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""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
Author(s): Vincent Rouvreau
Copyright (C) 2016 Inria
Modification(s):
- YYYY/MM Author: Description of the modification
"""
from gudhi import SimplexTree, __GUDHI_USE_EIGEN3
import pytest
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
def test_insertion():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([0, 1]) == True
assert st.dimension() == 1
assert st.insert([0, 1, 2], filtration=4.0) == True
assert st.dimension() == 2
assert st.num_simplices() == 7
assert st.num_vertices() == 3
# find test
assert st.find([0, 1, 2]) == True
assert st.find([0, 1]) == True
assert st.find([0, 2]) == True
assert st.find([0]) == True
assert st.find([1]) == True
assert st.find([2]) == True
assert st.find([3]) == False
assert st.find([0, 3]) == False
assert st.find([1, 3]) == False
assert st.find([2, 3]) == False
# filtration test
assert st.filtration([0, 1, 2]) == 4.0
assert st.filtration([0, 2]) == 4.0
assert st.filtration([1, 2]) == 4.0
assert st.filtration([2]) == 4.0
assert st.filtration([0, 1]) == 0.0
assert st.filtration([0]) == 0.0
assert st.filtration([1]) == 0.0
# skeleton test
assert list(st.get_skeleton(2)) == [
([0, 1, 2], 4.0),
([0, 1], 0.0),
([0, 2], 4.0),
([0], 0.0),
([1, 2], 4.0),
([1], 0.0),
([2], 4.0),
]
assert list(st.get_skeleton(1)) == [
([0, 1], 0.0),
([0, 2], 4.0),
([0], 0.0),
([1, 2], 4.0),
([1], 0.0),
([2], 4.0),
]
assert list(st.get_skeleton(0)) == [([0], 0.0), ([1], 0.0), ([2], 4.0)]
# remove_maximal_simplex test
assert st.get_cofaces([0, 1, 2], 1) == []
st.remove_maximal_simplex([0, 1, 2])
assert list(st.get_skeleton(2)) == [
([0, 1], 0.0),
([0, 2], 4.0),
([0], 0.0),
([1, 2], 4.0),
([1], 0.0),
([2], 4.0),
]
assert st.find([0, 1, 2]) == False
assert st.find([0, 1]) == True
assert st.find([0, 2]) == True
assert st.find([0]) == True
assert st.find([1]) == True
assert st.find([2]) == True
assert st.persistence(persistence_dim_max=True) == [
(1, (4.0, float("inf"))),
(0, (0.0, float("inf"))),
]
assert st.__is_persistence_defined() == True
assert st.betti_numbers() == [1, 1]
assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0]
assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0]
assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0]
assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1]
assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1]
def test_expansion():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([3, 2], 0.1) == True
assert st.insert([2, 0], 0.2) == True
assert st.insert([1, 0], 0.3) == True
assert st.insert([3, 1], 0.4) == True
assert st.insert([2, 1], 0.5) == True
assert st.insert([6, 5], 0.6) == True
assert st.insert([4, 2], 0.7) == True
assert st.insert([3, 0], 0.8) == True
assert st.insert([6, 4], 0.9) == True
assert st.insert([6, 3], 1.0) == True
assert st.num_vertices() == 7
assert st.num_simplices() == 17
assert list(st.get_filtration()) == [
([2], 0.1),
([3], 0.1),
([2, 3], 0.1),
([0], 0.2),
([0, 2], 0.2),
([1], 0.3),
([0, 1], 0.3),
([1, 3], 0.4),
([1, 2], 0.5),
([5], 0.6),
([6], 0.6),
([5, 6], 0.6),
([4], 0.7),
([2, 4], 0.7),
([0, 3], 0.8),
([4, 6], 0.9),
([3, 6], 1.0),
]
st.expansion(3)
assert st.num_vertices() == 7
assert st.num_simplices() == 22
assert list(st.get_filtration()) == [
([2], 0.1),
([3], 0.1),
([2, 3], 0.1),
([0], 0.2),
([0, 2], 0.2),
([1], 0.3),
([0, 1], 0.3),
([1, 3], 0.4),
([1, 2], 0.5),
([0, 1, 2], 0.5),
([1, 2, 3], 0.5),
([5], 0.6),
([6], 0.6),
([5, 6], 0.6),
([4], 0.7),
([2, 4], 0.7),
([0, 3], 0.8),
([0, 1, 3], 0.8),
([0, 2, 3], 0.8),
([0, 1, 2, 3], 0.8),
([4, 6], 0.9),
([3, 6], 1.0),
]
def test_automatic_dimension():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([0, 1, 3], filtration=0.5) == True
assert st.insert([0, 1, 2], filtration=1.0) == True
assert st.num_vertices() == 4
assert st.num_simplices() == 11
assert st.dimension() == 2
assert st.upper_bound_dimension() == 2
assert st.prune_above_filtration(0.6) == True
assert st.dimension() == 2
assert st.upper_bound_dimension() == 2
st.assign_filtration([0, 1, 3], 0.7)
assert st.filtration([0, 1, 3]) == 0.7
st.remove_maximal_simplex([0, 1, 3])
assert st.upper_bound_dimension() == 2
assert st.dimension() == 1
assert st.upper_bound_dimension() == 1
def test_make_filtration_non_decreasing():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# Inserted simplex:
# 1
# o
# /X\
# o---o---o---o
# 2 0 3\X/4
# o
# 5
assert st.insert([2, 1, 0], filtration=2.0) == True
assert st.insert([3, 0], filtration=2.0) == True
assert st.insert([3, 4, 5], filtration=2.0) == True
assert st.make_filtration_non_decreasing() == False
# Because of non decreasing property of simplex tree, { 0 } , { 1 } and
# { 0, 1 } are going to be set from value 2.0 to 1.0
st.insert([0, 1, 6, 7], filtration=1.0)
assert st.make_filtration_non_decreasing() == False
# Modify specific values to test make_filtration_non_decreasing
st.assign_filtration([0, 1, 6, 7], 0.8)
st.assign_filtration([0, 1, 6], 0.9)
st.assign_filtration([0, 6], 0.6)
st.assign_filtration([3, 4, 5], 1.2)
st.assign_filtration([3, 4], 1.1)
st.assign_filtration([4, 5], 1.99)
assert st.make_filtration_non_decreasing() == True
assert st.filtration([0, 1, 6, 7]) == 1.0
assert st.filtration([0, 1, 6]) == 1.0
assert st.filtration([0, 1]) == 1.0
assert st.filtration([0]) == 1.0
assert st.filtration([1]) == 1.0
assert st.filtration([3, 4, 5]) == 2.0
assert st.filtration([3, 4]) == 2.0
assert st.filtration([4, 5]) == 2.0
def test_extend_filtration():
# Inserted simplex:
# 5 4
# o o
# / \ /
# o o
# /2\ /3
# o o
# 1 0
st = SimplexTree()
st.insert([0,2])
st.insert([1,2])
st.insert([0,3])
st.insert([2,5])
st.insert([3,4])
st.insert([3,5])
st.assign_filtration([0], 1.)
st.assign_filtration([1], 2.)
st.assign_filtration([2], 3.)
st.assign_filtration([3], 4.)
st.assign_filtration([4], 5.)
st.assign_filtration([5], 6.)
assert list(st.get_filtration()) == [
([0, 2], 0.0),
([1, 2], 0.0),
([0, 3], 0.0),
([3, 4], 0.0),
([2, 5], 0.0),
([3, 5], 0.0),
([0], 1.0),
([1], 2.0),
([2], 3.0),
([3], 4.0),
([4], 5.0),
([5], 6.0)
]
st.extend_filtration()
assert list(st.get_filtration()) == [
([6], -3.0),
([0], -2.0),
([1], -1.8),
([2], -1.6),
([0, 2], -1.6),
([1, 2], -1.6),
([3], -1.4),
([0, 3], -1.4),
([4], -1.2),
([3, 4], -1.2),
([5], -1.0),
([2, 5], -1.0),
([3, 5], -1.0),
([5, 6], 1.0),
([4, 6], 1.2),
([3, 6], 1.4),
([3, 4, 6], 1.4),
([3, 5, 6], 1.4),
([2, 6], 1.6),
([2, 5, 6], 1.6),
([1, 6], 1.8),
([1, 2, 6], 1.8),
([0, 6], 2.0),
([0, 2, 6], 2.0),
([0, 3, 6], 2.0)
]
dgms = st.extended_persistence(min_persistence=-1.)
assert dgms[0][0][1][0] == pytest.approx(2.)
assert dgms[0][0][1][1] == pytest.approx(3.)
assert dgms[1][0][1][0] == pytest.approx(5.)
assert dgms[1][0][1][1] == pytest.approx(4.)
assert dgms[2][0][1][0] == pytest.approx(1.)
assert dgms[2][0][1][1] == pytest.approx(6.)
assert dgms[3][0][1][0] == pytest.approx(6.)
assert dgms[3][0][1][1] == pytest.approx(1.)
def test_simplices_iterator():
st = SimplexTree()
assert st.insert([0, 1, 2], filtration=4.0) == True
assert st.insert([2, 3, 4], filtration=2.0) == True
for simplex in st.get_simplices():
print("simplex is: ", simplex[0])
assert st.find(simplex[0]) == True
print("filtration is: ", simplex[1])
assert st.filtration(simplex[0]) == simplex[1]
def test_collapse_edges():
st = SimplexTree()
assert st.insert([0, 1], filtration=1.0) == True
assert st.insert([1, 2], filtration=1.0) == True
assert st.insert([2, 3], filtration=1.0) == True
assert st.insert([0, 3], filtration=1.0) == True
assert st.insert([0, 2], filtration=2.0) == True
assert st.insert([1, 3], filtration=2.0) == True
assert st.num_simplices() == 10
if __GUDHI_USE_EIGEN3:
st.collapse_edges()
assert st.num_simplices() == 9
assert st.find([1, 3]) == False
for simplex in st.get_skeleton(0):
assert simplex[1] == 1.
else:
# If no Eigen3, collapse_edges throws an exception
with pytest.raises(RuntimeError):
st.collapse_edges()
def test_reset_filtration():
st = SimplexTree()
assert st.insert([0, 1, 2], 3.) == True
assert st.insert([0, 3], 2.) == True
assert st.insert([3, 4, 5], 3.) == True
assert st.insert([0, 1, 6, 7], 4.) == True
# Guaranteed by construction
for simplex in st.get_simplices():
assert st.filtration(simplex[0]) >= 2.
# dimension until 5 even if simplex tree is of dimension 3 to test the limits
for dimension in range(5, -1, -1):
st.reset_filtration(0., dimension)
for simplex in st.get_skeleton(3):
print(simplex)
if len(simplex[0]) < (dimension) + 1:
assert st.filtration(simplex[0]) >= 2.
else:
assert st.filtration(simplex[0]) == 0.
def test_boundaries_iterator():
st = SimplexTree()
assert st.insert([0, 1, 2, 3], filtration=1.0) == True
assert st.insert([1, 2, 3, 4], filtration=2.0) == True
assert list(st.get_boundaries([1, 2, 3])) == [([1, 2], 1.0), ([1, 3], 1.0), ([2, 3], 1.0)]
assert list(st.get_boundaries([2, 3, 4])) == [([2, 3], 1.0), ([2, 4], 2.0), ([3, 4], 2.0)]
assert list(st.get_boundaries([2])) == []
with pytest.raises(RuntimeError):
list(st.get_boundaries([]))
with pytest.raises(RuntimeError):
list(st.get_boundaries([0, 4])) # (0, 4) does not exist
with pytest.raises(RuntimeError):
list(st.get_boundaries([6])) # (6) does not exist
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