(control)
# assert_array_equal(fs.density, [[.9, 1.0, .9, .1, 0, 0, 0, 0, 0, 0, 0], [0, 1.0, .9, .9, .1, 0, 0, 0, 0, 0, 0]])
assert_array_almost_equal(fs.density, [[0.9, 1.0, 0.9, 0.1, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0]])
control[1][:] += 2.0
fs = ca.fs(control)
assert_array_almost_equal(
fs.density, np.array([[0.9, 1.8, 1.8, 1.8, 1.8, 1.8, 1.8], [2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 1.0]])
)
def test_two_length():
beta_op.beta = 50.0
# beta_op.beta = 0.8
beta_op.factor = 1.02
beta_op.beta = 100.0
beta_op.factor = 1.02
beta_op.factor = 1.000
beta = 100.0
beta_op.beta_admm_factor = 1.000
beta_op.inner_iters = 100
n, t = 2, 2
scen_full = Scenario.blank(n, t)
scen_full.ic.mainline[1] = 0.5
sln = CtmAdjointAdmm.from_full_scenario(scen_full, 1, beta=beta, n_iters=20).solve()
sln.density_summary()
cl = sln.l.construct_control(sln.cl)
cr = sln.r.construct_control(sln.cr)
assert_array_almost_equal(cl[0][-2:, :], cr[0][:2, :])
assert_array_almost_equal(cl[1], [0, 0, 0.5, 0], 2)
assert_array_almost_equal(cr[1], [0, 0.5, 0, 0], 2)
assert_almost_equals(sln.history.x[-1], 0.0, 2)
assert_almost_equals(sln.history.y[-1], 0.0, 2)
def test_plotting_positions():
# Regression test for #1256
pos = mstats.plotting_positions(np.arange(3), 0, 0)
assert_array_almost_equal(pos.data, np.array([0.25, 0.5, 0.75]))
def test_triinterp():
# Test points within triangles of masked triangulation.
x, y = np.meshgrid(np.arange(4), np.arange(4))
x = x.ravel()
y = y.ravel()
z = 1.23*x - 4.79*y
triangles = [[0, 1, 4], [1, 5, 4], [1, 2, 5], [2, 6, 5], [2, 3, 6],
[3, 7, 6], [4, 5, 8], [5, 9, 8], [5, 6, 9], [6, 10, 9],
[6, 7, 10], [7, 11, 10], [8, 9, 12], [9, 13, 12], [9, 10, 13],
[10, 14, 13], [10, 11, 14], [11, 15, 14]]
mask = np.zeros(len(triangles))
mask[8:10] = 1
triang = mtri.Triangulation(x, y, triangles, mask)
linear_interp = mtri.LinearTriInterpolator(triang, z)
cubic_min_E = mtri.CubicTriInterpolator(triang, z)
cubic_geom = mtri.CubicTriInterpolator(triang, z, kind='geom')
xs = np.linspace(0.25, 2.75, 6)
ys = [0.25, 0.75, 2.25, 2.75]
xs, ys = np.meshgrid(xs, ys) # Testing arrays with array.ndim = 2
for interp in (linear_interp, cubic_min_E, cubic_geom):
zs = interp(xs, ys)
assert_array_almost_equal(zs, (1.23*xs - 4.79*ys))
# Test points outside triangulation.
xs = [-0.25, 1.25, 1.75, 3.25]
ys = xs
xs, ys = np.meshgrid(xs, ys)
for interp in (linear_interp, cubic_min_E, cubic_geom):
zs = linear_interp(xs, ys)
assert_array_equal(zs.mask, [[True]*4]*4)
# Test mixed configuration (outside / inside).
xs = np.linspace(0.25, 1.75, 6)
ys = [0.25, 0.75, 1.25, 1.75]
xs, ys = np.meshgrid(xs, ys)
for interp in (linear_interp, cubic_min_E, cubic_geom):
zs = interp(xs, ys)
matest.assert_array_almost_equal(zs, (1.23*xs - 4.79*ys))
mask = (xs >= 1) * (xs <= 2) * (ys >= 1) * (ys <= 2)
assert_array_equal(zs.mask, mask)
# 2nd order patch test: on a grid with an 'arbitrary shaped' triangle,
# patch test shall be exact for quadratic functions and cubic
# interpolator if *kind* = user
(a, b, c) = (1.23, -4.79, 0.6)
def quad(x, y):
return a*(x-0.5)**2 + b*(y-0.5)**2 + c*x*y
def gradient_quad(x, y):
return (2*a*(x-0.5) + c*y, 2*b*(y-0.5) + c*x)
x = np.array([0.2, 0.33367, 0.669, 0., 1., 1., 0.])
y = np.array([0.3, 0.80755, 0.4335, 0., 0., 1., 1.])
triangles = np.array([[0, 1, 2], [3, 0, 4], [4, 0, 2], [4, 2, 5],
[1, 5, 2], [6, 5, 1], [6, 1, 0], [6, 0, 3]])
triang = mtri.Triangulation(x, y, triangles)
z = quad(x, y)
dz = gradient_quad(x, y)
# test points for 2nd order patch test
xs = np.linspace(0., 1., 5)
ys = np.linspace(0., 1., 5)
xs, ys = np.meshgrid(xs, ys)
cubic_user = mtri.CubicTriInterpolator(triang, z, kind='user', dz=dz)
interp_zs = cubic_user(xs, ys)
assert_array_almost_equal(interp_zs, quad(xs, ys))
(interp_dzsdx, interp_dzsdy) = cubic_user.gradient(x, y)
(dzsdx, dzsdy) = gradient_quad(x, y)
assert_array_almost_equal(interp_dzsdx, dzsdx)
assert_array_almost_equal(interp_dzsdy, dzsdy)
# Cubic improvement: cubic interpolation shall perform better than linear
# on a sufficiently dense mesh for a quadratic function.
n = 11
x, y = np.meshgrid(np.linspace(0., 1., n+1), np.linspace(0., 1., n+1))
x = x.ravel()
y = y.ravel()
z = quad(x, y)
triang = mtri.Triangulation(x, y, triangles=meshgrid_triangles(n+1))
xs, ys = np.meshgrid(np.linspace(0.1, 0.9, 5), np.linspace(0.1, 0.9, 5))
xs = xs.ravel()
ys = ys.ravel()
linear_interp = mtri.LinearTriInterpolator(triang, z)
cubic_min_E = mtri.CubicTriInterpolator(triang, z)
cubic_geom = mtri.CubicTriInterpolator(triang, z, kind='geom')
zs = quad(xs, ys)
diff_lin = np.abs(linear_interp(xs, ys) - zs)
for interp in (cubic_min_E, cubic_geom):
diff_cubic = np.abs(interp(xs, ys) - zs)
assert np.max(diff_lin) >= 10 * np.max(diff_cubic)
assert (np.dot(diff_lin, diff_lin) >=
100 * np.dot(diff_cubic, diff_cubic))
def test_simplest():
scen, control = smallest_possible()
u = control.flatten()
adjoint = CTMAdjoint(scen)
assert_array_almost_equal(adjoint.grad(u), adjoint.grad_fd(u))
def test_triinterp_transformations():
# 1) Testing that the interpolation scheme is invariant by rotation of the
# whole figure.
# Note: This test is non-trivial for a CubicTriInterpolator with
# kind='min_E'. It does fail for a non-isotropic stiffness matrix E of
# :class:`_ReducedHCT_Element` (tested with E=np.diag([1., 1., 1.])), and
# provides a good test for :meth:`get_Kff_and_Ff`of the same class.
#
# 2) Also testing that the interpolation scheme is invariant by expansion
# of the whole figure along one axis.
n_angles = 20
n_radii = 10
min_radius = 0.15
def z(x, y):
r1 = np.hypot(0.5 - x, 0.5 - y)
theta1 = np.arctan2(0.5 - x, 0.5 - y)
r2 = np.hypot(-x - 0.2, -y - 0.2)
theta2 = np.arctan2(-x - 0.2, -y - 0.2)
z = -(2*(np.exp((r1/10)**2)-1)*30. * np.cos(7.*theta1) +
(np.exp((r2/10)**2)-1)*30. * np.cos(11.*theta2) +
0.7*(x**2 + y**2))
return (np.max(z)-z)/(np.max(z)-np.min(z))
# First create the x and y coordinates of the points.
radii = np.linspace(min_radius, 0.95, n_radii)
angles = np.linspace(0 + n_angles, 2*np.pi + n_angles,
n_angles, endpoint=False)
angles = np.repeat(angles[..., np.newaxis], n_radii, axis=1)
angles[:, 1::2] += np.pi/n_angles
x0 = (radii*np.cos(angles)).flatten()
y0 = (radii*np.sin(angles)).flatten()
triang0 = mtri.Triangulation(x0, y0) # Delaunay triangulation
z0 = z(x0, y0)
# Then create the test points
xs0 = np.linspace(-1., 1., 23)
ys0 = np.linspace(-1., 1., 23)
xs0, ys0 = np.meshgrid(xs0, ys0)
xs0 = xs0.ravel()
ys0 = ys0.ravel()
interp_z0 = {}
for i_angle in range(2):
# Rotating everything
theta = 2*np.pi / n_angles * i_angle
x = np.cos(theta)*x0 + np.sin(theta)*y0
y = -np.sin(theta)*x0 + np.cos(theta)*y0
xs = np.cos(theta)*xs0 + np.sin(theta)*ys0
ys = -np.sin(theta)*xs0 + np.cos(theta)*ys0
triang = mtri.Triangulation(x, y, triang0.triangles)
linear_interp = mtri.LinearTriInterpolator(triang, z0)
cubic_min_E = mtri.CubicTriInterpolator(triang, z0)
cubic_geom = mtri.CubicTriInterpolator(triang, z0, kind='geom')
dic_interp = {'lin': linear_interp,
'min_E': cubic_min_E,
'geom': cubic_geom}
# Testing that the interpolation is invariant by rotation...
for interp_key in ['lin', 'min_E', 'geom']:
interp = dic_interp[interp_key]
if i_angle == 0:
interp_z0[interp_key] = interp(xs0, ys0) # storage
else:
interpz = interp(xs, ys)
matest.assert_array_almost_equal(interpz,
interp_z0[interp_key])
scale_factor = 987654.3210
for scaled_axis in ('x', 'y'):
# Scaling everything (expansion along scaled_axis)
if scaled_axis == 'x':
x = scale_factor * x0
y = y0
xs = scale_factor * xs0
ys = ys0
else:
x = x0
y = scale_factor * y0
xs = xs0
ys = scale_factor * ys0
triang = mtri.Triangulation(x, y, triang0.triangles)
linear_interp = mtri.LinearTriInterpolator(triang, z0)
cubic_min_E = mtri.CubicTriInterpolator(triang, z0)
cubic_geom = mtri.CubicTriInterpolator(triang, z0, kind='geom')
dic_interp = {'lin': linear_interp,
'min_E': cubic_min_E,
'geom': cubic_geom}
# Test that the interpolation is invariant by expansion along 1 axis...
for interp_key in ['lin', 'min_E', 'geom']:
interpz = dic_interp[interp_key](xs, ys)
matest.assert_array_almost_equal(interpz, interp_z0[interp_key])