/
test_morphsnakes.py
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/
test_morphsnakes.py
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import numpy as np
from morphsnakes import (morphological_chan_vese,
morphological_geodesic_active_contour,
inverse_gaussian_gradient,
circle_level_set, checkerboard_level_set)
from numpy.testing import assert_array_equal
import pytest
def gaussian_blob():
coords = np.mgrid[-5:6, -5:6]
sqrdistances = (coords ** 2).sum(0)
return np.exp(-sqrdistances / 10)
def test_morphsnakes_incorrect_image_shape():
img = np.zeros((10, 10, 3))
ls = np.zeros((10, 9))
with pytest.raises(ValueError):
morphological_chan_vese(img, iterations=1, init_level_set=ls)
with pytest.raises(ValueError):
morphological_geodesic_active_contour(img, iterations=1,
init_level_set=ls)
def test_morphsnakes_incorrect_ndim():
img = np.zeros((4, 4, 4, 4))
ls = np.zeros((4, 4, 4, 4))
with pytest.raises(ValueError):
morphological_chan_vese(img, iterations=1, init_level_set=ls)
with pytest.raises(ValueError):
morphological_geodesic_active_contour(img, iterations=1,
init_level_set=ls)
def test_morphsnakes_black():
img = np.zeros((11, 11))
ls = circle_level_set(img.shape, (5, 5), 3)
ref_zeros = np.zeros(img.shape, dtype=np.int8)
ref_ones = np.ones(img.shape, dtype=np.int8)
acwe_ls = morphological_chan_vese(img, iterations=6, init_level_set=ls)
assert_array_equal(acwe_ls, ref_zeros)
gac_ls = morphological_geodesic_active_contour(img, iterations=6,
init_level_set=ls)
assert_array_equal(gac_ls, ref_zeros)
gac_ls2 = morphological_geodesic_active_contour(img, iterations=6,
init_level_set=ls,
balloon=1, threshold=-1,
smoothing=0)
assert_array_equal(gac_ls2, ref_ones)
assert acwe_ls.dtype == gac_ls.dtype == gac_ls2.dtype == np.int8
def test_morphsnakes_simple_shape_chan_vese():
img = gaussian_blob()
ls1 = circle_level_set(img.shape, (5, 5), 3)
ls2 = circle_level_set(img.shape, (5, 5), 6)
acwe_ls1 = morphological_chan_vese(img, iterations=10, init_level_set=ls1)
acwe_ls2 = morphological_chan_vese(img, iterations=10, init_level_set=ls2)
assert_array_equal(acwe_ls1, acwe_ls2)
assert acwe_ls1.dtype == acwe_ls2.dtype == np.int8
def test_morphsnakes_simple_shape_geodesic_active_contour():
img = np.float_(circle_level_set((11, 11), (5, 5), 3.5))
gimg = inverse_gaussian_gradient(img, alpha=10.0, sigma=1.0)
ls = circle_level_set(img.shape, (5, 5), 6)
ref = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
dtype=np.int8)
gac_ls = morphological_geodesic_active_contour(gimg, iterations=10,
init_level_set=ls,
balloon=-1)
assert_array_equal(gac_ls, ref)
assert gac_ls.dtype == np.int8
def test_init_level_sets():
image = np.zeros((6, 6))
checkerboard_ls = morphological_chan_vese(image, 0, 'checkerboard')
checkerboard_ref = np.array([[0, 0, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 1],
[1, 1, 1, 1, 1, 0]], dtype=np.int8)
circle_ls = morphological_geodesic_active_contour(image, 0, 'circle')
circle_ref = np.array([[0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0],
[0, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1],
[0, 0, 1, 1, 1, 0]], dtype=np.int8)
ellipsoid_ls = morphological_chan_vese(np.zeros((7, 9)), 0, 'ellipsoid')
ellipsoid_ref = np.array(
[[0, 0, 1, 1, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 1, 1, 0, 0]],
dtype=np.uint8
)
assert_array_equal(checkerboard_ls, checkerboard_ref)
assert_array_equal(circle_ls, circle_ref)
assert_array_equal(ellipsoid_ls, ellipsoid_ref)
def test_morphsnakes_3d():
image = np.zeros((7, 7, 7))
evolution = []
def callback(x):
evolution.append(x.sum())
ls = morphological_chan_vese(image, 5, 'circle',
iter_callback=callback)
# Check that the initial circle level set is correct
assert evolution[0] == 81
# Check that the final level set is correct
assert ls.sum() == 0
# Check that the contour is shrinking at every iteration
for v1, v2 in zip(evolution[:-1], evolution[1:]):
assert v1 >= v2
if __name__ == "__main__":
np.testing.run_module_suite()