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, 15)
guess = np.array([[6, 13]])
actual = tp.feature.refine(image, image, 6, guess, characterize=False,
engine=self.engine)[:, :2][:, ::-1]
assert_allclose(actual, expected, atol=0.1)
guess = np.array([[7, 12]])
actual = tp.feature.refine(image, image, 6, guess, characterize=False,
engine=self.engine)[:, :2][:, ::-1]
assert_allclose(actual, expected, atol=0.1)
guess = np.array([[7, 14]])
actual = tp.feature.refine(image, image, 6, guess, characterize=False,
engine=self.engine)[:, :2][:, ::-1]
assert_allclose(actual, expected, atol=0.1)
guess = np.array([[6, 12]])
actual = tp.feature.refine(image, image, 6, guess, characterize=False,
engine=self.engine)[:, :2][:, ::-1]
assert_allclose(actual, expected, atol=0.1)
def test_separation_fast(self):
separation = 20
for angle in np.arange(0, 360, 15):
im = np.zeros((128, 128), dtype=np.uint8)
pos = [[64, 64], [64 + separation * np.sin(angle/180*np.pi),
64 + separation * np.cos(angle/180*np.pi)]]
# setup features: features with equal signal will always be
# detected by a grey dilation, so make them unequal
draw_feature(im, pos[0], 3, 240)
draw_feature(im, pos[1], 3, 250)
# find both of them
f = grey_dilation(im, separation - 1, precise=False)
assert_coordinates_close(f, pos, atol=1)
# find only the brightest
if angle in [45, 135, 225, 315]:
# for unprecise, a too small square kernel is used, which is
# perfect for 45-degree angles
f = grey_dilation(im, separation + 1, precise=False)
assert_coordinates_close(f, pos[1:], atol=1)
else:
# but too small by a factor of sqrt(ndim) for 90-degree angles
f = grey_dilation(im, separation*np.sqrt(2) + 1, precise=False)
assert_coordinates_close(f, pos[1:], atol=1)
def test_separation_fast(self):
separation = 20
for angle in np.arange(0, 360, 15):
im = np.zeros((128, 128), dtype=np.uint8)
pos = [[64, 64],
[
64 + separation * np.sin(angle / 180 * np.pi),
64 + separation * np.cos(angle / 180 * np.pi)
]]
# setup features: features with equal signal will always be
# detected by a grey dilation, so make them unequal
draw_feature(im, pos[0], 3, 240)
draw_feature(im, pos[1], 3, 250)
# find both of them
f = grey_dilation(im, separation - 1, precise=False)
assert_coordinates_close(f, pos, atol=1)
# find only the brightest
if angle in [45, 135, 225, 315]:
# for unprecise, a too small square kernel is used, which is
# perfect for 45-degree angles
f = grey_dilation(im, separation + 1, precise=False)
assert_coordinates_close(f, pos[1:], atol=1)
else:
# but too small by a factor of sqrt(ndim) for 90-degree angles
f = grey_dilation(im,
separation * np.sqrt(2) + 1,
precise=False)
assert_coordinates_close(f, pos[1:], atol=1)
def test_reject_peaks_near_edge(self):
"""Check whether local maxima near the edge of the image
are properly rejected, so as not to cause crashes later."""
N = 30
diameter = 9
y = np.arange(20, 10*N + 1, 20)
x = np.linspace(diameter / 2. - 2, diameter * 1.5, len(y))
cols = ['y', 'x']
expected = DataFrame(np.vstack([y, x]).T, columns=cols)
dims = (y.max() - y.min() + 5*diameter, int(4 * diameter) - 2)
image = np.ones(dims, dtype='uint8')
for ypos, xpos in expected[['y', 'x']].values:
draw_feature(image, [ypos, xpos], 27, max_value=100)
def locate(image, **kwargs):
return tp.locate(image, diameter, 1, preprocess=False,
engine=self.engine, **kwargs)[cols]
# All we care about is that this doesn't crash
actual = locate(image)
assert len(actual)
# Check the other sides
actual = locate(np.fliplr(image))
assert len(actual)
actual = locate(image.transpose())
assert len(actual)
actual = locate(np.flipud(image.transpose()))
assert len(actual)
def test_one_centered_gaussian_3D_anisotropic(self):
self.check_skip()
L = 21
dims = (L, L + 2, L + 4) # avoid square images in tests
pos = [7, 13, 9]
cols = ['z', 'y', 'x']
expected = DataFrame(np.asarray(pos).reshape(1, -1), columns=cols)
image = np.ones(dims, dtype='uint8')
draw_feature(image, pos, (21, 27, 27))
actual = tp.locate(image, (7, 9, 9), 1, preprocess=False,
engine=self.engine)[cols]
assert_allclose(actual, expected, atol=0.1)
def test_float_image(self):
separation = 20
angle = 45
im = np.zeros((128, 128), dtype=np.float64)
pos = [[64, 64], [64 + separation * np.sin(angle/180*np.pi),
64 + separation * np.cos(angle/180*np.pi)]]
# setup features: features with equal signal will always be
# detected by a grey dilation, so make them unequal
draw_feature(im, pos[0], 3, 240)
draw_feature(im, pos[1], 3, 250)
# find both of them
f = grey_dilation(im, separation - 1, precise=False)
assert_coordinates_close(f, pos, atol=1)
def test_size_anisotropic(self):
# The separate columns 'size_x' and 'size_y' reflect the radii of
# gyration in the two separate directions.
self.check_skip()
L = 101
SIZE = 5
dims = (L, L + 2) # avoid square images in tests
pos = [50, 55]
for ar in [1.1, 1.5, 2]:
image = np.zeros(dims, dtype='uint8')
draw_feature(image, pos, [int(SIZE*8*ar), SIZE*8], rg=0.25)
f = tp.locate(image, [int(SIZE*4*ar) * 2 - 1, SIZE*8 - 1], 1,
preprocess=False, engine=self.engine)
assert_allclose(f['size_x'], SIZE, rtol=0.1)
assert_allclose(f['size_y'], SIZE*ar, rtol=0.1)
def test_float_image(self):
separation = 20
angle = 45
im = np.zeros((128, 128), dtype=np.float64)
pos = [[64, 64],
[
64 + separation * np.sin(angle / 180 * np.pi),
64 + separation * np.cos(angle / 180 * np.pi)
]]
# setup features: features with equal signal will always be
# detected by a grey dilation, so make them unequal
draw_feature(im, pos[0], 3, 240)
draw_feature(im, pos[1], 3, 250)
# find both of them
f = grey_dilation(im, separation - 1, precise=False)
assert_coordinates_close(f, pos, atol=1)
def test_separation_anisotropic(self):
separation = (10, 20)
for angle in np.arange(0, 360, 15):
im = np.zeros((128, 128), dtype=np.uint8)
pos = [[64, 64], [64 + separation[0] * np.sin(angle/180*np.pi),
64 + separation[1] * np.cos(angle/180*np.pi)]]
# setup features: features with equal signal will always be
# detected by a grey dilation, so make them unequal
draw_feature(im, pos[0], 3, 240)
draw_feature(im, pos[1], 3, 250)
# find both of them
f = grey_dilation(im, (9, 19))
assert_coordinates_close(f, pos, atol=1)
# find only the brightest
f = grey_dilation(im, (11, 21))
assert_coordinates_close(f, pos[1:], atol=1)
def test_separation(self):
separation = 20
for angle in np.arange(0, 360, 15):
im = np.zeros((128, 128), dtype=np.uint8)
pos = [[64, 64], [64 + separation * np.sin(angle/180*np.pi),
64 + separation * np.cos(angle/180*np.pi)]]
# setup features: features with equal signal will always be
# detected by grey_dilation_legacy, so make them unequal
draw_feature(im, pos[0], 3, 240)
draw_feature(im, pos[1], 3, 250)
# find both of them
f = grey_dilation_legacy(im, separation - 1)
assert_coordinates_close(f, pos, atol=1)
# find only the brightest
f = grey_dilation_legacy(im, separation + 1)
assert_coordinates_close(f, pos[1:], atol=1)
def test_minmass_maxsize(self):
# Test the mass- and sizebased filtering here on 4 different features.
self.check_skip()
L = 64
dims = (L, L + 2)
cols = ['y', 'x']
PRECISION = 1 # we are not testing for subpx precision here
image = np.zeros(dims, dtype=np.uint8)
pos1 = np.array([15, 20])
pos2 = np.array([40, 40])
pos3 = np.array([25, 50])
pos4 = np.array([35, 15])
draw_feature(image, pos1, size=2.5)
draw_feature(image, pos2, size=5)
draw_feature(image, pos3, size=0.8)
draw_feature(image, pos4, size=3.2)
# filter on mass
actual = tp.locate(image,
15,
engine=self.engine,
preprocess=False,
minmass=6500,
separation=10)[cols]
actual = pandas_sort(actual, cols)
expected = pandas_sort(DataFrame([pos2, pos4], columns=cols), cols)
assert_allclose(actual, expected, atol=PRECISION)
# filter on size
actual = tp.locate(image,
15,
engine=self.engine,
preprocess=False,
maxsize=3.0,
separation=10)[cols]
actual = pandas_sort(actual, cols)
expected = pandas_sort(DataFrame([pos1, pos3], columns=cols), cols)
assert_allclose(actual, expected, atol=PRECISION)
# filter on both mass and size
actual = tp.locate(image,
15,
engine=self.engine,
preprocess=False,
minmass=600,
maxsize=4.0,
separation=10)[cols]
actual = pandas_sort(actual, cols)
expected = pandas_sort(DataFrame([pos1, pos4], columns=cols), cols)
assert_allclose(actual, expected, atol=PRECISION)
def get_image(self,
noise=0,
signal_dev=0.,
size_dev=0.,
separation=None,
N=None):
if N is None:
N = self.repeats
if separation is None:
separation = self.separation
margin = self.separation
Nsqrt = int(N**(1 / self.ndim) + 0.9999)
pos = np.meshgrid(*[np.arange(0, s * Nsqrt, s) for s in separation],
indexing='ij')
pos = np.array([p.ravel() for p in pos], dtype=np.float).T[:N] + margin
pos += (np.random.random(pos.shape) - 0.5
) #randomize subpixel location
shape = tuple(np.max(pos, axis=0).astype(np.int) + margin)
if signal_dev > 0:
signal = self.signal * np.random.uniform(1 - signal_dev,
1 + signal_dev, N)
else:
signal = np.repeat(self.signal, N)
if size_dev > 0:
size = np.array([self.size]) * np.random.uniform(
1 - size_dev, 1 + size_dev, (N, 1))
else:
size = np.repeat([self.size], N, axis=0)
image = np.zeros(shape, dtype=self.dtype)
for _pos, _signal, _size in zip(pos, signal, size):
draw_feature(image, _pos, _size, _signal, self.feat_func,
**self.feat_kwargs)
if self.isotropic:
size = size[:, 0]
if noise > 0:
image = image + np.random.poisson(noise, shape)
if image.max() <= 255:
image = image.astype(np.uint8)
return image, (pos, signal, size)
def test_ep_anisotropic(self):
# The separate columns 'ep_x' and 'ep_y' reflect the static errors
# in the two separate directions. The error in the direction with the
# smallest mask size should be lowest; their ratio is equal to the
# mask aspect ratio.
self.check_skip()
L = 101
SIZE = 5
dims = (L, L + 2) # avoid square images in tests
pos = [50, 55]
noise = 0.2
for ar in [1.1, 1.5, 2]: # sizeY / sizeX
image = np.random.randint(0, int(noise*255), dims).astype('uint8')
draw_feature(image, pos, [int(SIZE*8*ar), SIZE*8],
max_value=int((1-noise)*255))
f = tp.locate(image, [int(SIZE*4*ar) * 2 - 1, SIZE*8 - 1],
threshold=int(noise*64), topn=1,
engine=self.engine).loc[0]
assert_allclose(f['ep_y'] / f['ep_x'], ar, rtol=0.1)
def test_size(self):
# To draw Gaussians with radii 2, 3, 5, and 7 px, we supply the draw
# function with rg=0.25. This means that the radius of gyration will be
# one fourth of the max radius in the draw area, which is diameter/2.
# The 'size' comes out to be within 3%, which is because of the
# pixelation of the Gaussian.
# The IDL code has mistake in this area, documented here:
# http://www.physics.emory.edu/~weeks/idl/radius.html
self.check_skip()
L = 101
dims = (L, L + 2) # avoid square images in tests
for pos in [[50, 55], [50.2, 55], [50.5, 55]]:
for SIZE in [2, 3, 5, 7]:
image = np.zeros(dims, dtype='uint8')
draw_feature(image, pos, SIZE*8, rg=0.25)
actual = tp.locate(image, SIZE*8 - 1, 1, preprocess=False,
engine=self.engine)['size']
assert_allclose(actual, SIZE, rtol=0.1)
def test_eccentricity(self):
# Eccentricity (elongation) is measured with good accuracy and
# ~0.02 precision, as long as the mask is large enough to cover
# the whole object.
self.check_skip()
L = 501
dims = (L + 2, L) # avoid square images in tests
pos = [50, 55]
cols = ['y', 'x']
ECC = 0
image = np.ones(dims, dtype='uint8')
draw_feature(image, pos, 27, ecc=ECC)
actual = tp.locate(image, 21, 1, preprocess=False,
engine=self.engine)['ecc']
expected = ECC
assert_allclose(actual, expected, atol=0.02)
ECC = 0.2
image = np.ones(dims, dtype='uint8')
draw_feature(image, pos, 27, ecc=ECC)
actual = tp.locate(image, 21, 1, preprocess=False,
engine=self.engine)['ecc']
expected = ECC
assert_allclose(actual, expected, atol=0.1)
ECC = 0.5
image = np.ones(dims, dtype='uint8')
draw_feature(image, pos, 27, ecc=ECC)
actual = tp.locate(image, 21, 1, preprocess=False,
engine=self.engine)['ecc']
expected = ECC
assert_allclose(actual, expected, atol=0.1)
def test_separation_anisotropic(self):
separation = (10, 20)
for angle in np.arange(0, 360, 15):
im = np.zeros((128, 128), dtype=np.uint8)
pos = [[64, 64],
[
64 + separation[0] * np.sin(angle / 180 * np.pi),
64 + separation[1] * np.cos(angle / 180 * np.pi)
]]
# setup features: features with equal signal will always be
# detected by a grey dilation, so make them unequal
draw_feature(im, pos[0], 3, 240)
draw_feature(im, pos[1], 3, 250)
# find both of them
f = grey_dilation(im, (9, 19))
assert_coordinates_close(f, pos, atol=1)
# find only the brightest
f = grey_dilation(im, (11, 21))
assert_coordinates_close(f, pos[1:], atol=1)
def test_separation(self):
separation = 20
for angle in np.arange(0, 360, 15):
im = np.zeros((128, 128), dtype=np.uint8)
pos = [[64, 64],
[
64 + separation * np.sin(angle / 180 * np.pi),
64 + separation * np.cos(angle / 180 * np.pi)
]]
# setup features: features with equal signal will always be
# detected by grey_dilation_legacy, so make them unequal
draw_feature(im, pos[0], 3, 240)
draw_feature(im, pos[1], 3, 250)
# find both of them
f = grey_dilation_legacy(im, separation - 1)
assert_coordinates_close(f, pos, atol=1)
# find only the brightest
f = grey_dilation_legacy(im, separation + 1)
assert_coordinates_close(f, pos[1:], atol=1)
def test_uncertainty_failure(self):
"""When the uncertainty ("ep") calculation results in a nonsense negative
value, it should return NaN instead.
"""
self.check_skip()
L = 21
dims = (L, L + 2) # avoid square images in tests
pos = np.array([7, 13])
cols = ['x', 'y']
expected = DataFrame(pos[::-1].reshape(1, -1), columns=cols)
image = 100*np.ones(dims, dtype='uint8')
# For a feature to have a negative uncertainty, its integrated mass
# must be less than if it were not there at all (replaced
# with the average background intensity). So our feature will be a
# small bright spot surrounded by a dark annulus.
draw_feature(image, pos, 6, max_value=-100)
draw_feature(image, pos, 4, max_value=200)
actual = tp.locate(image, 9, 1, preprocess=False, engine=self.engine)
assert np.allclose(actual[['x', 'y']], expected[['x', 'y']])
assert np.isnan(np.asscalar(actual.ep))
def get_image(self, noise=0, signal_dev=0., size_dev=0., separation=None,
N=None):
if N is None:
N = self.repeats
if separation is None:
separation = self.separation
margin = self.separation
Nsqrt = int(N**(1/self.ndim) + 0.9999)
pos = np.meshgrid(*[np.arange(0, s * Nsqrt, s) for s in separation],
indexing='ij')
pos = np.array([p.ravel() for p in pos], dtype=np.float).T[:N] + margin
pos += (np.random.random(pos.shape) - 0.5) #randomize subpixel location
shape = tuple(np.max(pos, axis=0).astype(np.int) + margin)
if signal_dev > 0:
signal = self.signal * np.random.uniform(1-signal_dev, 1+signal_dev,
N)
else:
signal = np.repeat(self.signal, N)
if size_dev > 0:
size = np.array([self.size]) * np.random.uniform(1-size_dev,
1+size_dev,
(N, 1))
else:
size = np.repeat([self.size], N, axis=0)
image = np.zeros(shape, dtype=self.dtype)
for _pos, _signal, _size in zip(pos, signal, size):
draw_feature(image, _pos, _size, _signal,
self.feat_func, **self.feat_kwargs)
if self.isotropic:
size = size[:, 0]
if noise > 0:
image = image + np.random.poisson(noise, shape)
if image.max() <= 255:
image = image.astype(np.uint8)
return image, (pos, signal, size)
def test_minmass_maxsize(self):
# Test the mass- and sizebased filtering here on 4 different features.
self.check_skip()
L = 64
dims = (L, L + 2)
cols = ['y', 'x']
PRECISION = 1 # we are not testing for subpx precision here
image = np.zeros(dims, dtype=np.uint8)
pos1 = np.array([15, 20])
pos2 = np.array([40, 40])
pos3 = np.array([25, 45])
pos4 = np.array([35, 15])
draw_feature(image, pos1, 15)
draw_feature(image, pos2, 30)
draw_feature(image, pos3, 5)
draw_feature(image, pos4, 20)
# filter on mass
actual = tp.locate(image, 15, engine=self.engine, preprocess=False,
minmass=6500)[cols]
actual = actual.sort(cols)
expected = DataFrame([pos2, pos4], columns=cols).sort(cols)
assert_allclose(actual, expected, atol=PRECISION)
# filter on size
actual = tp.locate(image, 15, engine=self.engine, preprocess=False,
maxsize=3.0)[cols]
actual = actual.sort(cols)
expected = DataFrame([pos1, pos3], columns=cols).sort(cols)
assert_allclose(actual, expected, atol=PRECISION)
# filter on both mass and size
actual = tp.locate(image, 15, engine=self.engine, preprocess=False,
minmass=600, maxsize=4.0)[cols]
actual = actual.sort(cols)
expected = DataFrame([pos1, pos4], columns=cols).sort(cols)
assert_allclose(actual, expected, atol=PRECISION)