def test_constraint_global_noisy(self):
hard_radius = 1.
constraints = dimer_global(1, self.im.ndim)
self.im.clear()
self.im.draw_clusters(10, 2, hard_radius, 2*self.separation,
2*self.diameter)
f0 = self.im.f(noise=self.pos_err)
f0['signal'] = 180
f0['size'] = 6.
result = refine_leastsq(f0, self.im.noisy_image(0.2*self.signal),
self.diameter, self.separation,
constraints=constraints,
param_mode=dict(signal='global',
size='global'),
options=dict(maxiter=1000))
dists = []
for _, f_cl in result.groupby('cluster'):
pos = result[['y', 'x']].values
dists.append(np.sqrt(np.sum(((pos[0] - pos[1])/np.array(self.im.size))**2)))
assert_allclose(dists, 2*hard_radius, atol=0.1)
assert_coordinates_close(result[self.im.pos_columns].values,
self.im.coords, 0.1)
assert_allclose(result['signal'].values, 200, atol=2)
assert_allclose(result['size'].values, 5.25, atol=1)
def test_constraint_global_noisy(self):
hard_radius = 1.
constraints = dimer_global(1, self.im.ndim)
self.im.clear()
self.im.draw_clusters(10, 2, hard_radius, 2 * self.separation,
2 * self.diameter)
f0 = self.im.f(noise=self.pos_err)
f0['signal'] = 180
f0['size'] = 6.
result = refine_leastsq(f0,
self.im.noisy_image(0.2 * self.signal),
self.diameter,
self.separation,
constraints=constraints,
param_mode=dict(signal='global',
size='global'),
options=dict(maxiter=1000))
dists = []
for _, f_cl in result.groupby('cluster'):
pos = result[['y', 'x']].values
dists.append(
np.sqrt(np.sum(
((pos[0] - pos[1]) / np.array(self.im.size))**2)))
assert_allclose(dists, 2 * hard_radius, atol=0.1)
assert_coordinates_close(result[self.im.pos_columns].values,
self.im.coords, 0.1)
assert_allclose(result['signal'].values, 200, atol=2)
assert_allclose(result['size'].values, 5.25, atol=1)
def test_constraint_global_dimer(self):
hard_radius = 1.
constraints = dimer_global(1, self.im.ndim)
self.im.clear()
self.im.draw_clusters(10, 2, hard_radius, 2 * self.separation,
2 * self.diameter)
f0 = self.im.f(noise=self.pos_err)
result = refine_leastsq(f0,
self.im(),
self.diameter,
self.separation,
constraints=constraints,
options=dict(maxiter=1000))
dists = []
for _, f_cl in result.groupby('cluster'):
pos = result[['y', 'x']].values
dists.append(
np.sqrt(np.sum(
((pos[0] - pos[1]) / np.array(self.im.size))**2)))
assert_allclose(dists, 2 * hard_radius, atol=0.01)
assert_coordinates_close(result[self.im.pos_columns].values,
self.im.coords, 0.1)
def refine_cluster(self, cluster_size, hard_radius, pos_diff=None,
signal_dev=None, size_dev=None, noise=None,
param_mode=None, angle=None, **kwargs):
"""
Parameters
----------
noise : integer
noise level
pos_diff :
pixels deviation of p0 from true feature location
signal_dev :
deviation of feature signal with respect to p0
size_dev :
deviation of feature size with respect to p0
"""
if param_mode is None:
param_mode = self.param_mode
else:
param_mode = dict(self.param_mode, **param_mode)
if pos_diff is None:
pos_diff = self.pos_diff
if signal_dev is None:
signal_dev = self.signal_dev
if size_dev is None:
size_dev = self.size_dev
if noise is None:
noise = self.noise
# generate image with array of features and deviating signal and size
image, expected, clusters = self.get_image_clusters(cluster_size,
hard_radius,
noise, signal_dev,
size_dev, angle)
expected_pos, expected_signal, expected_size = expected
expected_center, expected_angle = clusters
p0_pos = self.gen_p0_coords(expected_pos, pos_diff)
f0 = self.to_dataframe(p0_pos, self.signal, self.size, cluster_size)
# Set an estimate for the background value. Helps convergence,
# especially for 3D tests with high noise (tested here: S/N = 3)
f0['background'] = noise / 2
actual = refine_leastsq(f0, image, self.diameter, separation=None,
param_mode=dict(self.param_mode, **param_mode),
param_val=self.param_val,
pos_columns=self.pos_columns,
t_column='frame',
fit_function=self.fit_func,
bounds=self.bounds, **kwargs)
assert not np.any(np.isnan(actual['cost']))
assert np.all(actual['cluster_size'] <= cluster_size)
actual = self.from_dataframe(actual)
actual_pos, actual_signal, actual_size, pos_err = actual
deviations = self.get_deviations(actual_pos, expected_pos, cluster_size,
expected_center, expected_angle)
return self.compute_deviations_cluster(actual, expected, deviations)
def refine(self,
pos_diff=None,
signal_dev=None,
size_dev=None,
noise=None,
param_mode=None,
**kwargs):
"""
Parameters
----------
noise : integer
noise level
pos_diff :
pixels deviation of p0 from true feature location
signal_dev :
deviation of feature signal with respect to p0
size_dev :
deviation of feature size with respect to p0
"""
if param_mode is None:
param_mode = self.param_mode
else:
param_mode = dict(self.param_mode, **param_mode)
if pos_diff is None:
pos_diff = self.pos_diff
if signal_dev is None:
signal_dev = self.signal_dev
if size_dev is None:
size_dev = self.size_dev
if noise is None:
noise = self.noise
# generate image with array of features and deviating signal and size
image, expected = self.get_image(noise, signal_dev, size_dev)
expected_pos, expected_signal, expected_size = expected
p0_pos = self.gen_p0_coords(expected_pos, pos_diff)
f0 = self.to_dataframe(p0_pos, self.signal, self.size)
# Set an estimate for the background value. Helps convergence,
# especially for 3D tests with high noise (tested here: S/N = 3)
f0['background'] = noise / 2
actual = refine_leastsq(f0,
image,
self.diameter,
separation=None,
param_mode=dict(self.param_mode, **param_mode),
param_val=self.param_val,
pos_columns=self.pos_columns,
t_column='frame',
fit_function=self.fit_func,
bounds=self.bounds,
**kwargs)
assert not np.any(np.isnan(actual['cost']))
actual = self.from_dataframe(actual)
return self.compute_deviations(actual, expected)
def test_multiple_overlapping(self):
self.im.clear()
self.im.draw_features(100, 15, self.diameter)
f0 = self.im.f(noise=self.pos_err)
result = refine_leastsq(f0, self.im(), self.diameter, self.separation)
assert_coordinates_close(result[self.im.pos_columns].values,
self.im.coords, 0.1)
def test_multiple_overlapping(self):
self.im.clear()
self.im.draw_features(100, 15, self.diameter)
f0 = self.im.f(noise=self.pos_err)
result = refine_leastsq(f0, self.im(), self.diameter, self.separation)
assert_coordinates_close(result[self.im.pos_columns].values,
self.im.coords, 0.1)
def test_var_global(self):
self.im.clear()
self.im.draw_features(100, 15, self.diameter)
f0 = self.im.f(noise=self.pos_err)
f0['signal'] = 180
result = refine_leastsq(f0, self.im(), self.diameter, self.separation,
param_mode=dict(signal='global'),
options=dict(maxiter=10000))
assert_coordinates_close(result[self.im.pos_columns].values,
self.im.coords, 0.1)
assert (result['signal'].values[1:] == result['signal'].values[:-1]).all()
assert_allclose(result['signal'].values, 200, atol=5)
def test_var_global(self):
self.im.clear()
self.im.draw_features(100, 15, self.diameter)
f0 = self.im.f(noise=self.pos_err)
f0['signal'] = 180
result = refine_leastsq(f0, self.im(), self.diameter, self.separation,
param_mode=dict(signal='global'),
options=dict(maxiter=10000))
assert_coordinates_close(result[self.im.pos_columns].values,
self.im.coords, 0.1)
assert (result['signal'].values[1:] == result['signal'].values[:-1]).all()
assert_allclose(result['signal'].values, 200, atol=5)
def test_constraint_global_dimer(self):
hard_radius = 1.
constraints = dimer_global(1, self.im.ndim)
self.im.clear()
self.im.draw_clusters(10, 2, hard_radius, 2*self.separation,
2*self.diameter)
f0 = self.im.f(noise=self.pos_err)
result = refine_leastsq(f0, self.im(), self.diameter,
self.separation, constraints=constraints,
options=dict(maxiter=1000))
dists = []
for _, f_cl in result.groupby('cluster'):
pos = result[['y', 'x']].values
dists.append(np.sqrt(np.sum(((pos[0] - pos[1])/np.array(self.im.size))**2)))
assert_allclose(dists, 2*hard_radius, atol=0.01)
assert_coordinates_close(result[self.im.pos_columns].values,
self.im.coords, 0.1)