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automated_test.py
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import pytest
import numpy as np
import fastmorph
def test_spherical_dilate():
labels = np.zeros((10,10,10), dtype=bool)
res = fastmorph.spherical_dilate(labels, radius=1000)
assert np.all(res == False)
labels[5,5,5] = True
radius = 5 * np.sqrt(3) + 0.000001
res = fastmorph.spherical_dilate(labels, radius=radius)
assert np.all(res == True)
res = fastmorph.spherical_dilate(labels, radius=1)
assert np.count_nonzero(res) == 7
res = fastmorph.spherical_dilate(labels, radius=np.sqrt(2))
assert np.count_nonzero(res) == 19
res = fastmorph.spherical_dilate(labels, radius=np.sqrt(3))
assert np.count_nonzero(res) == 27
def test_spherical_erode():
labels = np.ones((10,10,10), dtype=bool)
res = fastmorph.spherical_erode(labels, radius=1000)
assert np.all(res == False)
def test_fill_holes():
labels = np.ones((10,10,10), dtype=np.uint8)
labels[:,:,:5] = 2
labels[5,5,2] = 0
labels[5,5,7] = 0
assert np.count_nonzero(labels) == 998
res, ct = fastmorph.fill_holes(labels, return_fill_count=True)
assert np.count_nonzero(res) == 1000
assert list(np.unique(res)) == [1,2]
assert res[5,5,2] == 2
assert res[5,5,7] == 1
assert ct[1] == 1
assert ct[2] == 1
labels = np.ones((10,10,10), dtype=int)
labels[5,5,2] = 777
res, removed = fastmorph.fill_holes(labels, remove_enclosed=True, return_removed=True)
assert removed == set([777])
labels = np.ones((10,10,10), dtype=bool)
labels[5,5,2] = 0
res = fastmorph.fill_holes(labels, return_fill_count=False)
assert np.all(res == True)
res = fastmorph.fill_holes(labels, return_fill_count=True)
assert np.all(res[0] == True)
assert res[1] == 1
res = fastmorph.fill_holes(labels, return_removed=True)
assert np.all(res[0] == True)
assert res[1] == set()
res = fastmorph.fill_holes(labels, return_fill_count=True, return_removed=True)
assert np.all(res[0] == True)
assert res[1] == 1
assert res[2] == set()
def test_fill_fix_borders():
labels = np.ones([100,100,100], dtype=np.uint8)
labels[40:60,40:60,:] = 0
labels[40:60,:,40:60] = 0
labels[:,40:60,40:60] = 0
res, cts = fastmorph.fill_holes(
labels,
fix_borders=False,
return_fill_count=True,
morphological_closing=False,
)
assert cts[1] == 0
assert np.all(res == labels)
res, cts = fastmorph.fill_holes(
labels,
fix_borders=True,
return_fill_count=True,
morphological_closing=False,
)
assert cts[1] == np.count_nonzero(labels == 0)
assert np.all(res == 1)
def test_complex_fill():
import crackle
labels = crackle.load("test_data/complex_soma.ckl.gz")
ans = crackle.load("test_data/complex_soma_result.ckl.gz")
res = fastmorph.fill_holes(
labels,
remove_enclosed=True,
fix_borders=True,
morphological_closing=True,
)
assert np.all(res == ans)
def test_spherical_open_close_run():
labels = np.zeros((10,10,10), dtype=bool)
res = fastmorph.spherical_open(labels, radius=1)
res = fastmorph.spherical_close(labels, radius=1)
def test_spherical_close():
labels = np.zeros((10,10,10), dtype=bool)
labels[4:7,4:7,4:7] = True
labels[5,5,5] = False
res = fastmorph.spherical_close(labels, radius=1)
assert res[5,5,5] == True
def test_multilabel_dilate_3d():
labels = np.zeros((3,3,3), dtype=bool)
out = fastmorph.dilate(labels)
assert not np.any(out)
labels[1,1,1] = True
out = fastmorph.dilate(labels)
assert np.all(out)
labels = np.zeros((3,3,3), dtype=bool)
labels[0,0,0] = True
out = fastmorph.dilate(labels)
ans = np.zeros((3,3,3), dtype=bool)
ans[:2,:2,:2] = True
assert np.all(out == ans)
labels = np.zeros((3,3,3), dtype=int)
labels[0,1,1] = 1
labels[2,1,1] = 2
out = fastmorph.dilate(labels)
ans = np.ones((3,3,3), dtype=int)
ans[2,:,:] = 2
assert np.all(ans == out)
labels = np.zeros((3,3,3), dtype=int, order="F")
labels[0,1,1] = 1
labels[1,1,1] = 2
labels[2,1,1] = 2
out = fastmorph.dilate(labels)
ans = np.ones((3,3,3), dtype=int, order="F")
ans[1:,:,:] = 2
assert np.all(ans == out)
def test_multilabel_dilate_2d():
labels = np.zeros((3,3), dtype=bool)
out = fastmorph.dilate(labels)
assert not np.any(out)
labels[1,1] = True
out = fastmorph.dilate(labels)
assert np.all(out)
labels = np.zeros((3,3), dtype=bool)
labels[0,0] = True
out = fastmorph.dilate(labels)
ans = np.zeros((3,3), dtype=bool)
ans[:2,:2] = True
assert np.all(out == ans)
labels = np.zeros((3,3), dtype=int)
labels[0,1] = 1
labels[2,1] = 2
out = fastmorph.dilate(labels)
ans = np.ones((3,3), dtype=int)
ans[2,:] = 2
assert np.all(ans == out)
labels = np.zeros((3,3), dtype=int, order="F")
labels[0,1] = 1
labels[1,1] = 2
labels[2,1] = 2
out = fastmorph.dilate(labels)
ans = np.ones((3,3), dtype=int, order="F")
ans[1:,:] = 2
assert np.all(ans == out)
labels = np.zeros([2411,2101], dtype=bool, order="F")
labels[10:-10,10:-10] = 1
for i in range(20):
labels = fastmorph.dilate(labels)
assert np.all(labels)
def test_multilabel_erode_3d():
labels = np.ones((3,3,3), dtype=bool)
out = fastmorph.erode(labels)
assert np.sum(out) == 1 and out[1,1,1] == True
out = fastmorph.erode(out)
assert not np.any(out)
out = fastmorph.erode(out)
assert not np.any(out)
labels = np.ones((3,3,3), dtype=int, order="F")
labels[0,:,:] = 1
labels[1,:,:] = 2
labels[2,:,:] = 3
out = fastmorph.erode(labels)
ans = np.zeros((3,3,3), dtype=int, order="F")
assert np.all(ans == out)
labels = np.zeros((5,5,5), dtype=bool)
labels[1:4,1:4,1:4] = True
out = fastmorph.erode(labels)
assert np.sum(out) == 1 and out[2,2,2] == True
labels = np.ones((5,5,5), dtype=bool)
out = fastmorph.erode(labels)
assert np.sum(out) == 27
labels = np.ones((5,5,5), dtype=bool)
out = fastmorph.erode(labels, erode_border=False, iterations=5)
assert np.sum(out) == 125
def test_multilabel_erode_2d():
labels = np.ones((3,3), dtype=bool)
out = fastmorph.erode(labels)
assert np.sum(out) == 1 and out[1,1] == True
out = fastmorph.erode(out)
assert not np.any(out)
out = fastmorph.erode(out)
assert not np.any(out)
labels = np.ones((3,3), dtype=int, order="F")
labels[0,:] = 1
labels[1,:] = 2
labels[2,:] = 3
out = fastmorph.erode(labels)
ans = np.zeros((3,3), dtype=int, order="F")
assert np.all(ans == out)
labels = np.zeros((5,5), dtype=bool)
labels[1:4,1:4] = True
out = fastmorph.erode(labels)
assert np.sum(out) == 1 and out[2,2] == True
labels = np.ones((5,5), dtype=bool)
out = fastmorph.erode(labels)
assert np.sum(out) == 9
labels = np.ones((5,5), dtype=bool)
out = fastmorph.erode(labels, iterations=5, erode_border=False)
assert np.sum(out) == 25
labels = np.array([
[1, 1, 1, 0],
[1, 1, 0, 0],
[0, 0, 0, 0],
], dtype=bool).T
out = fastmorph.erode(labels, erode_border=False)
ans = np.array([
[1, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
], dtype=bool).T
assert np.all(out == ans)
@pytest.mark.parametrize('dtype', [
np.uint8,np.uint16,np.uint32,np.uint64,
np.int8,np.int16,np.int32,np.int64,
])
def test_grey_erode(dtype):
labels = np.arange(9, dtype=dtype).reshape((3,3), order="F")
out = fastmorph.erode(labels, mode=fastmorph.Mode.grey)
ans = np.array([
[0, 0, 1],
[0, 0, 1],
[3, 3, 4],
], dtype=dtype).T
assert np.all(out == ans)
out = fastmorph.erode(out, mode=fastmorph.Mode.grey)
assert np.all(out == 0)
labels = np.arange(27, dtype=dtype).reshape((3,3,3), order="F")
out = fastmorph.erode(labels, mode=fastmorph.Mode.grey)
ans = np.array([
[
[0, 0, 1],
[0, 0, 1],
[3, 3, 4],
],
[
[0, 0, 1],
[0, 0, 1],
[3, 3, 4],
],
[
[9, 9, 10],
[9, 9, 10],
[12, 12, 13],
],
], dtype=dtype).T
assert np.all(out == ans)
out = fastmorph.erode(out, mode=fastmorph.Mode.grey)
assert np.all(out == 0)
@pytest.mark.parametrize('dtype', [
np.uint8,np.uint16,np.uint32,np.uint64,
np.int8,np.int16,np.int32,np.int64,
])
def test_grey_dilate(dtype):
L = 5
H = 10
labels = np.zeros((3,3), dtype=dtype)
labels[0,0] = L
labels[2,2] = H
out = fastmorph.dilate(labels, mode=fastmorph.Mode.grey)
ans = np.array([
[L, L, 0],
[L, H, H],
[0, H, H],
], dtype=dtype).T
assert np.all(out == ans)
labels = np.zeros((3,3,3), dtype=dtype)
labels[0,0,0] = L
labels[2,2,2] = H
out = fastmorph.dilate(labels, mode=fastmorph.Mode.grey)
ans = np.array([
[
[L, L, 0],
[L, L, 0],
[0, 0, 0],
],
[
[L, L, 0],
[L, H, H],
[0, H, H],
],
[
[0, 0, 0],
[0, H, H],
[0, H, H],
],
], dtype=dtype).T
assert np.all(out == ans)
out = fastmorph.dilate(out, mode=fastmorph.Mode.grey)
assert np.all(out == H)
def test_grey_dilate_bool():
labels = np.zeros((3,3,3), dtype=bool)
labels[1,1,1] = True
out = fastmorph.dilate(labels, mode=fastmorph.Mode.grey)
assert np.all(out == True)
labels = np.zeros((3,3), dtype=bool)
labels[1,1] = True
out = fastmorph.dilate(labels, mode=fastmorph.Mode.grey)
assert np.all(out == True)