def test_yule_data():
ar, v, c = aryule([1,-1,1,1,1],2, norm='biased')
assert_almost_equal(ar[0], 0.0+0.j)
assert_almost_equal(ar[1], -0.2+0.j)
assert_almost_equal(v, 0.95999999999999996)
assert_almost_equal(c[0], 0.0+0.j)
assert_almost_equal(c[1], -0.2+0.j)
def test_decimate():
"""Test decimation of digitizer headshapes with too many points."""
# load headshape and convert to meters
hsp_mm = _get_ico_surface(5)['rr'] * 100
hsp_m = hsp_mm / 1000.
# save headshape to a file in mm in temporary directory
tempdir = _TempDir()
sphere_hsp_path = op.join(tempdir, 'test_sphere.txt')
np.savetxt(sphere_hsp_path, hsp_mm)
# read in raw data using spherical hsp, and extract new hsp
with warnings.catch_warnings(record=True) as w:
raw = read_raw_kit(sqd_path, mrk_path, elp_txt_path, sphere_hsp_path)
assert_true(any('more than' in str(ww.message) for ww in w))
# collect headshape from raw (should now be in m)
hsp_dec = np.array([dig['r'] for dig in raw.info['dig']])[8:]
# with 10242 points and _decimate_points set to resolution of 5 mm, hsp_dec
# should be a bit over 5000 points. If not, something is wrong or
# decimation resolution has been purposefully changed
assert_true(len(hsp_dec) > 5000)
# should have similar size, distance from center
dist = np.sqrt(np.sum((hsp_m - np.mean(hsp_m, axis=0))**2, axis=1))
dist_dec = np.sqrt(np.sum((hsp_dec - np.mean(hsp_dec, axis=0))**2, axis=1))
hsp_rad = np.mean(dist)
hsp_dec_rad = np.mean(dist_dec)
assert_almost_equal(hsp_rad, hsp_dec_rad, places=3)
def test_applyaction(self):
action = Action(1.0, 0.0)
world = WorldSim(10, 10, default_x=5.0, default_y=5.0)
world.applyaction(action)
# Test just the linear change
assert_equal(world.x, 5.0 + WorldSim.TICK_DURATION)
action = Action(0.0, 1.0)
world.reset()
world.applyaction(action)
# Test just the angular change
assert_equal(world.theta, WorldSim.TICK_DURATION)
action = Action(1.0, 1 / WorldSim.TICK_DURATION * math.pi / 2)
world.reset()
world.applyaction(action)
# Test just the linear change
assert_equal(world.y, 5.0 + WorldSim.TICK_DURATION)
world = WorldSim(10.0, 10.0, default_x=0.0, default_y=0.0)
action = Action(1 / WorldSim.TICK_DURATION * 9 * math.sqrt(2),
1 / WorldSim.TICK_DURATION * math.pi / 4)
world.applyaction(action)
assert_almost_equal(world.x, 9)
assert_almost_equal(world.y, 9)
def test_energy():
# make sure that energy as computed by ssvm is the same as by lp
np.random.seed(0)
for inference_method in ["lp", "ad3"]:
found_fractional = False
crf = EdgeFeatureGraphCRF(n_states=3,
inference_method=inference_method,
n_edge_features=2)
while not found_fractional:
x = np.random.normal(size=(7, 8, 3))
edge_list = make_grid_edges(x, 4, return_lists=True)
edges = np.vstack(edge_list)
edge_features = edge_list_to_features(edge_list)
x = (x.reshape(-1, 3), edges, edge_features)
unary_params = np.random.normal(size=(3, 3))
pw1 = np.random.normal(size=(3, 3))
pw2 = np.random.normal(size=(3, 3))
w = np.hstack([unary_params.ravel(), pw1.ravel(), pw2.ravel()])
res, energy = crf.inference(x, w, relaxed=True, return_energy=True)
found_fractional = np.any(np.max(res[0], axis=-1) != 1)
psi = crf.psi(x, res)
energy_svm = np.dot(psi, w)
assert_almost_equal(energy, -energy_svm)
if not found_fractional:
# exact discrete labels, test non-relaxed version
res, energy = crf.inference(x, w, relaxed=False,
return_energy=True)
psi = crf.psi(x, res)
energy_svm = np.dot(psi, w)
assert_almost_equal(energy, -energy_svm)
def test_keep_top_k_epitopes():
arg_parser = make_variant_sequences_arg_parser()
args = arg_parser.parse_args([
"--vcf", data_path("b16.f10/b16.f10.Phip.vcf"),
"--bam", data_path("b16.f10/b16.combined.sorted.bam"),
])
reads_generator = allele_reads_generator_from_args(args)
variants = variant_collection_from_args(args)
keep_k_epitopes = 3
core_logic = VaxrankCoreLogic(
reads_generator=reads_generator,
mhc_predictor=random_binding_predictor,
variants=variants,
vaccine_peptide_length=15,
padding_around_mutation=5,
min_alt_rna_reads=1,
min_variant_sequence_coverage=1,
variant_sequence_assembly=True,
max_vaccine_peptides_per_variant=1,
num_mutant_epitopes_to_keep=keep_k_epitopes)
ranked_list = core_logic.ranked_vaccine_peptides()
for variant, vaccine_peptides in ranked_list:
vaccine_peptide = vaccine_peptides[0]
eq_(keep_k_epitopes, len(vaccine_peptide.mutant_epitope_predictions))
# recompute the expected score, make sure the top-k argument from ranked_vaccine_peptides()
# propagated as expected
mutant_epitope_score = sum(
p.logistic_epitope_score() for p in vaccine_peptide.mutant_epitope_predictions)
assert_almost_equal(mutant_epitope_score, vaccine_peptide.mutant_epitope_score)
def test_covar_15_ip():
af, pf, ab, pb, pbv = arcovar_marple(marple_data, 15)
assert_almost_equal(pf, 0.0031358526195905032)
assert_almost_equal(pb, 0.0026095580050847235)
assert_array_almost_equal(af[0:15], array([ 3.14064291e+00 -0.53085796j, 6.71499124e+00 -2.02047795j,
1.06218919e+01 -4.91215366j, 1.40604378e+01 -8.88144555j,
1.56600743e+01-13.2925649j , 1.52808636e+01-17.26357445j,
1.29553371e+01-20.19441487j, 9.56479043e+00-21.35967801j,
5.76086019e+00-20.39407074j, 2.35478080e+00-17.25236853j,
-1.39883911e-02-12.63099132j, -1.01307484e+00 -7.71542788j,
-1.00735874e+00 -3.71449987j, -5.47782956e-01 -1.24481265j,
-1.63739470e-01 -0.22820697j]))
assert_array_almost_equal(ab[0:15], array([ 3.06854326 +0.4396126j , 6.52836187 +1.85223579j,
10.14250939 +4.53484335j, 13.27104933 +8.16295648j,
14.65282324+12.10370542j, 14.30283278+15.67072521j,
12.13984749+18.32533332j, 9.02885933+19.34952244j,
5.49933445+18.38815454j, 2.39313549+15.41172794j,
0.23240843+11.16952573j, -0.69430878 +6.74812076j,
-0.75349882 +3.21552564j, -0.42710881 +1.07407686j,
-0.13625884 +0.18990667j]))
assert_array_almost_equal(pbv, array([23.002882564886164,
14.963158025030376, 11.46060060362683,
8.8047876198403294, 8.464718707735825,
6.7595928955003961, 3.9194229830412644,
3.4283223276191257, 2.2528330561384045,
1.174361182536527, 0.53260425403862111,
0.30138304540853789, 0.1893577453852136,
0.13685257356088598]))
def test_query_resolution():
bbox = (-180, -90, 180, 90)
init_res = (4.5, 6.7)
query = mapnik.Query(mapnik.Box2d(*bbox), init_res)
r = query.resolution
assert_almost_equal(r[0], init_res[0], places=7)
assert_almost_equal(r[1], init_res[1], places=7)
def test_match_velocities():
regression_data=yaml.load(open(os.path.join(os.path.dirname(__file__),'match_velocities.yml')))
boid_data=regression_data["before"]
match_velocities(boid_data)
for after,before in zip(regression_data["after"],boid_data):
for after_value,before_value in zip(after,before):
assert_almost_equal(after_value,before_value,delta=0.01)
def test_bad_boids_regression():
regression_data=yaml.load(open(os.path.join(os.path.dirname(__file__),'fixture.yml')))
boid_data=regression_data["before"]
update_boids(boid_data)
for after,before in zip(regression_data["after"],boid_data):
for after_value,before_value in zip(after,before):
assert_almost_equal(after_value,before_value,delta=0.01)
def test_fly_towards_middle():
regression_data=yaml.load(open(os.path.join(os.path.dirname(__file__),'fly_towards_middle.yml')))
boid_data=regression_data["before"]
fly_towards_middle(boid_data)
for after,before in zip(regression_data["after"],boid_data):
for after_value,before_value in zip(after,before):
assert_almost_equal(after_value,before_value,delta=0.01)
def test_avoid_nearby_birds():
regression_data=yaml.load(open(os.path.join(os.path.dirname(__file__),'avoid_nearby_boids.yml')))
boid_data=regression_data["before"]
avoid_nearby_boids(boid_data)
for after,before in zip(regression_data["after"],boid_data):
for after_value,before_value in zip(after,before):
assert_almost_equal(after_value,before_value,delta=0.01)
def test_length(self):
l = session.query(Lake).get(1)
r = session.query(Road).get(1)
s = session.query(Spot).get(1)
assert_almost_equal(session.scalar(l.lake_geom.length), 0.30157858985653774)
assert_almost_equal(session.scalar(r.road_geom.length), 0.8551694164147895)
ok_(not session.scalar(s.spot_location.length))
def _check_marginal_samples_match_scores(server, row, fi):
row = loom.query.protobuf_to_data_row(row.diff)
row[fi] = None
to_sample = [i == fi for i in range(len(row))]
samples = server.sample(to_sample, row, SAMPLE_COUNT)
val = samples[0][fi]
base_score = server.score(row)
if isinstance(val, bool) or isinstance(val, int):
probs_dict = {}
samples = [sample[fi] for sample in samples]
for sample in set(samples):
row[fi] = sample
probs_dict[sample] = numpy.exp(
server.score(row) - base_score)
if len(probs_dict) == 1:
assert_almost_equal(probs_dict[sample], 1., places=SCORE_PLACES)
return
if min(probs_dict.values()) < MIN_CATEGORICAL_PROB:
return
gof = discrete_goodness_of_fit(samples, probs_dict, plot=True)
elif isinstance(val, float):
probs = numpy.exp([
server.score(sample) - base_score
for sample in samples
])
samples = [sample[fi] for sample in samples]
gof = density_goodness_of_fit(samples, probs, plot=True)
assert_greater(gof, MIN_GOODNESS_OF_FIT)
def test_y(self):
s = session.query(Spot).get(1)
assert_almost_equal(float(session.scalar(s.spot_location.y)), 42.9480095987261)
s = session.query(Spot).filter(and_(Spot.spot_location.y < 0, Spot.spot_location.y > 42)).all()
ok_(s is not None)
assert_almost_equal(float(session.scalar(functions.y(WKTSpatialElement('POINT(-88.3655256496815 43.1402866687898)', geometry_type=Point.name)))),
43.1402866687898)
def test_logging():
iris = load_iris()
X, y = iris.data, iris.target
X_ = [(np.atleast_2d(x), np.empty((0, 2), dtype=np.int)) for x in X]
Y = y.reshape(-1, 1)
X_train, X_test, y_train, y_test = train_test_split(X_, Y, random_state=1)
_, file_name = mkstemp()
pbl = GraphCRF(n_features=4, n_states=3, inference_method=inference_method)
logger = SaveLogger(file_name)
svm = NSlackSSVM(pbl, C=100, n_jobs=1, logger=logger)
svm.fit(X_train, y_train)
score_current = svm.score(X_test, y_test)
score_auto_saved = logger.load().score(X_test, y_test)
alt_file_name = file_name + "alt"
logger.save(svm, alt_file_name)
logger.file_name = alt_file_name
logger.load()
score_manual_saved = logger.load().score(X_test, y_test)
assert_less(.97, score_current)
assert_less(.97, score_auto_saved)
assert_less(.97, score_manual_saved)
assert_almost_equal(score_auto_saved, score_manual_saved)
def test_multilabel_fully():
# test inference and energy with fully connected model
n_features = 5
n_labels = 4
edges = np.vstack([x for x in itertools.combinations(range(n_labels), 2)])
model = MultiLabelClf(n_labels=n_labels, n_features=n_features,
edges=edges)
rnd = np.random.RandomState(0)
x = rnd.normal(size=n_features)
w = rnd.normal(size=n_features * n_labels + 4 * len(edges))
y = model.inference(x, w)
# test joint_feature / energy
joint_feature = model.joint_feature(x, y)
energy = compute_energy(model._get_unary_potentials(x, w),
model._get_pairwise_potentials(x, w), edges, y)
assert_almost_equal(energy, np.dot(joint_feature, w))
# for continuous y
#y_cont = model.inference(x, w, relaxed=True)
y_continuous = np.zeros((n_labels, 2))
pairwise_marginals = []
for edge in edges:
# indicator of one of four possible states of the edge
pw = np.zeros((2, 2))
pw[y[edge[0]], y[edge[1]]] = 1
pairwise_marginals.append(pw)
pairwise_marginals = np.vstack(pairwise_marginals)
y_continuous[np.arange(n_labels), y] = 1
assert_array_almost_equal(
joint_feature, model.joint_feature(x, (y_continuous, pairwise_marginals)))
def test_x(self):
s = session.query(Spot).get(1)
assert_almost_equal(float(session.scalar(s.spot_location.x)), -88.594586159235689)
s = session.query(Spot).filter(and_(Spot.spot_location.x < 0, Spot.spot_location.y > 42)).all()
ok_(s is not None)
assert_almost_equal(float(session.scalar(functions.x(WKTSpatialElement('POINT(-88.3655256496815 43.1402866687898)', geometry_type=Point.name)))),
-88.3655256496815)
def test_analyze_lifetime(self):
resA = self.analyzer.analyze_lifetime(self.trajectory, self.stateA)
resB = self.analyzer.analyze_lifetime(self.trajectory, self.stateB)
assert_equal(resA.n_frames.tolist(), [3, 1, 2]) # A->B
assert_equal(resB.n_frames.tolist(), [2, 1, 1, 11]) # B->A
assert_almost_equal(resA.times.mean(), 6.0/3.0*0.1)
assert_almost_equal(resB.times.mean(), 15.0/4.0*0.1)
def test_multilabel_independent():
# test inference and energy with independent model
edges = np.zeros((0, 2), dtype=np.int)
n_features = 5
n_labels = 4
model = MultiLabelClf(n_labels=n_labels, n_features=n_features,
edges=edges)
rnd = np.random.RandomState(0)
x = rnd.normal(size=5)
w = rnd.normal(size=n_features * n_labels)
# test inference
y = model.inference(x, w)
y_ = np.dot(w.reshape(n_labels, n_features), x) > 0
assert_array_equal(y, y_)
# test joint_feature / energy
joint_feature = model.joint_feature(x, y)
energy = compute_energy(model._get_unary_potentials(x, w),
model._get_pairwise_potentials(x, w), edges, y)
assert_almost_equal(energy, np.dot(joint_feature, w))
# for continuous y
y_continuous = np.zeros((n_labels, 2))
y_continuous[np.arange(n_labels), y] = 1
assert_array_almost_equal(
joint_feature, model.joint_feature(x, (y_continuous, np.zeros((0, n_labels, n_labels)))))
def test_ap_amplitude_from_voltagebase1():
"""basic: Test AP_amplitude_from_voltagebase 1"""
import efel
import numpy
stim_start = 500.0
stim_end = 900.0
data = numpy.loadtxt('testdata/basic/mean_frequency_1.txt')
time = data[:, 0]
voltage = data[:, 1]
trace = {}
trace['T'] = time
trace['V'] = voltage
trace['stim_start'] = [stim_start]
trace['stim_end'] = [stim_end]
features = ['AP_amplitude_from_voltagebase',
'peak_voltage', 'voltage_base']
feature_values = \
efel.getFeatureValues(
[trace],
features)
voltage_base = feature_values[0]['voltage_base'][0]
for peak_voltage, ap_amplitude_from_voltagebase in zip(
feature_values[0]['peak_voltage'],
feature_values[0]['AP_amplitude_from_voltagebase']):
nt.assert_almost_equal(peak_voltage - voltage_base,
ap_amplitude_from_voltagebase)
def test_f_divergence(places=1):
"""
Tests various known relations of f-divergences to other divergences.
"""
def f_alpha(alpha):
if alpha == 1:
def f(x):
return x * np.log2(x)
elif alpha == -1:
def f(x):
return - np.log2(x)
else:
def f(x):
return 4. / (1. - alpha*alpha) * (1. - np.power(x, (1. + alpha)/2))
return f
def f_tsallis(alpha):
def f(x):
return (np.power(x, 1. - alpha) - 1.) / (alpha - 1.)
return f
test_functions = []
alphas = [0.1, 0.5, 1.1]
for alpha in alphas:
test_functions.append((f_alpha(alpha), partial(alpha_divergence, alpha=alpha)))
test_functions.append((f_tsallis(alpha), partial(tsallis_divergence, alpha=alpha)))
dists = get_dists_3()
for dist1 in dists:
for dist2 in dists:
if dist1 == dist2:
continue
for f, div_func in test_functions:
div1 = f_divergence(dist1, dist2, f)
div2 = div_func(dist1, dist2)
assert_almost_equal(div1, div2, places=1)
def test_call_with_linear_momentum_fix(self):
toy_modifier = SingleAtomVelocityDirectionModifier(
delta_v=[1.0, 2.0],
subset_mask=[1, 2],
remove_linear_momentum=True
)
new_toy_snap = toy_modifier(self.toy_snapshot)
velocities = new_toy_snap.velocities
momenta = velocities * new_toy_snap.masses[:, np.newaxis]
assert_array_almost_equal(sum(momenta), np.array([0.0]*2))
double_ke = sum(sum(momenta * velocities))
assert_almost_equal(double_ke, 86.0)
u_vel = old_div(u.nanometer, u.picosecond)
u_mass = old_div(u.dalton, u.AVOGADRO_CONSTANT_NA)
openmm_modifier = SingleAtomVelocityDirectionModifier(
delta_v=1.2*u_vel,
remove_linear_momentum=False
)
new_openmm_snap = openmm_modifier(self.openmm_snap)
velocities = new_openmm_snap.velocities
momenta = velocities * new_openmm_snap.masses[:, np.newaxis]
zero_momentum = 0 * u_vel * u_mass
total_momenta = sum(momenta, zero_momentum)
assert_array_almost_equal(total_momenta,
np.array([0.0]*3) * u_vel * u_mass)
def test_remove_momentum_rescale_energy_openmm(self):
# don't actually need to do everything with OpenMM, but do need to
# add units
u_vel = old_div(u.nanometer, u.picosecond)
u_mass = old_div(u.dalton, u.AVOGADRO_CONSTANT_NA)
u_energy = old_div(u.kilojoule_per_mole, u.AVOGADRO_CONSTANT_NA)
velocities = \
np.array([[1.5, -1.0], [-1.0, 2.0], [0.25, -1.0]]) * u_vel
masses = np.array([1.0, 1.5, 4.0]) * u_mass
new_vel = self.openmm_modifier._remove_linear_momentum(
velocities=velocities,
masses=masses
)
new_momenta = new_vel * masses[:, np.newaxis]
total_momenta = sum(new_momenta, new_momenta[0])
assert_array_almost_equal(total_momenta,
np.array([0.0]*2) * u_vel * u_mass)
new_vel = self.openmm_modifier._rescale_kinetic_energy(
velocities=velocities,
masses=masses,
double_KE=20.0 * u_energy
)
new_momenta = new_vel * masses[:, np.newaxis]
total_momenta = sum(new_momenta, new_momenta[0])
zero_energy = 0.0 * u_energy
new_ke = sum(sum(new_momenta * new_vel, zero_energy), zero_energy)
# tests require that the linear momentum be 0, and KE be correct
assert_array_almost_equal(total_momenta,
np.array([0.0]*2) * u_vel * u_mass)
assert_equal(new_ke.unit, (20.0 * u_energy).unit)
assert_almost_equal(new_ke._value, (20.0 * u_energy)._value)
def test_initial_value():
m = Minuit(func3, pedantic=False, x=1., y=2., error_x=3., print_level=0)
assert_almost_equal(m.args[0], 1.)
assert_almost_equal(m.args[1], 2.)
assert_almost_equal(m.values['x'], 1.)
assert_almost_equal(m.values['y'], 2.)
assert_almost_equal(m.errors['x'], 3.)
def test_intercepts_from_means_with_true_normalization(self):
expected_intercepts = self.true_intercepts_series
true_normalization = ['m3', 2.0]
calc_intercepts, calc_mean = wf.intercepts_from_means(
self.data, true_normalization, self.true_loadings_series)
assert_series_equal(calc_intercepts, expected_intercepts)
assert_almost_equal(calc_mean, 0.0, places=2)
def test_fit_background_C(self):
self.m["B_K"].active = False
self.m.fit_background()
nt.assert_almost_equal(self.m["Offset"].offset.value,
1.71212121212)
nt.assert_false(self.m["B_K"].active)
nt.assert_true(self.m["C_K"].active)
def check_consistency_in_mesh1d(macro_grid, element_orders, var_list):
my_mesh1d = Mesh1D(macro_grid, element_orders, var_list)
# Testing mesh attributes
numpy.testing.assert_allclose(my_mesh1d.macro_grid, macro_grid)
numpy.testing.assert_array_equal(my_mesh1d.element_orders, element_orders)
assert_equal(my_mesh1d.variables, var_list)
assert_equal(my_mesh1d.dof, (sum(element_orders) + 1) * len(var_list))
# Testing list of elements
for idx_var, var in enumerate(var_list):
for idx_el, element in enumerate(my_mesh1d.elem):
if idx_var == 0:
mesh_pos_1 = my_mesh1d.gm[idx_el][element.pos[var]][0]
mesh_pos_2 = sum(my_mesh1d.elem[el].order for el in range(idx_el))
numpy.testing.assert_array_equal(mesh_pos_1, mesh_pos_2)
else:
mesh_pos_1 = my_mesh1d.gm[idx_el][element.pos[previous_var]] + my_mesh1d.dof_1v
mesh_pos_2 = my_mesh1d.gm[idx_el][element.pos[var]]
numpy.testing.assert_array_equal(mesh_pos_1, mesh_pos_2)
previous_var = var
# Testing linear and quadratic integration
domain_integral_a = sum(el.w_1v.dot(el.x_1v) for el in my_mesh1d.elem)
domain_integral_b = sum(el.w_1v.dot(el.x_1v ** 2) for el in my_mesh1d.elem)
assert_almost_equal(domain_integral_a, (my_mesh1d.macro_grid[-1]**2 - my_mesh1d.macro_grid[0]**2) / 2)
assert_almost_equal(domain_integral_b, (my_mesh1d.macro_grid[-1]**3 - my_mesh1d.macro_grid[0]**3) / 3)
def test_call(self):
new_toy_snap = self.toy_modifier(self.toy_snapshot)
assert_array_almost_equal(new_toy_snap.coordinates,
self.toy_snapshot.coordinates)
new_vel = new_toy_snap.velocities
old_vel = self.toy_snapshot.velocities
same_vel = [np.allclose(new_vel[i], old_vel[i])
for i in range(len(new_vel))]
assert_equal(Counter(same_vel), Counter({True: 2, False: 1}))
for new_v, old_v in zip(new_vel, old_vel):
assert_almost_equal(sum([v**2 for v in new_v]),
sum([v**2 for v in old_v]))
new_omm_snap = self.openmm_modifier(self.openmm_snap)
n_atoms = len(self.openmm_snap.coordinates)
assert_array_almost_equal(new_omm_snap.coordinates,
self.openmm_snap.coordinates)
new_vel = new_omm_snap.velocities
old_vel = self.openmm_snap.velocities
same_vel = [np.allclose(new_vel[i], old_vel[i])
for i in range(len(new_vel))]
same_vel = [np.allclose(new_vel[i], old_vel[i])
for i in range(len(new_vel))]
assert_equal(Counter(same_vel), Counter({True: n_atoms-1, False: 1}))
u_vel_sq = (old_div(u.nanometers, u.picoseconds))**2
for new_v, old_v in zip(new_vel, old_vel):
assert_almost_equal(
sum([(v**2).value_in_unit(u_vel_sq) for v in new_v]),
sum([(v**2).value_in_unit(u_vel_sq) for v in old_v])
)
def test_generate_og_receptive_field():
xpixels = 500 # simulated screen width
ypixels = 500 # simulated screen height
ppd = 1 # simulated visual angle
scale_factor = 1.0 # simulated stimulus resampling rate
distance = 5 # standard deviations to compute gauss out to
xcenter = 0 # x coordinate of the pRF center
ycenter = 0 # y coordinate of the pRF center
sigma = 1 # width of the pRF
test_value = 6 # this is the sum of a gaussian given 1 ppd
# and a 1 sigma prf centered on (0,0)
# generate the visuotopic coordinates
dx,dy = generate_coordinate_matrices(xpixels,
ypixels,
ppd,
scale_factor)
# generate a pRF at (0,0) and 1 sigma wide
rf = generate_og_receptive_field(xcenter, ycenter, sigma, dx, dy)
# divide by integral
rf /= 2 * np.pi * sigma ** 2
# compare the volume of the pRF to a known value
nt.assert_almost_equal(np.sum(rf),1)
def test_mean_frequency1():
"""basic: Test mean_frequency 1"""
import efel
import numpy
stim_start = 500.0
stim_end = 900.0
data = numpy.loadtxt('testdata/basic/mean_frequency_1.txt')
time = data[:, 0]
voltage = data[:, 1]
trace = {}
trace['T'] = time
trace['V'] = voltage
trace['stim_start'] = [stim_start]
trace['stim_end'] = [stim_end]
features = ['mean_frequency']
feature_values = \
efel.getFeatureValues(
[trace],
features)
nt.assert_almost_equal(feature_values[0]['mean_frequency'], 15.2858453)
def test_ttest():
"""Test univariate t-test functions"""
ds = datasets.get_uv()
print(test.ttest('fltvar', ds=ds))
print(test.ttest('fltvar', 'A', ds=ds))
print(test.ttest('fltvar', 'A%B', ds=ds))
print(test.ttest('fltvar', 'A', match='rm', ds=ds))
print(test.ttest('fltvar', 'A', 'a1', match='rm', ds=ds))
print(test.ttest('fltvar', 'A%B', ('a1', 'b1'), match='rm', ds=ds))
# Prepare data for scipy
a1_index = ds.eval("A == 'a1'")
a2_index = ds.eval("A == 'a2'")
b1_index = ds.eval("B == 'b1'")
a1_in_b1_index = np.logical_and(a1_index, b1_index)
a2_in_b1_index = np.logical_and(a2_index, b1_index)
# TTest1Samp
res = test.TTest1Sample('fltvar', ds=ds)
t, p = scipy.stats.ttest_1samp(ds['fltvar'], 0)
assert_almost_equal(res.t, t, 10)
assert_almost_equal(res.p, p, 10)
res = test.TTest1Sample('fltvar', ds=ds, tail=1)
assert_almost_equal(res.t, t, 10)
assert_almost_equal(res.p, p / 2., 10)
# TTestInd
res = test.TTestInd('fltvar', 'A', 'a1', 'a2', ds=ds)
t, p = scipy.stats.ttest_ind(ds[a1_index, 'fltvar'], ds[a2_index,
'fltvar'])
assert_almost_equal(res.t, t, 10)
assert_almost_equal(res.p, p, 10)
# TTestRel
res = test.TTestRel('fltvar', 'A', 'a1', 'a2', 'rm', "B=='b1'", ds)
a1 = ds[a1_in_b1_index, 'fltvar'].x
a2 = ds[a2_in_b1_index, 'fltvar'].x
diff = a1 - a2
t, p = scipy.stats.ttest_rel(a1, a2)
assert_array_equal(res.diff.x, diff)
eq_(res.df, len(a1) - 1)
eq_(res.tail, 0)
assert_almost_equal(res.t, t, 10)
assert_almost_equal(res.p, p, 10)
print(res)
print(asfmtext(res))
res = test.TTestRel('fltvar', 'A', 'a1', 'a2', 'rm', "B=='b1'", ds, 1)
assert_array_equal(res.diff.x, diff)
eq_(res.df, len(a1) - 1)
eq_(res.tail, 1)
assert_almost_equal(res.t, t, 10)
assert_almost_equal(res.p, p / 2 if t > 0 else 1 - p / 2, 10)
print(res)
print(asfmtext(res))
res = test.TTestRel('fltvar', 'A', 'a1', 'a2', 'rm', "B=='b1'", ds, -1)
assert_array_equal(res.diff.x, diff)
eq_(res.df, len(a1) - 1)
eq_(res.tail, -1)
assert_almost_equal(res.t, t, 10)
assert_almost_equal(res.p, p / 2 if t < 0 else 1 - p / 2, 10)
print(res)
print(asfmtext(res))
def test_that_can_convert_julian_tai_to_datetime_obj(self):
import numpy as np
sec = 1.0 / (24.0 * 60.0 * 60.0)
days_since_standard_epoch = 143541.0 # Almost, but not quite 365.2425*393.0, not sure why...
a = np.arange(6).reshape(2, 3)
b = convert_sec_since_to_std_time(a, dt.datetime(1993, 1, 1))
eq_(a.shape, b.shape)
assert_almost_equal(b[0][0], days_since_standard_epoch)
assert_almost_equal(b[0][1], days_since_standard_epoch + 1 * sec)
assert_almost_equal(b[0][2], days_since_standard_epoch + 2 * sec)
assert_almost_equal(b[1][0], days_since_standard_epoch + 3 * sec)
assert_almost_equal(b[1][1], days_since_standard_epoch + 4 * sec)
assert_almost_equal(b[1][2], days_since_standard_epoch + 5 * sec)
def test_that_can_convert_masked_tai_to_datetime_obj(self):
import numpy.ma as ma
sec = 1.0 / (24.0 * 60.0 * 60.0)
days_since_standard_epoch = 143541.0 # Almost, but not quite 365.2425*393.0, not sure why...
a = ma.array([0, 1, 2, 3, 4, 5],
mask=[False, False, True, False, False,
False]).reshape(2, 3)
b = convert_sec_since_to_std_time(a, dt.datetime(1993, 1, 1))
eq_(a.shape, b.shape)
assert_almost_equal(b[0][0], days_since_standard_epoch)
assert_almost_equal(b[0][1], days_since_standard_epoch + 1 * sec)
assert_almost_equal(b.filled()[0][2], b.fill_value)
assert_almost_equal(b[1][0], days_since_standard_epoch + 3 * sec)
assert_almost_equal(b[1][1], days_since_standard_epoch + 4 * sec)
assert_almost_equal(b[1][2], days_since_standard_epoch + 5 * sec)
def test_number_density():
ethanol = from_atom_frac({'C': 2, 'H': 6, 'O': 1}, density=0.78900)
obs = ethanol.number_density()
exp = 9.2825E22
assert_almost_equal(obs / exp, 1.0, 4)
def test_mass_density():
ethanol = from_atom_frac({'C': 2, 'H': 6, 'O': 1})
atom_density_ethanol = 9.282542841E22 # atom density not molecule density
mass_density = ethanol.mass_density(atom_density_ethanol)
expected_mass_density = 0.78900
assert_almost_equal(mass_density, expected_mass_density, 4)
def test_even_probabilities(self):
assert_almost_equal(calculate_renyi(self.ok, 2), log(2))
assert_almost_equal(calculate_renyi(self.ok, 3), log(2))
assert_almost_equal(calculate_renyi(self.ok, 9), log(2))
def test_calculate_entropy(self):
assert_almost_equal(calculate_entropy(self.zeros), 0.0)
assert_almost_equal(calculate_entropy(self.ones), 0.0)
assert_almost_equal(calculate_entropy(self.negatives), 0.0)
assert_almost_equal(calculate_entropy(self.ok), log(2))
assert_almost_equal(calculate_entropy(self.ok_2), log(3))
def test_constraint_undirected(self):
constraint = nx.constraint(self.G)
assert_almost_equal(round(constraint['G'], 3), 0.400)
assert_almost_equal(round(constraint['A'], 3), 0.595)
assert_almost_equal(round(constraint['C'], 3), 1)
def test_constraint_directed(self):
constraint = nx.constraint(self.D)
assert_almost_equal(round(constraint[0], 3), 1.003)
assert_almost_equal(round(constraint[1], 3), 1.003)
assert_almost_equal(round(constraint[2], 3), 1.389)
def test_effective_size_undirected_borgatti(self):
effective_size = nx.effective_size(self.G)
assert_almost_equal(round(effective_size['G'], 2), 4.67)
assert_almost_equal(round(effective_size['A'], 2), 2.50)
assert_almost_equal(round(effective_size['C'], 2), 1)
def test_metric_minimum_average_direct_flip():
feature = dipymetric.IdentityFeature()
class MinimumAverageDirectFlipMetric(dipymetric.Metric):
def __init__(self, feature):
super(MinimumAverageDirectFlipMetric,
self).__init__(feature=feature)
@property
def is_order_invariant(self):
return True # Ordering is handled in the distance computation
def are_compatible(self, shape1, shape2):
return shape1[0] == shape2[0]
def dist(self, v1, v2):
average_euclidean = lambda x, y: np.mean(norm(x - y, axis=1))
dist_direct = average_euclidean(v1, v2)
dist_flipped = average_euclidean(v1, v2[::-1])
return min(dist_direct, dist_flipped)
for metric in [
MinimumAverageDirectFlipMetric(feature),
dipymetric.MinimumAverageDirectFlipMetric(feature)
]:
# Test special cases of the MDF distance.
assert_equal(metric.dist(s, s), 0.)
assert_equal(metric.dist(s, s[::-1]), 0.)
# Translation
offset = np.array([0.8, 1.3, 5], dtype=dtype)
assert_almost_equal(metric.dist(s, s + offset), norm(offset), 5)
# Scaling
M_scaling = np.diag([1.2, 2.8, 3]).astype(dtype)
s_mean = np.mean(s, axis=0)
s_zero_mean = s - s_mean
s_scaled = np.dot(M_scaling, s_zero_mean.T).T + s_mean
d = np.mean(norm((np.diag(M_scaling) - 1) * s_zero_mean, axis=1))
assert_almost_equal(metric.dist(s, s_scaled), d, 5)
# Rotation
from dipy.core.geometry import rodrigues_axis_rotation
rot_axis = np.array([1, 2, 3], dtype=dtype)
M_rotation = rodrigues_axis_rotation(rot_axis, 60.).astype(dtype)
s_mean = np.mean(s, axis=0)
s_zero_mean = s - s_mean
s_rotated = np.dot(M_rotation, s_zero_mean.T).T + s_mean
opposite = norm(np.cross(rot_axis, s_zero_mean),
axis=1) / norm(rot_axis)
distances = np.sqrt(2 * opposite**2 *
(1 - np.cos(60. * np.pi / 180.))).astype(dtype)
d = np.mean(distances)
assert_almost_equal(metric.dist(s, s_rotated), d, 5)
for s1, s2 in itertools.product(*[streamlines] *
2): # All possible pairs
# Extract features since metric doesn't work directly on streamlines
f1 = metric.feature.extract(s1)
f2 = metric.feature.extract(s2)
# Test method are_compatible
same_nb_points = f1.shape[0] == f2.shape[0]
assert_equal(metric.are_compatible(f1.shape, f2.shape),
same_nb_points)
# Test method dist if features are compatible
if metric.are_compatible(f1.shape, f2.shape):
distance = metric.dist(f1, f2)
if np.all(f1 == f2):
assert_equal(distance, 0.)
assert_almost_equal(distance, dipymetric.dist(metric, s1, s2))
assert_almost_equal(distance, dipymetric.mdf(s1, s2))
assert_true(distance >= 0.)
# This metric type is order invariant
assert_true(metric.is_order_invariant)
for s1, s2 in itertools.product(*[streamlines] *
2): # All possible pairs
f1 = metric.feature.extract(s1)
f2 = metric.feature.extract(s2)
if not metric.are_compatible(f1.shape, f2.shape):
continue
f1_flip = metric.feature.extract(s1[::-1])
f2_flip = metric.feature.extract(s2[::-1])
distance = metric.dist(f1, f2)
assert_almost_equal(metric.dist(f1_flip, f2_flip), distance)
if not np.all(f1_flip == f2_flip):
assert_true(np.allclose(metric.dist(f1, f2_flip), distance))
assert_true(np.allclose(metric.dist(f1_flip, f2), distance))
def test_effective_size_directed(self):
effective_size = nx.effective_size(self.D)
assert_almost_equal(round(effective_size[0], 3), 1.167)
assert_almost_equal(round(effective_size[1], 3), 1.167)
assert_almost_equal(round(effective_size[2], 3), 1)
def test_large_monty_prize():
assert_almost_equal(large_monty_prize.log_probability(
(True, True, 'A')), numpy.log(0.3))
assert_almost_equal(large_monty_prize.log_probability(
(True, False, 'C')), numpy.log(0.4))
assert_almost_equal(large_monty_prize.log_probability(
(False, True, 'B')), numpy.log(0.9))
assert_almost_equal(large_monty_prize.log_probability(
(False, False, 'A')), float("-inf"))
data = [[True, 'A', 'A', 'C', 1, True],
[True, 'A', 'A', 'C', 0, True],
[False, 'A', 'A', 'B', 1, False],
[False, 'A', 'A', 'A', 2, False],
[False, 'A', 'A', 'C', 1, False],
[False, 'B', 'B', 'B', 2, False],
[False, 'B', 'B', 'C', 0, False],
[True, 'C', 'C', 'A', 2, True],
[True, 'C', 'C', 'C', 1, False],
[True, 'C', 'C', 'C', 0, False],
[True, 'C', 'C', 'C', 2, True],
[True, 'C', 'B', 'A', 1, False]]
large_monty_network.fit(data)
assert_almost_equal(large_monty_prize.log_probability(
(True, True, 'C')), numpy.log(0.5))
assert_equal(large_monty_prize.log_probability(
(True, True, 'B')), float("-inf"))
a = large_monty_prize.log_probability((True, False, 'A'))
b = large_monty_prize.log_probability((True, False, 'B'))
c = large_monty_prize.log_probability((True, False, 'C'))
assert_almost_equal(a, b)
assert_almost_equal(b, c)
assert_equal(large_monty_prize.log_probability(
(False, False, 'C')), float("-inf"))
assert_almost_equal(large_monty_prize.log_probability(
(False, True, 'C')), numpy.log(2. / 3))
def test_float_from_string():
fv = sc.FloatType('2.01')
assert_almost_equal(fv, 2.01)
def test_titanic_network():
assert_almost_equal(passenger.log_probability('survive'), numpy.log(0.6))
assert_almost_equal(passenger.log_probability('survive'), numpy.log(0.6))
assert_almost_equal(gender.log_probability(('survive', 'male')), float("-inf"))
assert_almost_equal(gender.log_probability(('survive', 'female')), 0.0)
assert_almost_equal(gender.log_probability(('perish', 'male')), 0.0)
assert_almost_equal(gender.log_probability(('perish', 'female')), float("-inf"))
assert_almost_equal(tclass.log_probability(('survive', 'first')), float("-inf"))
assert_almost_equal(tclass.log_probability(('survive', 'second')), 0.0)
assert_almost_equal(tclass.log_probability(('survive', 'third')), float("-inf"))
assert_almost_equal(tclass.log_probability(('perish', 'first')), 0.0)
assert_almost_equal(tclass.log_probability(('perish', 'second')), float("-inf"))
assert_almost_equal(tclass.log_probability(('perish', 'third')), float("-inf"))
def test_metric_cosine():
feature = dipymetric.VectorBetweenEndpointsFeature()
class CosineMetric(dipymetric.Metric):
def __init__(self, feature):
super(CosineMetric, self).__init__(feature=feature)
def are_compatible(self, shape1, shape2):
# Cosine metric works on vectors.
return shape1 == shape2 and shape1[0] == 1
def dist(self, v1, v2):
# Check if we have null vectors
if norm(v1) == 0:
return 0. if norm(v2) == 0 else 1.
v1_normed = v1.astype(np.float64) / norm(v1.astype(np.float64))
v2_normed = v2.astype(np.float64) / norm(v2.astype(np.float64))
cos_theta = np.dot(v1_normed, v2_normed.T)
# Make sure it's in [-1, 1], i.e. within domain of arccosine
cos_theta = np.minimum(cos_theta, 1.)
cos_theta = np.maximum(cos_theta, -1.)
return np.arccos(cos_theta) / np.pi # Normalized cosine distance
for metric in [CosineMetric(feature), dipymetric.CosineMetric(feature)]:
# Test special cases of the cosine distance.
v0 = np.array([[0, 0, 0]], dtype=np.float32)
v1 = np.array([[1, 2, 3]], dtype=np.float32)
v2 = np.array([[1, -1. / 2, 0]], dtype=np.float32)
v3 = np.array([[-1, -2, -3]], dtype=np.float32)
assert_equal(metric.dist(v0, v0), 0.) # dot-dot
assert_equal(metric.dist(v0, v1), 1.) # dot-line
assert_equal(metric.dist(v1, v1), 0.) # collinear
assert_equal(metric.dist(v1, v2), 0.5) # orthogonal
assert_equal(metric.dist(v1, v3), 1.) # opposite
for s1, s2 in itertools.product(*[streamlines] *
2): # All possible pairs
# Extract features since metric doesn't work directly on streamlines
f1 = metric.feature.extract(s1)
f2 = metric.feature.extract(s2)
# Test method are_compatible
are_vectors = f1.shape[0] == 1 and f2.shape[0] == 1
same_dimension = f1.shape[1] == f2.shape[1]
assert_equal(metric.are_compatible(f1.shape, f2.shape), are_vectors
and same_dimension)
# Test method dist if features are compatible
if metric.are_compatible(f1.shape, f2.shape):
distance = metric.dist(f1, f2)
if np.all(f1 == f2):
assert_almost_equal(distance, 0.)
assert_almost_equal(distance, dipymetric.dist(metric, s1, s2))
assert_true(distance >= 0.)
assert_true(distance <= 1.)
# This metric type is not order invariant
assert_false(metric.is_order_invariant)
for s1, s2 in itertools.product(*[streamlines] *
2): # All possible pairs
f1 = metric.feature.extract(s1)
f2 = metric.feature.extract(s2)
if not metric.are_compatible(f1.shape, f2.shape):
continue
f1_flip = metric.feature.extract(s1[::-1])
f2_flip = metric.feature.extract(s2[::-1])
distance = metric.dist(f1, f2)
assert_almost_equal(metric.dist(f1_flip, f2_flip), distance)
if not np.all(f1_flip == f2_flip):
assert_false(metric.dist(f1, f2_flip) == distance)
assert_false(metric.dist(f1_flip, f2) == distance)
def test_chow_liu_structure_learning():
logps = -19.8282, -344.248785, -4842.40158, -603.2370
for X, logp in zip(datasets, logps):
model = BayesianNetwork.from_samples(X, algorithm='chow-liu')
assert_almost_equal(model.log_probability(X).sum(), logp, 4)
def test_large_monty_remaining():
model = large_monty_remaining
assert_almost_equal(model.log_probability(0), numpy.log(0.1))
assert_almost_equal(model.log_probability(1), numpy.log(0.7))
assert_almost_equal(model.log_probability(2), numpy.log(0.2))
data = [[True, 'A', 'A', 'C', 1, True],
[True, 'A', 'A', 'C', 0, True],
[False, 'A', 'A', 'B', 1, False],
[False, 'A', 'A', 'A', 2, False],
[False, 'A', 'A', 'C', 1, False],
[False, 'B', 'B', 'B', 2, False],
[False, 'B', 'B', 'C', 0, False],
[True, 'C', 'C', 'A', 2, True],
[True, 'C', 'C', 'C', 1, False],
[True, 'C', 'C', 'C', 0, False],
[True, 'C', 'C', 'C', 2, True],
[True, 'C', 'B', 'A', 1, False]]
large_monty_network.fit(data)
assert_almost_equal(model.log_probability(0), numpy.log(3. / 12))
assert_almost_equal(model.log_probability(1), numpy.log(5. / 12))
assert_almost_equal(model.log_probability(2), numpy.log(4. / 12))
def check_cp(transition, analysis, results):
# a little nested function to that does the actual check
for (i, ens) in enumerate(transition.ensembles):
cp_ens = analysis.crossing_probability(ens)
for x in results[i]:
assert_almost_equal(results[i][x], cp_ens(x))
def test_greedy_nan_structure_learning():
logps = -7.5239, -159.6505, -2058.5706, -203.7662
for X, logp in zip(datasets_nan, logps):
model = BayesianNetwork.from_samples(X, algorithm='greedy')
assert_almost_equal(model.log_probability(X).sum(), logp, 4)
def test_flux_matrix_pd_None(self):
series = flux_matrix_pd(self.fluxes, sort_method=None)
for idx in self.indices:
assert_almost_equal(series[idx], self.expected_series[idx])
def test_greedy_structure_learning():
logps = -19.8282, -345.9527, -4847.59688, -611.0356
for X, logp in zip(datasets, logps):
model = BayesianNetwork.from_samples(X, algorithm='greedy')
assert_almost_equal(model.log_probability(X).sum(), logp, 4)
def test_inventory_audit():
ev = get_sqlite_evaluator()
audit_resources = an.inventory_audit(ev,
agentids=[30])['ResourceId'].tolist()
ans_audit_resources = ev.eval('AgentStateInventories')['ResourceId']
assert_almost_equal(audit_resources, ans_audit_resources)
def test_rate_matrix_calculation(self):
mistis_analysis = self._make_tis_analysis(self.mistis)
mistis_rate = mistis_analysis.rate_matrix(steps=self.mistis_steps)
pairs = [(self.state_A, self.state_B), (self.state_B, self.state_A)]
for (vol_1, vol_2) in pairs:
assert_almost_equal(mistis_rate[(vol_1, vol_2)], 0.0125)
def assert_no_error(u, x, t, n):
u_e = exact_solution(x, t[n])
diff = abs(u - u_e).max()
nt.assert_almost_equal(diff, 0, places=13)
def test_with_minus_move_flux(self):
network = self.mstis
scheme = paths.DefaultScheme(network, engine=RandomMDEngine())
scheme.build_move_decision_tree()
# create the minus move steps
# `center` is the edge of the state/innermost interface
center = {self.state_A: 0.0, self.state_B: 1.0}
replica = {self.state_A: -1, self.state_B: -2}
minus_ensemble_to_mover = {m.minus_ensemble: m
for m in scheme.movers['minus']}
state_to_minus_ensemble = {ens.state_vol: ens
for ens in network.minus_ensembles}
minus_changes = []
# `delta` is the change on either side for in vs. out
for (state, delta) in [(self.state_A, 0.1), (self.state_B, -0.1)]:
minus_ens = state_to_minus_ensemble[state]
minus_mover = minus_ensemble_to_mover[minus_ens]
a_in = center[state] - delta
a_out = center[state] + delta
# note that these trajs are equivalent to minus move
# descriptions in TestMinusMoveFlux
seq_1 = [a_in] + [a_out]*2 + [a_in]*5 + [a_out]*5 + [a_in]
seq_2 = [a_in] + [a_out]*3 + [a_in]*3 + [a_out]*3 + [a_in]
for seq in [seq_1, seq_2]:
traj = make_1d_traj(seq)
assert_equal(minus_ens(traj), True)
samp = paths.Sample(trajectory=traj,
ensemble=minus_ens,
replica=replica[state])
sample_set = paths.SampleSet([samp])
change = paths.AcceptedSampleMoveChange(
samples=[samp],
mover=minus_mover,
details=paths.Details()
)
minus_changes.append(change)
active = self.mstis_steps[0].active
steps = []
cycle = -1
for m_change in minus_changes:
cycle += 1
active = active.apply_samples(m_change.samples)
step = paths.MCStep(mccycle=cycle,
active=active,
change=m_change)
steps.append(step)
for old_step in self.mstis_steps[1:]:
cycle += 1
active = active.apply_samples(old_step.change.samples)
step = paths.MCStep(mccycle=cycle,
active=active,
change=old_step.change)
steps.append(step)
analysis = StandardTISAnalysis(
network=self.mstis,
scheme=scheme,
max_lambda_calcs={t: {'bin_width': 0.1,
'bin_range': (-0.1, 1.1)}
for t in network.sampling_transitions},
steps=steps
)
# now we actually verify correctness
avg_t_in = (5.0 + 3.0) / 2
avg_t_out = (2.0 + 5.0 + 3.0 + 3.0) / 4
expected_flux = 1.0 / (avg_t_in + avg_t_out)
# NOTE: Apparently this approach screws up the TCP calculation. I
# think this is a problem in the fake data, not the simulation.
for flux in analysis.flux_matrix.values():
assert_almost_equal(flux, expected_flux)
def test_inequalities():
# Memorize the dataset.
hyperparameters = dict(
loss="custom:mse_with_inequalities",
peptide_amino_acid_encoding="one-hot",
activation="tanh",
layer_sizes=[16],
max_epochs=50,
minibatch_size=32,
random_negative_rate=0.0,
early_stopping=False,
validation_split=0.0,
locally_connected_layers=[
{
"filters": 8,
"activation": "tanh",
"kernel_size": 3
}
],
dense_layer_l1_regularization=0.0,
dropout_probability=0.0)
df = pandas.DataFrame()
df["peptide"] = random_peptides(1000, length=9)
# First half are binders
df["binder"] = df.index < len(df) / 2
df["value"] = df.binder.map({True: 100, False: 5000})
df.loc[:10, "value"] = 1.0 # some strong binders
df["inequality1"] = "="
df["inequality2"] = df.binder.map({True: "<", False: "="})
df["inequality3"] = df.binder.map({True: "=", False: ">"})
# "A" at start of peptide indicates strong binder
df["peptide"] = [
("C" if not row.binder else "A") + row.peptide[1:]
for _, row in df.iterrows()
]
fit_kwargs = {'verbose': 0}
# Prediction1 uses no inequalities (i.e. all are (=))
predictor = Class1NeuralNetwork(**hyperparameters)
predictor.fit(
df.peptide.values,
df.value.values,
inequalities=df.inequality1.values,
**fit_kwargs)
df["prediction1"] = predictor.predict(df.peptide.values)
# Prediction2 has a (<) inequality on binders and an (=) on non-binders
predictor = Class1NeuralNetwork(**hyperparameters)
predictor.fit(
df.peptide.values,
df.value.values,
inequalities=df.inequality2.values,
**fit_kwargs)
df["prediction2"] = predictor.predict(df.peptide.values)
# Prediction3 has a (=) inequality on binders and an (>) on non-binders
predictor = Class1NeuralNetwork(**hyperparameters)
predictor.fit(
df.peptide.values,
df.value.values,
inequalities=df.inequality3.values,
**fit_kwargs)
df["prediction3"] = predictor.predict(df.peptide.values)
df_binders = df.loc[df.binder]
df_nonbinders = df.loc[~df.binder]
print("***** Binders: *****")
print(df_binders.head(5))
print("***** Non-binders: *****")
print(df_nonbinders.head(5))
# Binders should always be given tighter predicted affinity than non-binders
assert_less(df_binders.prediction1.mean(), df_nonbinders.prediction1.mean())
assert_less(df_binders.prediction2.mean(), df_nonbinders.prediction2.mean())
assert_less(df_binders.prediction3.mean(), df_nonbinders.prediction3.mean())
# prediction2 binders should be tighter on average than prediction1
# binders, since prediction2 has a (<) inequality for binders.
# Non-binders should be about the same between prediction2 and prediction1
assert_less(df_binders.prediction2.mean(), df_binders.prediction1.mean())
assert_almost_equal(
df_nonbinders.prediction2.mean(),
df_nonbinders.prediction1.mean(),
delta=3000)
# prediction3 non-binders should be weaker on average than prediction2 (or 1)
# non-binders, since prediction3 has a (>) inequality for these peptides.
# Binders should be about the same.
assert_greater(
df_nonbinders.prediction3.mean(),
df_nonbinders.prediction2.mean())
assert_greater(
df_nonbinders.prediction3.mean(),
df_nonbinders.prediction1.mean())
assert_almost_equal(
df_binders.prediction3.mean(),
df_binders.prediction1.mean(),
delta=3000)
def test_shuffle_series():
"""
Test function to ensure Inference.shuffle_series() reorders data within columns.
If parameter 'only' is specified, only that column should be shuffled; otherwise
all columns must be shufffled.
"""
DF = coupled_random_walks( S1 = 100, S2 = 100, T = 10,
N = 200, mu1 = 0.1, mu2 = 0.02,
sigma1 = 0.01, sigma2 = 0.01,
alpha = 0.1, epsilon=0, lag = 2)
### Shuffling both time series S1 & S2
DF_shuffled = shuffle_series(DF)
# Ensure rows are shuffled but not lost
assert_almost_equal(np.mean(DF['S1']), np.mean(DF_shuffled['S1']))
assert_almost_equal(np.mean(DF['S2']), np.mean(DF_shuffled['S2']))
# Ensure rows are shuffled independently
assert not np.sum(DF['S1'].head(20)) == np.sum(DF_shuffled['S1'].head(20))
assert not DF.head(10).equals(DF_shuffled.head(10))
### Shuffling only time series S1
S1_shuffled = shuffle_series(DF, only=['S1'])
# Ensure rows are shuffled but not lost
assert_almost_equal(np.mean(DF['S1']), np.mean(S1_shuffled['S1']))
assert_almost_equal(np.mean(DF['S2']), np.mean(S1_shuffled['S2']))
# Ensure only S1 has been shuffled
assert DF['S2'].head(10).equals(S1_shuffled['S2'].head(10))
assert not DF['S1'].head(10).equals(S1_shuffled['S1'].head(10))
### Shuffling only time series S1
S2_shuffled = shuffle_series(DF, only=['S2'])
# Ensure rows are shuffled but not lost
assert_almost_equal(np.mean(DF['S1']), np.mean(S1_shuffled['S1']))
assert_almost_equal(np.mean(DF['S2']), np.mean(S1_shuffled['S2']))
# Ensure only S2 has been shuffled
assert DF['S1'].head(10).equals(S2_shuffled['S1'].head(10))
assert not DF['S2'].head(10).equals(S2_shuffled['S2'].head(10))
def the_local_topic_distribution_is(step, distribution):
distribution = json.loads(distribution)
for index, topic_dist in enumerate(world.local_topic_distribution):
assert_almost_equal(topic_dist["probability"],
distribution[index],
places=5)
def test_separable(c=np.pi):
"""
Verify the solver with a separable exact solution
u_e = X(x)Y(y)T(t)
where
X = Ax^3 - (3/2)*A*Lx*x**2
Y = By^3 - (3/2)*B*Ly*y**2
T = D*t
Uses a constant wave velocity q, and no damping, b = 0.
"""
import nose.tools as nt
class CubicSolution(WaveProblem):
def __init__(self, A, B, D, dx, dy, Lx, Ly, q_const=2.0):
self.A, self.B, self.D = A, B, D
self.dx, self.dy = dx, dy
self.Lx, self.Ly = Lx, Ly
self.q_const = q_const
self.b = 0
def X(self, x):
A, Lx = self.A, self.Lx
return A * x**3 - 1.5 * A * Lx * x**2
def Y(self, y):
B, Ly = self.B, self.Ly
return B * y**3 - 1.5 * B * Ly * y**2
def T(self, t):
D = self.D
return D * t
def u_e(self, x, y, t):
X, Y, T = self.X, self.Y, self.T
return X(x) * Y(y) * T(t)
def V(self, x, y):
X, Y = self.X, self.Y
return D * X(x) * Y(y)
def I(self, x, y):
return self.u_e(x, y, 0)
def f(self, x, y, t):
A, B, D = self.A, self.B, self.D
X, Y, T = self.X, self.Y, self.T
Lx, Ly = self.Lx, self.Ly
dx, dy = self.dx, self.dy
q = self.q_const
# Vector evaluated
if isinstance(x, np.ndarray) and isinstance(y, np.ndarray):
# All mesh points
fx = A * (6 * x[:, np.newaxis] - 3 * Lx) * Y(y[np.newaxis, :])
fy = B * (6 * y[np.newaxis, :] - 3 * Ly) * X(x[:, np.newaxis])
f = -q * (fx + fy) * T(t)
# Add extra contributions at boundaries
f[0, :] -= 2 * A * dx * q * Y(y[:]) * T(t)
f[-1, :] += 2 * A * dx * q * Y(y[:]) * T(t)
f[:, 0] -= 2 * B * dy * q * X(x[:]) * T(t)
f[:, -1] += 2 * B * dy * q * X(x[:]) * T(t)
# print "time ", t
# print f
# Pointwise evaluated
else:
fx = A * (6 * x - 3 * Lx) * Y(y)
fy = B * (6 * y - 3 * Ly) * X(x)
f = -q * (fx + fy) * T(t)
# Add extra contributions at boundaries
tol = 1e-14
if abs(x) < tol:
f -= 2 * A * dx * q * Y(y) * T(t)
if abs(x - Lx) < tol:
f += 2 * A * dx * q * Y(y) * T(t)
if abs(y) < tol:
f -= 2 * B * dy * q * X(x) * T(t)
if abs(y - Ly) < tol:
f += 2 * B * dy * q * X(x) * T(t)
return f
Lx = 0.3
Ly = 0.3
Nx = 3
Ny = 3
dx = Lx / float(Nx)
dy = Ly / float(Ny)
dt = 0.01
T = 10
q = 1.2
b = 0.0
A = 2.
B = 2.
D = 1.
problem = CubicSolution(A, B, D, dx, dy, Lx, Ly, q_const=q)
print "Verifying solver for a separable solution."
for v in ["scalar", "vectorized"]:
solver = WaveSolver(problem, Lx, Ly, Nx, Ny, dt, T, version=v)
x, y = solver.get_mesh()
u = solver.get_solution()
while solver.n < solver.Nt:
solver.advance()
t = solver.t[solver.n]
u_e = problem.u_e(x[:, np.newaxis], y[np.newaxis, :], t)
u = solver.get_solution()
diff = abs(u - u_e).max()
print "%10s: abs(u-u_e).max() = %e" % (v, diff)
nt.assert_almost_equal(diff, 0, places=12)
