def test_triplicate_name(self):
tied = prior.Uniform(-5, 5, name='dummy')
sphere = Sphere(n=prior.Uniform(1, 2, name='dummy'),
r=prior.Uniform(1, 2, name='dummy'),
center=[tied, tied, prior.Uniform(0, 10, name='z')])
model = AlphaModel(sphere)
expected = ['dummy', 'dummy_0', 'dummy_1', 'z']
self.assertEqual(model._parameter_names, expected)
def test_add_tie_updates_parameter_names(self):
tied = prior.Uniform(-5, 5)
sphere = Sphere(n=prior.Uniform(1, 2), r=prior.Uniform(1, 2),
center=[tied, tied, 10])
model = AlphaModel(sphere)
model.add_tie(['r', 'n'])
expected = ['n', 'center.0']
self.assertEqual(model._parameter_names, expected)
def test_subset_tempering():
holo = normalize(get_example_data('image0001'))
scat = Sphere(r=0.65e-6,n=1.58,center=[5.5e-6,5.8e-6,14e-6])
mod = AlphaModel(scat,noise_sd=.1, alpha=prior.Gaussian(0.7,0.1))
with warnings.catch_warnings():
warnings.simplefilter('ignore')
inf = sample.tempered_sample(mod, holo, nwalkers=4, samples=10, stages=1, stage_len=10, threads=None, seed=40)
assert_obj_close(inf.MAP,gold_alpha, rtol=1e-3)
def test_BaseModel_lnprior(self):
scat = Sphere(r=prior.Gaussian(1, 1),
n=prior.Gaussian(1, 1),
center=[10, 10, 10])
mod = Model(scat, noise_sd=0.1)
# Desired: log(sqrt(0.5/pi))-1/2
desired_sigma = -1.4189385332
assert_obj_close(mod.lnprior([0, 0]), desired_sigma * 2)
def test_parameters_checks_ties(self):
spheres = [Sphere(n=Uniform(0, 1), r=Uniform(0, 1)) for i in range(3)]
ties = {'r': ['0:r', '1:r', '2:r'], 'n': ['0:n', '1:n', '2:n']}
spheres = Spheres(spheres, ties=ties)
spheres.ties['n'].append('dummy_name')
msg = 'Tied parameter dummy_name not present in raw parameters'
with self.assertRaisesRegex(ValueError, msg):
spheres.parameters
def test_parameters_map(self):
tied = prior.Uniform(0, 1)
scatterer = Sphere(n=tied, r=prior.Uniform(0.5, 1.5),
center=[tied, 10, prior.Uniform(0, 10)])
model = AlphaModel(scatterer)
expected = [dict, [[['n', '_parameter_0'], ['r', '_parameter_1'],
['center', ['_parameter_0', 10, '_parameter_2']]]]]
self.assertEqual(model._maps['scatterer'], expected)
def test_from_parameters_keeps_attributes(self):
spheres = [
Sphere(n=np.random.rand(), r=0.1, center=[i, i, i])
for i in range(3)
]
spheres = Spheres(spheres, warn="TEST")
spheres = spheres.from_parameters(spheres.parameters)
self.assertEqual(spheres.warn, "TEST")
def test_parameterize_scatterer_spheres(self):
sphere = Sphere(r=0.5, n=1, center=[0, 0, 0])
model = make_default_model(Spheres([sphere, sphere], warn=False))
expected = {
'0:n', '1:n', '0:r', '1:r', 'alpha', '0:x', '0:y', '0:z', '1:x',
'1:y', '1:z'
}
self.assertEqual(set(model.parameters.keys()), expected)
def test_add_tie_specify_name(self):
tied = prior.Uniform(-5, 5)
sphere = Sphere(n=prior.Uniform(1, 2), r=prior.Uniform(1, 2),
center=[tied, tied, 10])
model = AlphaModel(sphere)
model.add_tie(['r', 'n'], new_name='dummy')
expected = ['dummy', 'center.0']
self.assertEqual(model._parameter_names, expected)
def make_scatterer(self, params):
center = self._make_center_priors(params)
index = prior.Uniform(
self._min_index, self._max_index, guess=params['n'])
radius = prior.Uniform(
self._min_radius, self._max_radius, guess=params['r'])
scatterer = Sphere(n=index, r=radius, center=center)
return scatterer
def test_add_tie_updates_map(self):
tied = prior.Uniform(-5, 5)
sphere = Sphere(n=prior.Uniform(1, 2), r=prior.Uniform(1, 2),
center=[tied, tied, 10])
model = AlphaModel(sphere)
model.add_tie(['r', 'n'])
expected = [dict, [[['n', '_parameter_0'], ['r', '_parameter_0'],
['center', ['_parameter_1', '_parameter_1', 10]]]]]
self.assertEqual(model._maps['scatterer'], expected)
def test_parameters_list(self):
tied = prior.Uniform(0, 1)
scatterer = Sphere(n=tied, r=prior.Uniform(0.5, 1.5),
center=[tied, 10, prior.Uniform(0, 10)])
model = AlphaModel(scatterer)
expected = [prior.Uniform(0, 1),
prior.Uniform(0.5, 1.5),
prior.Uniform(0, 10)]
self.assertEqual(model._parameters, expected)
def test_yaml_preserves_parameter_ties(self):
tied = prior.Uniform(0, 1)
sphere = Sphere(n=tied, r=prior.Uniform(0.6, 1, name='radius'),
center=[prior.Uniform(0.6, 1), tied, 10])
alpha = {'r': 0.6, 'g': prior.Uniform(0.8, 0.9)}
model = AlphaModel(sphere, alpha=alpha)
model.add_tie(['radius', 'center.0'])
post_model = take_yaml_round_trip(model)
self.assertEqual(model.parameters, post_model.parameters)
def test_yaml_preserves_parameter_names(self):
n = prior.ComplexPrior(prior.Uniform(1, 2), prior.Uniform(0, 0.1))
sphere = Sphere(n=n, r=prior.Uniform(0, 1.5, name='radius'),
center=[1, 1, prior.Uniform(10, 20)])
alpha = {'r': 0.6, 'g': prior.Uniform(0.6, 1.0)}
model = AlphaModel(sphere, alpha=alpha)
pre_names = model._parameter_names
post_names = take_yaml_round_trip(model)._parameter_names
self.assertEqual(pre_names, post_names)
def test_optics_from_schema(self):
model = AlphaModel(Sphere(), medium_index=prior.Uniform(1, 2))
schema = detector_grid(2, 2)
schema.attrs['illum_wavelen'] = 0.6
schema.attrs['illum_polarization'] = [1, 0]
found_optics = model._find_optics([1.5], schema)
expected = {'medium_index': 1.5, 'illum_wavelen': 0.6,
'illum_polarization': [1, 0]}
self.assertEqual(found_optics, expected)
def test_add_tie(self):
spheres = [Sphere(n=Uniform(0, 1), r=Uniform(0, 1)) for i in range(3)]
spheres = Spheres(spheres)
spheres.add_tie('0:r', '1:r')
spheres.add_tie('r', '2:r')
spheres.add_tie('0:n', '1:n')
spheres.add_tie('0:n', '2:n')
expected_keys = {'n', 'r'}
self.assertEqual(set(spheres.parameters.keys()), expected_keys)
def test_model_optics_take_precedence(self):
model = AlphaModel(Sphere(), medium_index=1.5, illum_wavelen=0.8)
schema = detector_grid(2, 2)
schema.attrs['illum_wavelen'] = 0.6
schema.attrs['illum_polarization'] = [1, 0]
found_optics = model._find_optics([], schema)
expected = {'medium_index': 1.5, 'illum_wavelen': 0.8,
'illum_polarization': [1, 0]}
self.assertEqual(found_optics, expected)
def test_optimization_with_maxiter_of_2():
gold_fit_dict = {
'0:r': 0.52480509800531849,
'1:center.1': 14.003687569304704,
'alpha': 0.93045027963762217,
'0:center.2': 19.93177549652841,
'1:r': 0.56292664494653732,
'0:center.1': 15.000340621607815,
'1:center.0': 14.020984607646726,
'0:center.0': 15.000222185576494,
'1:center.2': 20.115613202192328
}
#calculate a hologram with known particle positions to do a fit against
schema = detector_grid(shape=100, spacing=.1)
s1 = Sphere(center=(15, 15, 20), n=1.59, r=0.5)
s2 = Sphere(center=(14, 14, 20), n=1.59, r=0.5)
cluster = Spheres([s1, s2])
holo = calc_holo(schema, cluster, 1.33, .66, illum_polarization=(1, 0))
#trying to do a fast fit:
guess1 = Sphere(center=(prior.Uniform(5, 25, guess=15),
prior.Uniform(5, 25, 15), prior.Uniform(5, 25,
20)),
r=(prior.Uniform(.4, .6, guess=.45)),
n=1.59)
guess2 = Sphere(center=(prior.Uniform(5, 25, guess=14),
prior.Uniform(5, 25, 14), prior.Uniform(5, 25,
20)),
r=(prior.Uniform(.4, .6, guess=.45)),
n=1.59)
par_s = Spheres([guess1, guess2])
model = AlphaModel(par_s,
medium_index=1.33,
illum_wavelen=.66,
illum_polarization=(1, 0),
alpha=prior.Uniform(.1, 1, .6))
optimizer = Nmpfit(maxiter=2)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
result = optimizer.fit(model, holo)
assert_obj_close(gold_fit_dict, result.parameters, rtol=1e-5)
def test_raw_scat_matrs_same_as_mie(self):
theory_mie = Mie()
theory_tmat = Tmatrix()
pos = np.array([10, 0, 0])[:,None]
s = Sphere(n=1.59, r=0.9, center=(2, 2, 80))
s_mie = theory_mie._raw_scat_matrs(s, pos, 2*np.pi/.660, 1.33)
s_tmat = theory_tmat._raw_scat_matrs(s, pos, 2*np.pi/.660, 1.33)
self.assertTrue(np.allclose(s_mie, s_tmat))
def test_calc_holo_with_twocolor_alpha(self):
detector = detector_grid(
5, 1, extra_dims={'illumination': ['red', 'green']})
scatterer = Sphere(
r=0.5, n={'red': 1.5, 'green': 1.6}, center=(2, 2, 2))
alpha = {'red': 0.8, 'green': 0.9}
result = calc_holo(
detector, scatterer, scaling=alpha, illum_polarization=(0, 1),
illum_wavelen={'red': 0.66, 'green': 0.52}, medium_index=1.33)
assert result is not None
def test_save_and_open(self):
n = Uniform(0, 1)
r = Uniform(0, np.pi / 2)
spheres = [Sphere(n=n, r=r, center=[i, i, i]) for i in range(3)]
spheres = Spheres(spheres)
expected_keys = spheres.parameters.keys()
with tempfile.TemporaryDirectory() as tempdir:
hp.save(tempdir + '/test.out', spheres)
spheres = hp.load(tempdir + '/test.out')
self.assertEqual(spheres.parameters.keys(), expected_keys)
def test_ties(self):
n = Uniform(0, 1)
r = Uniform(0, 1)
spheres = [Sphere(n=n, r=r, center=[i, i, i]) for i in range(3)]
spheres = Spheres(spheres)
expected_ties = {
'n': ['0:n', '1:n', '2:n'],
'r': ['0:r', '1:r', '2:r']
}
self.assertEqual(spheres.ties, expected_ties)
def test_layered():
s = Sphere(n=(1, 2), r=(1, 2), center=(2, 2, 2))
sch = detector_grid((10, 10), .2)
hs = calc_holo(sch, s, 1, .66, (1, 0))
guess = LayeredSphere((1, 2), (Uniform(1, 1.01), Uniform(.99, 1)),
(2, 2, 2))
model = ExactModel(guess, calc_holo)
res = NmpfitStrategy().fit(model, hs)
assert_allclose(res.scatterer.t, (1, 1), rtol=1e-12)
def test_propagate_e_field():
e = calc_field(detector_grid(100, 0.1),
Sphere(1.59, .5, (5, 5, 5)),
illum_wavelen=0.66,
medium_index=1.33,
illum_polarization=(1, 0),
theory=Mie(False))
prop_e = propagate(e, 10)
verify(prop_e, 'propagate_e_field')
def test_equal_not_identical_do_not_tie(self):
scatterer = Sphere(n=prior.Uniform(1, 2), r=prior.Uniform(1, 2),
center=[10, 10, prior.Uniform(1, 2)])
model = AlphaModel(scatterer)
expected_priors = [prior.Uniform(1, 2),
prior.Uniform(1, 2),
prior.Uniform(1, 2)]
expected_names = ['n', 'r', 'center.2']
self.assertEqual(model._parameters, expected_priors)
self.assertEqual(model._parameter_names, expected_names)
def test_transformed_priors_are_tied(self):
base_prior = prior.Uniform(0, 2, name='x')
transformed = prior.TransformedPrior(np.sqrt, base_prior, name='y')
scatterer = Sphere(n=1.5, r=0.5, center=[base_prior, transformed,
prior.Uniform(5, 10)])
model = AlphaModel(scatterer)
expected_priors = [base_prior, prior.Uniform(5, 10)]
expected_names = ['x', 'center.2']
self.assertEqual(model._parameters, expected_priors)
self.assertEqual(model._parameter_names, expected_names)
def test_raw_fields_similar_to_mie(self):
theory_mie = Mie(False, False)
theory_tmat = Tmatrix()
pos = np.array([10, 0, 0])[:,None]
s = Sphere(n=1.59, r=0.9, center=(2, 2, 80))
pol = pd.Series([1, 0])
fields_mie = theory_mie._raw_fields(pos, s, 2*np.pi/.660, 1.33, pol)
fields_tmat = theory_tmat._raw_fields(pos, s, 2*np.pi/.660, 1.33, pol)
self.assertTrue(np.allclose(fields_mie, fields_tmat))
def residfunct(p, fjac=None):
# nmpfit calls residfunct w/fjac as a kwarg, we ignore
sphere = Sphere(n=p[0] + n_particle_imag * 1j, r=p[1], center=p[2:5])
thry = Mie(False)
calculated = calc_holo(holo, sphere, scaling=p[5], theory=thry)
status = 0
derivates = holo - calculated
return ([status, get_values(flat(derivates))])
def test_alpha_subset_tempering(self):
holo = normalize(get_example_data('image0001'))
scat = Sphere(r=0.65e-6, n=1.58, center=[5.5e-6, 5.8e-6, 14e-6])
mod = AlphaModel(scat, noise_sd=.1, alpha=prior.Gaussian(0.7, 0.1))
strat = TemperedStrategy(nwalkers=4, nsamples=10, stages=1,
stage_len=10, parallel=None, seed=40)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
inference_result = strat.sample(mod, holo)
desired_alpha = np.array([0.650348])
assert_allclose(inference_result._parameters, desired_alpha, rtol=5e-3)
def test_tied_parameter_naming(self):
n = Uniform(0, 1)
r = [Uniform(0, 1), Uniform(0, 1)]
spheres = [Sphere(n=n, r=r[i % 2]) for i in range(4)]
spheres = Spheres(spheres)
expected_ties = {
'n': ['0:n', '1:n', '2:n', '3:n'],
'r': ['0:r', '2:r'],
'1:r': ['1:r', '3:r']
}
self.assertEqual(spheres.ties, expected_ties)
