def test_push_tuple():
reference = ([1, 2], [-3, 4])
image = cle.push(reference)
result = cle.pull(image)
assert np.allclose(result, reference)
def test_push_np():
reference = np.asarray([[1, 2], [-3, 4]])
image = cle.push(reference)
result = cle.pull(image)
assert np.allclose(result, reference)
def test_push_list():
reference = [[1, 2], [-3, 4]]
image = cle.push(reference)
result = cle.pull(image)
assert np.allclose(result, reference)
def test_labelled_spots_to_pointlist():
gpu_input = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 0, 1, 0], [0, 0, 0, 0, 0],
[0, 0, 1, 0, 0], [0, 0, 0, 0, 1]]))
gpu_reference = cle.push(np.asarray([[1, 3, 2, 4], [1, 1, 3, 4]]))
gpu_output = cle.spots_to_pointlist(gpu_input)
a = cle.pull(gpu_output)
b = cle.pull(gpu_reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_connected_components_labeling_diamond():
gpu_input = cle.push(
np.asarray([[[0, 1, 0, 1], [0, 1, 0, 0], [1, 0, 0, 1]]]))
gpu_reference = cle.push(
np.asarray([[[0, 2, 0, 3], [0, 2, 0, 0], [1, 0, 0, 4]]]))
gpu_output = cle.connected_components_labeling_diamond(gpu_input)
a = cle.pull(gpu_output)
b = cle.pull(gpu_reference)
print(b)
print(a)
assert (np.array_equal(a, b))
def test_erode_sphere():
test = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 1, 1, 0], [0, 1, 1, 1, 0],
[0, 1, 1, 1, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]))
result = cle.create(test)
cle.erode_sphere(test, result)
print(result)
a = cle.pull(result)
b = cle.pull(reference)
assert (np.array_equal(a, b))
def test_dilate_labels_3d():
gpu_input = cle.push(
np.asarray([[
[0, 0, 0, 0, 0, 2],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 4, 0, 0],
[0, 0, 0, 0, 0, 0],
[5, 0, 0, 0, 0, 3],
],
[
[1, 0, 0, 0, 0, 2],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[5, 0, 0, 0, 0, 0],
]]))
gpu_reference = cle.push(
np.asarray([[
[1, 1, 0, 0, 2, 2],
[1, 1, 0, 0, 2, 2],
[0, 0, 4, 4, 4, 0],
[0, 0, 4, 4, 4, 0],
[5, 5, 4, 4, 4, 3],
[5, 5, 0, 0, 3, 3],
],
[
[1, 1, 0, 0, 2, 2],
[1, 1, 0, 0, 2, 2],
[0, 0, 4, 4, 4, 0],
[0, 0, 4, 4, 4, 0],
[5, 5, 4, 4, 4, 3],
[5, 5, 0, 0, 3, 3],
]]))
gpu_output = cle.extend_labels_with_maximum_radius(gpu_input, radius=1)
a = cle.pull(gpu_output)
b = cle.pull(gpu_reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_smaller_constant():
test1 = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 2, 3, 0], [0, 2, 3, 4, 0],
[0, 4, 5, 5, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[1, 1, 1, 1, 1], [1, 1, 1, 1, 1], [1, 1, 1, 0, 1],
[1, 0, 0, 0, 1], [1, 1, 1, 1, 1]]))
result = cle.create(test1)
cle.smaller_constant(test1, result, 4)
print(result)
a = cle.pull(result)
b = cle.pull(reference)
assert (np.array_equal(a, b))
def test_label_maximum_intensity_map_2d():
intensity = cle.push(np.asarray([[1, 1, 2], [4, 0, 0], [5, 3, 0]]))
labels = cle.push(np.asarray([[1, 1, 2], [1, 0, 0], [3, 3, 0]]))
reference = cle.push(np.asarray([[4, 4, 2], [4, 0, 0], [5, 5, 0]]))
result = cle.label_maximum_intensity_map(intensity, labels)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_set_ramp_z():
result = cle.push(
np.asarray([[[0, 0, 0], [3, 4, 3], [3, 4, 3]],
[[3, 4, 3], [3, 4, 3], [3, 4, 3]]]))
reference = cle.push(
np.asarray([[[0, 1, 2], [0, 1, 2], [0, 1, 2]],
[[0, 1, 2], [0, 1, 2], [0, 1, 2]]]))
cle.set_ramp_z(result)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
assert (np.allclose(a, b, 0.001))
def test_add_images_weighted_named_params():
output = cle.add_images_weighted(input1,
input2,
None,
factor1=1,
factor2=2)
result = cle.pull(output)
assert np.array_equal(result, reference)
def test_label_label_maximum_extension_map_2d():
labels = cle.push(np.asarray([[1, 1, 2], [1, 0, 0], [3, 3, 0]]))
reference = cle.push(
np.asarray([[0.74535596, 0.74535596, 0], [0.74535596, 0, 0],
[0.5, 0.5, 0]]))
result = cle.label_maximum_extension_map(labels)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
assert (np.allclose(a, b, 0.001))
def test_read_intensities_from_map():
intensities = cle.push(np.asarray([[1, 2, 3], [4, 5, 6], [7, 8, 9]]))
labels = cle.push(np.asarray([[8, 0, 7], [6, 5, 4], [3, 2, 1]]))
reference = cle.push(np.asarray([[2, 9, 8, 7, 6, 5, 4, 3, 1]]))
result = cle.read_intensities_from_map(labels, intensities)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_gradient_x():
test = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 2, 0, 0], [0, 1, 2, 0, 0],
[0, 1, 3, 0, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[0, 1, 2, 0, 0], [0, 1, 2, 0, 0], [0, 0, 1, 0, 0],
[0, -1, -2, 0, 0], [0, -1, -3, 0, 0]]))
result = cle.create(test)
cle.gradient_x(test, result)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
assert (np.array_equal(a, b))
def test_resample_upsample_3d():
test1 = cle.push(np.asarray([[[0, 2], [1, 4]], [[5, 5], [5, 5]]]))
reference = cle.push(
np.asarray([[[0, 0, 2, 2], [0, 0, 2, 2], [1, 1, 4, 4], [1, 1, 4, 4]],
[[0, 0, 2, 2], [0, 0, 2, 2], [1, 1, 4, 4], [1, 1, 4, 4]],
[[5, 5, 5, 5], [5, 5, 5, 5], [5, 5, 5, 5], [5, 5, 5, 5]],
[[5, 5, 5, 5], [5, 5, 5, 5], [5, 5, 5, 5], [5, 5, 5, 5]]]))
result = cle.resample(test1, factor_x=2, factor_y=2, factor_z=2)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_label_mean_intensity_map_2d():
intensity = cle.push(np.asarray([[1, 1, 2], [4, 0, 0], [5, 3, 0]]))
labels = cle.push(np.asarray([[1, 1, 2], [1, 0, 0], [3, 3, 0]]))
reference = cle.push(np.asarray([[2, 2, 2], [2, 0, 0], [4, 4, 0]]))
result = cle.label_mean_intensity_map(intensity, labels)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
assert (np.allclose(a, b, 0.001))
def test_pointlist_to_labelled_spots_2d():
positions_and_values = cle.push(
np.asarray([[0, 0, 2, 3, 5], [0, 1, 3, 2, 6]]))
reference = cle.push(
np.asarray([[1, 0, 0, 0, 0, 0], [2, 0, 0, 0, 0, 0], [0, 0, 0, 4, 0, 0],
[0, 0, 3, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 5]]))
result = cle.pointlist_to_labelled_spots(positions_and_values)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_minimum_box():
test1 = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 1, 1, 0], [0, 1, 1, 1, 0],
[0, 1, 1, 1, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]))
result = cle.create(test1)
cle.minimum_box(test1, result, 1, 1, 0)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
assert (np.array_equal(a, b))
def test_exponential():
test = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 1, 2, 0], [0, 2, 2, 3, 0],
[0, 3, 3, 4, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[1, 1, 1, 1, 1], [1, 2.7182817, 2.7182817, 7.389056, 1],
[1, 7.389056, 7.389056, 20.085537, 1],
[1, 20.085537, 20.085537, 54.59815, 1], [1, 1, 1, 1, 1]]))
result = cle.create(test)
cle.exponential(test, result)
print(result)
a = cle.pull(result)
b = cle.pull(reference)
assert (np.allclose(a, b, atol=0.00001))
def test_resample_3d_interpolation_x():
test1 = cle.push(np.asarray([[[0, 2]]]))
reference = cle.push(np.asarray([[
[0, 0.5, 1.5, 1.5],
]]))
result = cle.resample(test1,
factor_x=2,
factor_y=1,
factor_z=1,
linear_interpolation=True)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_flip():
test = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 2, 0, 0], [0, 1, 2, 0, 0],
[0, 1, 3, 0, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 0, 2, 1, 0], [0, 0, 2, 1, 0],
[0, 0, 3, 1, 0], [0, 0, 0, 0, 0]]))
result = cle.create(test)
cle.flip(test, result, True, False, False)
print(reference.get())
print(result.get())
a = cle.pull(result)
b = cle.pull(reference)
assert (np.array_equal(a, b))
def test_affine_shear_x_in_z_plane():
source = np.zeros((5, 5, 5))
source[1, 1, 1] = 1
reference = np.zeros((5, 5, 5))
reference[1, 1, 2] = 1
transform = cle.AffineTransform3D()
transform.shear_in_z_plane(angle_x_in_degrees=45)
result = cle.affine_transform(source, transform=transform)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_resample_downsample_3d():
test1 = cle.push(
np.asarray([[[-3, 0, 1, 2], [0, 5, 2, 7], [0, 1, 3, 4], [1, 6, 4, 8]],
[[-3, 0, 1, 2], [0, 5, 2, 7], [0, 1, 3, 4], [1, 6, 4, 8]],
[[5, 5, 5, 5], [5, 5, 5, 5], [5, 5, 5, 5], [5, 5, 5, 5]],
[[5, 5, 5, 5], [5, 5, 5, 5], [5, 5, 5, 5], [5, 5, 5, 5]]]))
reference = cle.push(
np.asarray([[[0, 2], [1, 4]], [[0, 2], [1, 4]], [[5, 5], [5, 5]],
[[5, 5], [5, 5]]]))
result = cle.downsample_slice_by_slice_half_median(test1)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
assert (np.array_equal(a, b))
def onlyzero_overwrite_maximum_diamond():
test1 = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 2, 3, 0], [0, 2, 3, 4, 0],
[0, 4, 4, 5, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[0, 1, 2, 3, 0], [1, 1, 2, 3, 3], [2, 2, 3, 4, 4],
[4, 4, 4, 5, 5], [0, 4, 4, 5, 0]]))
result = cle.create(test1)
flag = cle.create((1, 1, 1))
cle.onlyzero_overwrite_maximum_diamond(test1, flag, result)
print(result)
a = cle.pull(result)
b = cle.pull(reference)
assert (np.array_equal(a, b))
def test_laplace_diamond():
test1 = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 0, -1, 0, 0], [0, -1, 4, -1, 0],
[0, 0, -1, 0, 0], [0, 0, 0, 0, 0]]))
result = cle.create(test1)
cle.laplace_diamond(test1, result)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
assert (np.array_equal(a, b))
def test_exclude_large_labels_2d():
gpu_input = cle.push(
np.asarray([[1, 1, 2, 0, 3, 3], [1, 1, 2, 0, 3, 3], [0, 0, 0, 0, 0, 0],
[4, 4, 5, 6, 6, 6], [4, 4, 5, 6, 6, 6]]))
gpu_reference = cle.push(
np.asarray([[0, 0, 1, 0, 0, 0], [0, 0, 1, 0, 0, 0], [0, 0, 0, 0, 0, 0],
[0, 0, 2, 0, 0, 0], [0, 0, 2, 0, 0, 0]]))
gpu_output = cle.exclude_large_labels(gpu_input, gpu_input, minimum_size=3)
a = cle.pull(gpu_output)
b = cle.pull(gpu_reference)
print(a)
print(b)
assert (np.array_equal(a, b))
def test_mean_box():
test1 = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 9, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 1, 1, 1, 0], [0, 1, 1, 1, 0],
[0, 1, 1, 1, 0], [0, 0, 0, 0, 0]]))
result = cle.create(test1)
cle.mean_box(test1, result, 1, 1, 0)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
assert (np.allclose(a, b))
def test_standard_deviation_sphere():
test1 = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]))
reference = cle.push(
np.asarray([[0, 0, 0, 0, 0], [0, 0, 0.4, 0, 0], [0, 0.4, 0.4, 0.4, 0],
[0, 0, 0.4, 0, 0], [0, 0, 0, 0, 0]]))
result = cle.create(test1)
cle.standard_deviation_sphere(test1, result, 1, 1, 0)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
assert (np.allclose(a, b, 0.01))
def test_maximum_y_projection2():
test1 = cle.push(
np.asarray([
[1, 0, 0, 0, 9],
[0, 2, 0, 8, 0],
[3, 0, 1, 0, 10],
]))
reference = cle.push(np.asarray([[3, 2, 1, 8, 10]]))
result = cle.maximum_y_projection(test1)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
assert (np.array_equal(a, b))
def test_deskew_y():
source = np.zeros((5, 5, 5))
source[1, 1, 1] = 1
reference = np.zeros((2, 7, 5))
reference[0, 5, 1] = 1
result = cle.deskew_y(source, angle_in_degrees=30)
a = cle.pull(result)
b = cle.pull(reference)
print(a)
print(b)
print(a.shape)
print(b.shape)
assert (np.array_equal(a, b))
