def test_whole_pixel_shifts(self):
self.check_skip()
L = 21
dims = (L, L + 2) # avoid square images in tests
pos = [7, 13]
expected = np.array([pos])
image = np.ones(dims, dtype='uint8')
draw_feature(image, pos, 3.75)
guess = np.array([[6, 13]])
actual = refine_com(image, image, 6, guess,characterize=False,
engine=self.engine)[:, :2][:, ::-1]
assert_allclose(actual, expected, atol=0.1)
guess = np.array([[7, 12]])
actual = refine_com(image, image, 6, guess, characterize=False,
engine=self.engine)[:, :2][:, ::-1]
assert_allclose(actual, expected, atol=0.1)
guess = np.array([[7, 14]])
actual = refine_com(image, image, 6, guess, characterize=False,
engine=self.engine)[:, :2][:, ::-1]
assert_allclose(actual, expected, atol=0.1)
guess = np.array([[6, 12]])
actual = refine_com(image, image, 6, guess, characterize=False,
engine=self.engine)[:, :2][:, ::-1]
assert_allclose(actual, expected, atol=0.1)
def refine_com(self, pos_diff=None, signal_dev=None, size_dev=None,
noise=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 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)
actual = refine_com(image, image, self.radius, p0_pos, **kwargs)
actual = self.from_tp_ndarray(actual)
return self.compute_deviations(actual, expected)
def refine_com(self,
pos_diff=None,
signal_dev=None,
size_dev=None,
noise=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 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)
actual = refine_com(image, image, self.radius, p0_pos, **kwargs)
actual = self.from_dataframe(actual)
return self.compute_deviations(actual, expected)
def refine_cluster_com(self,
cluster_size,
hard_radius,
pos_diff=None,
signal_dev=None,
size_dev=None,
noise=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 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)
actual = refine_com(image, image, self.radius, p0_pos, **kwargs)
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_cluster_com(self, cluster_size, hard_radius, pos_diff=None,
signal_dev=None, size_dev=None, noise=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 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)
actual = refine_com(image, image, self.radius, p0_pos, **kwargs)
actual = self.from_tp_ndarray(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)