diff options
Diffstat (limited to 'src/python/test/test_simplex_tree.py')
| -rwxr-xr-x | src/python/test/test_simplex_tree.py | 365 |
1 files changed, 225 insertions, 140 deletions
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 54bafed5..2ccbfbf5 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -249,6 +249,7 @@ def test_make_filtration_non_decreasing(): assert st.filtration([3, 4]) == 2.0 assert st.filtration([4, 5]) == 2.0 + def test_extend_filtration(): # Inserted simplex: @@ -257,86 +258,87 @@ def test_extend_filtration(): # / \ / # 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) + # 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], 1.0) + st.assign_filtration([1], 2.0) + st.assign_filtration([2], 3.0) + st.assign_filtration([3], 4.0) + st.assign_filtration([4], 5.0) + st.assign_filtration([5], 6.0) + + 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), + + 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) + ([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.) + dgms = st.extended_persistence(min_persistence=-1.0) assert len(dgms) == 4 # Sort by (death-birth) descending - we are only interested in those with the longest life span for idx in range(4): - dgms[idx] = sorted(dgms[idx], key=lambda x:(-abs(x[1][0]-x[1][1]))) + dgms[idx] = sorted(dgms[idx], key=lambda x: (-abs(x[1][0] - x[1][1]))) + + assert dgms[0][0][1][0] == pytest.approx(2.0) + assert dgms[0][0][1][1] == pytest.approx(3.0) + assert dgms[1][0][1][0] == pytest.approx(5.0) + assert dgms[1][0][1][1] == pytest.approx(4.0) + assert dgms[2][0][1][0] == pytest.approx(1.0) + assert dgms[2][0][1][1] == pytest.approx(6.0) + assert dgms[3][0][1][0] == pytest.approx(6.0) + assert dgms[3][0][1][1] == pytest.approx(1.0) - 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 @@ -346,9 +348,10 @@ def test_simplices_iterator(): 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 @@ -360,31 +363,33 @@ def test_collapse_edges(): st.collapse_edges() assert st.num_simplices() == 9 - assert st.find([0, 2]) == False # [1, 3] would be fine as well + assert st.find([0, 2]) == False # [1, 3] would be fine as well for simplex in st.get_skeleton(0): - assert simplex[1] == 1. + assert simplex[1] == 1.0 + 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 + + assert st.insert([0, 1, 2], 3.0) == True + assert st.insert([0, 3], 2.0) == True + assert st.insert([3, 4, 5], 3.0) == True + assert st.insert([0, 1, 6, 7], 4.0) == True # Guaranteed by construction for simplex in st.get_simplices(): - assert st.filtration(simplex[0]) >= 2. - + assert st.filtration(simplex[0]) >= 2.0 + # 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) + st.reset_filtration(0.0, dimension) for simplex in st.get_skeleton(3): print(simplex) if len(simplex[0]) < (dimension) + 1: - assert st.filtration(simplex[0]) >= 2. + assert st.filtration(simplex[0]) >= 2.0 else: - assert st.filtration(simplex[0]) == 0. + assert st.filtration(simplex[0]) == 0.0 + def test_boundaries_iterator(): st = SimplexTree() @@ -400,16 +405,17 @@ def test_boundaries_iterator(): list(st.get_boundaries([])) with pytest.raises(RuntimeError): - list(st.get_boundaries([0, 4])) # (0, 4) does not exist + list(st.get_boundaries([0, 4])) # (0, 4) does not exist with pytest.raises(RuntimeError): - list(st.get_boundaries([6])) # (6) does not exist + list(st.get_boundaries([6])) # (6) does not exist + def test_persistence_intervals_in_dimension(): # Here is our triangulation of a 2-torus - taken from https://dioscuri-tda.org/Paris_TDA_Tutorial_2021.html # 0-----3-----4-----0 # | \ | \ | \ | \ | - # | \ | \ | \| \ | + # | \ | \ | \| \ | # 1-----8-----7-----1 # | \ | \ | \ | \ | # | \ | \ | \ | \ | @@ -418,50 +424,52 @@ def test_persistence_intervals_in_dimension(): # | \ | \ | \ | \ | # 0-----3-----4-----0 st = SimplexTree() - st.insert([0,1,8]) - st.insert([0,3,8]) - st.insert([3,7,8]) - st.insert([3,4,7]) - st.insert([1,4,7]) - st.insert([0,1,4]) - st.insert([1,2,5]) - st.insert([1,5,8]) - st.insert([5,6,8]) - st.insert([6,7,8]) - st.insert([2,6,7]) - st.insert([1,2,7]) - st.insert([0,2,3]) - st.insert([2,3,5]) - st.insert([3,4,5]) - st.insert([4,5,6]) - st.insert([0,4,6]) - st.insert([0,2,6]) + st.insert([0, 1, 8]) + st.insert([0, 3, 8]) + st.insert([3, 7, 8]) + st.insert([3, 4, 7]) + st.insert([1, 4, 7]) + st.insert([0, 1, 4]) + st.insert([1, 2, 5]) + st.insert([1, 5, 8]) + st.insert([5, 6, 8]) + st.insert([6, 7, 8]) + st.insert([2, 6, 7]) + st.insert([1, 2, 7]) + st.insert([0, 2, 3]) + st.insert([2, 3, 5]) + st.insert([3, 4, 5]) + st.insert([4, 5, 6]) + st.insert([0, 4, 6]) + st.insert([0, 2, 6]) st.compute_persistence(persistence_dim_max=True) - + H0 = st.persistence_intervals_in_dimension(0) - assert np.array_equal(H0, np.array([[ 0., float("inf")]])) + assert np.array_equal(H0, np.array([[0.0, float("inf")]])) H1 = st.persistence_intervals_in_dimension(1) - assert np.array_equal(H1, np.array([[ 0., float("inf")], [ 0., float("inf")]])) + assert np.array_equal(H1, np.array([[0.0, float("inf")], [0.0, float("inf")]])) H2 = st.persistence_intervals_in_dimension(2) - assert np.array_equal(H2, np.array([[ 0., float("inf")]])) + assert np.array_equal(H2, np.array([[0.0, float("inf")]])) # Test empty case assert st.persistence_intervals_in_dimension(3).shape == (0, 2) + def test_equality_operator(): st1 = SimplexTree() st2 = SimplexTree() assert st1 == st2 - st1.insert([1,2,3], 4.) + st1.insert([1, 2, 3], 4.0) assert st1 != st2 - st2.insert([1,2,3], 4.) + st2.insert([1, 2, 3], 4.0) assert st1 == st2 + def test_simplex_tree_deep_copy(): st = SimplexTree() - st.insert([1, 2, 3], 0.) + st.insert([1, 2, 3], 0.0) # compute persistence only on the original st.compute_persistence() @@ -480,14 +488,15 @@ def test_simplex_tree_deep_copy(): for a_splx in a_filt_list: assert a_splx in st_filt_list - + # test double free del st del st_copy + def test_simplex_tree_deep_copy_constructor(): st = SimplexTree() - st.insert([1, 2, 3], 0.) + st.insert([1, 2, 3], 0.0) # compute persistence only on the original st.compute_persistence() @@ -506,56 +515,132 @@ def test_simplex_tree_deep_copy_constructor(): for a_splx in a_filt_list: assert a_splx in st_filt_list - + # test double free del st del st_copy + def test_simplex_tree_constructor_exception(): with pytest.raises(TypeError): - st = SimplexTree(other = "Construction from a string shall raise an exception") + st = SimplexTree(other="Construction from a string shall raise an exception") + + +def test_create_from_array(): + a = np.array([[1, 4, 13, 6], [4, 3, 11, 5], [13, 11, 10, 12], [6, 5, 12, 2]]) + st = SimplexTree.create_from_array(a, max_filtration=5.0) + assert list(st.get_filtration()) == [([0], 1.0), ([3], 2.0), ([1], 3.0), ([0, 1], 4.0), ([1, 3], 5.0)] + + +def test_insert_edges_from_coo_matrix(): + try: + from scipy.sparse import coo_matrix + from scipy.spatial import cKDTree + except ImportError: + print("Skipping, no SciPy") + return + + st = SimplexTree() + st.insert([1, 2, 7], 7) + row = np.array([2, 5, 3]) + col = np.array([1, 4, 6]) + dat = np.array([1, 2, 3]) + edges = coo_matrix((dat, (row, col))) + st.insert_edges_from_coo_matrix(edges) + assert list(st.get_filtration()) == [ + ([1], 1.0), + ([2], 1.0), + ([1, 2], 1.0), + ([4], 2.0), + ([5], 2.0), + ([4, 5], 2.0), + ([3], 3.0), + ([6], 3.0), + ([3, 6], 3.0), + ([7], 7.0), + ([1, 7], 7.0), + ([2, 7], 7.0), + ([1, 2, 7], 7.0), + ] + + pts = np.random.rand(100, 2) + tree = cKDTree(pts) + edges = tree.sparse_distance_matrix(tree, max_distance=0.15, output_type="coo_matrix") + st = SimplexTree() + st.insert_edges_from_coo_matrix(edges) + assert 100 < st.num_simplices() < 1000 + + +def test_insert_batch(): + st = SimplexTree() + # vertices + st.insert_batch(np.array([[6, 1, 5]]), np.array([-5.0, 2.0, -3.0])) + # triangles + st.insert_batch(np.array([[2, 10], [5, 0], [6, 11]]), np.array([4.0, 0.0])) + # edges + st.insert_batch(np.array([[1, 5], [2, 5]]), np.array([1.0, 3.0])) + + assert list(st.get_filtration()) == [ + ([6], -5.0), + ([5], -3.0), + ([0], 0.0), + ([10], 0.0), + ([0, 10], 0.0), + ([11], 0.0), + ([0, 11], 0.0), + ([10, 11], 0.0), + ([0, 10, 11], 0.0), + ([1], 1.0), + ([2], 1.0), + ([1, 2], 1.0), + ([2, 5], 4.0), + ([2, 6], 4.0), + ([5, 6], 4.0), + ([2, 5, 6], 4.0), + ] + def test_expansion_with_blocker(): - st=SimplexTree() - st.insert([0,1],0) - st.insert([0,2],1) - st.insert([0,3],2) - st.insert([1,2],3) - st.insert([1,3],4) - st.insert([2,3],5) - st.insert([2,4],6) - st.insert([3,6],7) - st.insert([4,5],8) - st.insert([4,6],9) - st.insert([5,6],10) - st.insert([6],10) + st = SimplexTree() + st.insert([0, 1], 0) + st.insert([0, 2], 1) + st.insert([0, 3], 2) + st.insert([1, 2], 3) + st.insert([1, 3], 4) + st.insert([2, 3], 5) + st.insert([2, 4], 6) + st.insert([3, 6], 7) + st.insert([4, 5], 8) + st.insert([4, 6], 9) + st.insert([5, 6], 10) + st.insert([6], 10) def blocker(simplex): try: # Block all simplices that contain vertex 6 simplex.index(6) - print(simplex, ' is blocked') + print(simplex, " is blocked") return True except ValueError: - print(simplex, ' is accepted') - st.assign_filtration(simplex, st.filtration(simplex) + 1.) + print(simplex, " is accepted") + st.assign_filtration(simplex, st.filtration(simplex) + 1.0) return False st.expansion_with_blocker(2, blocker) assert st.num_simplices() == 22 assert st.dimension() == 2 - assert st.find([4,5,6]) == False - assert st.filtration([0,1,2]) == 4. - assert st.filtration([0,1,3]) == 5. - assert st.filtration([0,2,3]) == 6. - assert st.filtration([1,2,3]) == 6. + assert st.find([4, 5, 6]) == False + assert st.filtration([0, 1, 2]) == 4.0 + assert st.filtration([0, 1, 3]) == 5.0 + assert st.filtration([0, 2, 3]) == 6.0 + assert st.filtration([1, 2, 3]) == 6.0 st.expansion_with_blocker(3, blocker) assert st.num_simplices() == 23 assert st.dimension() == 3 - assert st.find([4,5,6]) == False - assert st.filtration([0,1,2]) == 4. - assert st.filtration([0,1,3]) == 5. - assert st.filtration([0,2,3]) == 6. - assert st.filtration([1,2,3]) == 6. - assert st.filtration([0,1,2,3]) == 7. + assert st.find([4, 5, 6]) == False + assert st.filtration([0, 1, 2]) == 4.0 + assert st.filtration([0, 1, 3]) == 5.0 + assert st.filtration([0, 2, 3]) == 6.0 + assert st.filtration([1, 2, 3]) == 6.0 + assert st.filtration([0, 1, 2, 3]) == 7.0 |