def test_filtered_alpha():
point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
filtered_alpha = AlphaComplex(points=point_list)
simplex_tree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25)
assert simplex_tree.num_simplices() == 8
assert simplex_tree.num_vertices() == 4
assert point_list[0] == filtered_alpha.get_point(0)
assert point_list[1] == filtered_alpha.get_point(1)
assert point_list[2] == filtered_alpha.get_point(2)
assert point_list[3] == filtered_alpha.get_point(3)
assert filtered_alpha.get_point(4) == []
assert filtered_alpha.get_point(125) == []
assert simplex_tree.get_filtration() == [
([0], 0.0),
([1], 0.0),
([2], 0.0),
([3], 0.0),
([0, 1], 0.25),
([0, 2], 0.25),
([1, 3], 0.25),
([2, 3], 0.25),
]
assert simplex_tree.get_star([0]) == [([0], 0.0), ([0, 1], 0.25),
([0, 2], 0.25)]
assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)]
def _filtered_alpha(precision):
point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
filtered_alpha = AlphaComplex(points=point_list, precision = precision)
simplex_tree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25)
assert simplex_tree.num_simplices() == 8
assert simplex_tree.num_vertices() == 4
assert point_list[0] == filtered_alpha.get_point(0)
assert point_list[1] == filtered_alpha.get_point(1)
assert point_list[2] == filtered_alpha.get_point(2)
assert point_list[3] == filtered_alpha.get_point(3)
with pytest.raises(IndexError):
filtered_alpha.get_point(len(point_list))
assert list(simplex_tree.get_filtration()) == [
([0], 0.0),
([1], 0.0),
([2], 0.0),
([3], 0.0),
([0, 1], 0.25),
([0, 2], 0.25),
([1, 3], 0.25),
([2, 3], 0.25),
]
assert simplex_tree.get_star([0]) == [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)]
assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)]
def _3d_tetrahedrons(precision):
points = 10*np.random.rand(10, 3)
alpha = AlphaComplex(points = points, precision = precision)
st_alpha = alpha.create_simplex_tree(default_filtration_value = False)
# New AlphaComplex for get_point to work
delaunay = AlphaComplex(points = points, precision = precision)
st_delaunay = delaunay.create_simplex_tree(default_filtration_value = True)
delaunay_tetra = []
for sk in st_delaunay.get_skeleton(4):
if len(sk[0]) == 4:
tetra = [delaunay.get_point(sk[0][0]),
delaunay.get_point(sk[0][1]),
delaunay.get_point(sk[0][2]),
delaunay.get_point(sk[0][3]) ]
delaunay_tetra.append(sorted(tetra, key=lambda tup: tup[0]))
alpha_tetra = []
for sk in st_alpha.get_skeleton(4):
if len(sk[0]) == 4:
tetra = [alpha.get_point(sk[0][0]),
alpha.get_point(sk[0][1]),
alpha.get_point(sk[0][2]),
alpha.get_point(sk[0][3]) ]
alpha_tetra.append(sorted(tetra, key=lambda tup: tup[0]))
# Check the tetrahedrons from one list are in the second one
assert len(alpha_tetra) == len(delaunay_tetra)
for tetra_from_del in delaunay_tetra:
assert tetra_from_del in alpha_tetra
def _delaunay_complex(precision):
point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
filtered_alpha = AlphaComplex(points=point_list, precision=precision)
simplex_tree = filtered_alpha.create_simplex_tree(
default_filtration_value=True)
assert simplex_tree.num_simplices() == 11
assert simplex_tree.num_vertices() == 4
assert point_list[0] == filtered_alpha.get_point(0)
assert point_list[1] == filtered_alpha.get_point(1)
assert point_list[2] == filtered_alpha.get_point(2)
assert point_list[3] == filtered_alpha.get_point(3)
try:
filtered_alpha.get_point(4) == []
except IndexError:
pass
else:
assert False
try:
filtered_alpha.get_point(125) == []
except IndexError:
pass
else:
assert False
for filtered_value in simplex_tree.get_filtration():
assert math.isnan(filtered_value[1])
for filtered_value in simplex_tree.get_star([0]):
assert math.isnan(filtered_value[1])
for filtered_value in simplex_tree.get_cofaces([0], 1):
assert math.isnan(filtered_value[1])
def _infinite_alpha(precision):
point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
alpha_complex = AlphaComplex(points=point_list, precision = precision)
assert alpha_complex.__is_defined() == True
simplex_tree = alpha_complex.create_simplex_tree()
assert simplex_tree.__is_persistence_defined() == False
assert simplex_tree.num_simplices() == 11
assert simplex_tree.num_vertices() == 4
assert list(simplex_tree.get_filtration()) == [
([0], 0.0),
([1], 0.0),
([2], 0.0),
([3], 0.0),
([0, 1], 0.25),
([0, 2], 0.25),
([1, 3], 0.25),
([2, 3], 0.25),
([1, 2], 0.5),
([0, 1, 2], 0.5),
([1, 2, 3], 0.5),
]
assert simplex_tree.get_star([0]) == [
([0], 0.0),
([0, 1], 0.25),
([0, 1, 2], 0.5),
([0, 2], 0.25),
]
assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)]
assert point_list[0] == alpha_complex.get_point(0)
assert point_list[1] == alpha_complex.get_point(1)
assert point_list[2] == alpha_complex.get_point(2)
assert point_list[3] == alpha_complex.get_point(3)
with pytest.raises(IndexError):
alpha_complex.get_point(len(point_list))
def test_infinite_alpha():
point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
alpha_complex = AlphaComplex(points=point_list)
assert alpha_complex.__is_defined() == True
simplex_tree = alpha_complex.create_simplex_tree()
assert simplex_tree.__is_persistence_defined() == False
assert simplex_tree.num_simplices() == 11
assert simplex_tree.num_vertices() == 4
assert simplex_tree.get_filtration() == [
([0], 0.0),
([1], 0.0),
([2], 0.0),
([3], 0.0),
([0, 1], 0.25),
([0, 2], 0.25),
([1, 3], 0.25),
([2, 3], 0.25),
([1, 2], 0.5),
([0, 1, 2], 0.5),
([1, 2, 3], 0.5),
]
assert simplex_tree.get_star([0]) == [
([0], 0.0),
([0, 1], 0.25),
([0, 1, 2], 0.5),
([0, 2], 0.25),
]
assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)]
assert point_list[0] == alpha_complex.get_point(0)
assert point_list[1] == alpha_complex.get_point(1)
assert point_list[2] == alpha_complex.get_point(2)
assert point_list[3] == alpha_complex.get_point(3)
assert alpha_complex.get_point(4) == []
assert alpha_complex.get_point(125) == []
def _filtered_alpha(precision):
point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
filtered_alpha = AlphaComplex(points=point_list, precision=precision)
simplex_tree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25)
assert simplex_tree.num_simplices() == 8
assert simplex_tree.num_vertices() == 4
assert point_list[0] == filtered_alpha.get_point(0)
assert point_list[1] == filtered_alpha.get_point(1)
assert point_list[2] == filtered_alpha.get_point(2)
assert point_list[3] == filtered_alpha.get_point(3)
try:
filtered_alpha.get_point(4) == []
except IndexError:
pass
else:
assert False
try:
filtered_alpha.get_point(125) == []
except IndexError:
pass
else:
assert False
assert list(simplex_tree.get_filtration()) == [
([0], 0.0),
([1], 0.0),
([2], 0.0),
([3], 0.0),
([0, 1], 0.25),
([0, 2], 0.25),
([1, 3], 0.25),
([2, 3], 0.25),
]
assert simplex_tree.get_star([0]) == [([0], 0.0), ([0, 1], 0.25),
([0, 2], 0.25)]
assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)]
else:
print("[0, 1] Not found...")
if simplex_tree.find([4]):
print("[4] Found !!")
else:
print("[4] Not found...")
if simplex_tree.insert([0, 1, 2], filtration=4.0):
print("[0, 1, 2] Inserted !!")
else:
print("[0, 1, 2] Not inserted...")
if simplex_tree.insert([0, 1, 4], filtration=4.0):
print("[0, 1, 4] Inserted !!")
else:
print("[0, 1, 4] Not inserted...")
if simplex_tree.find([4]):
print("[4] Found !!")
else:
print("[4] Not found...")
print("dimension=", simplex_tree.dimension())
print("filtrations=", simplex_tree.get_filtration())
print("star([0])=", simplex_tree.get_star([0]))
print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
print("point[0]=", alpha_complex.get_point(0))
print("point[5]=", alpha_complex.get_point(5))