150 lines
5.6 KiB
Python
150 lines
5.6 KiB
Python
import numpy as np
|
|
from skimage.segmentation import (morphological_chan_vese,
|
|
morphological_geodesic_active_contour,
|
|
inverse_gaussian_gradient,
|
|
circle_level_set,
|
|
disk_level_set)
|
|
|
|
from skimage._shared import testing
|
|
from skimage._shared.testing import assert_array_equal
|
|
from skimage._shared._warnings import expected_warnings
|
|
|
|
|
|
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 testing.raises(ValueError):
|
|
morphological_chan_vese(img, iterations=1, init_level_set=ls)
|
|
with testing.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 testing.raises(ValueError):
|
|
morphological_chan_vese(img, iterations=1, init_level_set=ls)
|
|
with testing.raises(ValueError):
|
|
morphological_geodesic_active_contour(img, iterations=1,
|
|
init_level_set=ls)
|
|
|
|
|
|
def test_morphsnakes_black():
|
|
img = np.zeros((11, 11))
|
|
ls = disk_level_set(img.shape, center=(5, 5), radius=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 = disk_level_set(img.shape, center=(5, 5), radius=3)
|
|
ls2 = disk_level_set(img.shape, center=(5, 5), radius=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 = (disk_level_set((11, 11), center=(5, 5), radius=3.5)).astype(float)
|
|
gimg = inverse_gaussian_gradient(img, alpha=10.0, sigma=1.0)
|
|
ls = disk_level_set(img.shape, center=(5, 5), radius=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_deprecated_circle_level_set():
|
|
img = gaussian_blob()
|
|
with expected_warnings(['circle_level_set is deprecated']):
|
|
ls1 = circle_level_set(img.shape, (5, 5), 3)
|
|
|
|
|
|
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)
|
|
|
|
disk_ls = morphological_geodesic_active_contour(image, 0, 'disk')
|
|
disk_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)
|
|
|
|
assert_array_equal(checkerboard_ls, checkerboard_ref)
|
|
assert_array_equal(disk_ls, disk_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, 'disk',
|
|
iter_callback=callback)
|
|
|
|
# Check that the initial disk 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
|