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-rwxr-xr-xsrc/python/test/test_alpha_complex.py38
-rwxr-xr-xsrc/python/test/test_bottleneck_distance.py4
-rwxr-xr-xsrc/python/test/test_cover_complex.py4
-rwxr-xr-xsrc/python/test/test_cubical_complex.py63
-rwxr-xr-xsrc/python/test/test_euclidean_witness_complex.py4
-rwxr-xr-xsrc/python/test/test_reader_utils.py6
-rwxr-xr-xsrc/python/test/test_representations.py12
-rwxr-xr-xsrc/python/test/test_rips_complex.py6
-rwxr-xr-xsrc/python/test/test_simplex_tree.py4
-rwxr-xr-xsrc/python/test/test_subsampling.py4
-rwxr-xr-xsrc/python/test/test_tangential_complex.py4
-rwxr-xr-xsrc/python/test/test_wasserstein_distance.py48
-rwxr-xr-xsrc/python/test/test_witness_complex.py4
13 files changed, 173 insertions, 28 deletions
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index 24f8bf53..0d9e9e45 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -1,5 +1,3 @@
-from gudhi import AlphaComplex, SimplexTree
-
""" 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
@@ -10,6 +8,17 @@ from gudhi import AlphaComplex, SimplexTree
- YYYY/MM Author: Description of the modification
"""
+from gudhi import AlphaComplex, SimplexTree
+import math
+import numpy as np
+import pytest
+try:
+ # python3
+ from itertools import zip_longest
+except ImportError:
+ # python2
+ from itertools import izip_longest as zip_longest
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
@@ -88,3 +97,28 @@ def test_filtered_alpha():
]
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 test_safe_alpha_persistence_comparison():
+ #generate periodic signal
+ time = np.arange(0, 10, 1)
+ signal = [math.sin(x) for x in time]
+ delta = math.pi
+ delayed = [math.sin(x + delta) for x in time]
+
+ #construct embedding
+ embedding1 = [[signal[i], -signal[i]] for i in range(len(time))]
+ embedding2 = [[signal[i], delayed[i]] for i in range(len(time))]
+
+ #build alpha complex and simplex tree
+ alpha_complex1 = AlphaComplex(points=embedding1)
+ simplex_tree1 = alpha_complex1.create_simplex_tree()
+
+ alpha_complex2 = AlphaComplex(points=embedding2)
+ simplex_tree2 = alpha_complex2.create_simplex_tree()
+
+ diag1 = simplex_tree1.persistence()
+ diag2 = simplex_tree2.persistence()
+
+ for (first_p, second_p) in zip_longest(diag1, diag2):
+ assert first_p[0] == pytest.approx(second_p[0])
+ assert first_p[1] == pytest.approx(second_p[1])
diff --git a/src/python/test/test_bottleneck_distance.py b/src/python/test/test_bottleneck_distance.py
index f5f019b9..70b2abad 100755
--- a/src/python/test/test_bottleneck_distance.py
+++ b/src/python/test/test_bottleneck_distance.py
@@ -1,5 +1,3 @@
-import gudhi
-
""" 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
@@ -10,6 +8,8 @@ import gudhi
- YYYY/MM Author: Description of the modification
"""
+import gudhi
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
diff --git a/src/python/test/test_cover_complex.py b/src/python/test/test_cover_complex.py
index 8cd12272..32bc5a26 100755
--- a/src/python/test/test_cover_complex.py
+++ b/src/python/test/test_cover_complex.py
@@ -1,5 +1,3 @@
-from gudhi import CoverComplex
-
""" 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
@@ -10,6 +8,8 @@ from gudhi import CoverComplex
- YYYY/MM Author: Description of the modification
"""
+from gudhi import CoverComplex
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2018 Inria"
__license__ = "MIT"
diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py
index 68f54fbe..8c1b2600 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -1,5 +1,3 @@
-from gudhi import CubicalComplex
-
""" 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
@@ -10,6 +8,9 @@ from gudhi import CubicalComplex
- YYYY/MM Author: Description of the modification
"""
+from gudhi import CubicalComplex, PeriodicCubicalComplex
+import numpy as np
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
@@ -56,7 +57,7 @@ def test_dimension_or_perseus_file_constructor():
assert cub.__is_persistence_defined() == False
-def test_dimension_simple_constructor():
+def simple_constructor(cub):
cub = CubicalComplex(
dimensions=[3, 3], top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9]
)
@@ -67,12 +68,22 @@ def test_dimension_simple_constructor():
assert cub.betti_numbers() == [1, 0, 0]
assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0]
-
-def test_user_case_simple_constructor():
+def test_simple_constructor_from_top_cells():
cub = CubicalComplex(
dimensions=[3, 3],
- top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+ top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
)
+ simple_constructor(cub)
+
+def test_simple_constructor_from_numpy_array():
+ cub = CubicalComplex(
+ top_dimensional_cells=np.array([[1, 2, 3],
+ [4, 5, 6],
+ [7, 8, 9]])
+ )
+ simple_constructor(cub)
+
+def user_case_simple_constructor(cub):
assert cub.__is_defined() == True
assert cub.__is_persistence_defined() == False
assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
@@ -83,6 +94,20 @@ def test_user_case_simple_constructor():
)
assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
+def test_user_case_simple_constructor_from_top_cells():
+ cub = CubicalComplex(
+ dimensions=[3, 3],
+ top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+ )
+ user_case_simple_constructor(cub)
+
+def test_user_case_simple_constructor_from_numpy_array():
+ cub = CubicalComplex(
+ top_dimensional_cells=np.array([[float("inf"), 0.0, 0.0],
+ [0.0, 1.0, 0.0],
+ [0.0, 0.0, 0.0]])
+ )
+ user_case_simple_constructor(cub)
def test_dimension_file_constructor():
# Create test file
@@ -96,3 +121,29 @@ def test_dimension_file_constructor():
assert cub.__is_persistence_defined() == True
assert cub.betti_numbers() == [1, 0, 0]
assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]
+
+def test_connected_sublevel_sets():
+ array_cells = np.array([[3, 3], [2, 2], [4, 4]])
+ linear_cells = [3, 3, 2, 2, 4, 4]
+ dimensions = [2, 3]
+ periodic_dimensions = [False, False]
+ # with a numpy array version
+ cub = CubicalComplex(top_dimensional_cells = array_cells)
+ assert cub.persistence() == [(0, (2.0, float("inf")))]
+ assert cub.betti_numbers() == [1, 0, 0]
+ # with vector of dimensions
+ cub = CubicalComplex(dimensions = dimensions,
+ top_dimensional_cells = linear_cells)
+ assert cub.persistence() == [(0, (2.0, float("inf")))]
+ assert cub.betti_numbers() == [1, 0, 0]
+ # periodic with a numpy array version
+ cub = PeriodicCubicalComplex(top_dimensional_cells = array_cells,
+ periodic_dimensions = periodic_dimensions)
+ assert cub.persistence() == [(0, (2.0, float("inf")))]
+ assert cub.betti_numbers() == [1, 0, 0]
+ # periodic with vector of dimensions
+ cub = PeriodicCubicalComplex(dimensions = dimensions,
+ top_dimensional_cells = linear_cells,
+ periodic_dimensions = periodic_dimensions)
+ assert cub.persistence() == [(0, (2.0, float("inf")))]
+ assert cub.betti_numbers() == [1, 0, 0]
diff --git a/src/python/test/test_euclidean_witness_complex.py b/src/python/test/test_euclidean_witness_complex.py
index f5eae5fa..c18d2484 100755
--- a/src/python/test/test_euclidean_witness_complex.py
+++ b/src/python/test/test_euclidean_witness_complex.py
@@ -1,5 +1,3 @@
-import gudhi
-
""" 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
@@ -10,6 +8,8 @@ import gudhi
- YYYY/MM Author: Description of the modification
"""
+import gudhi
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
diff --git a/src/python/test/test_reader_utils.py b/src/python/test/test_reader_utils.py
index 4c7b32c2..90da6651 100755
--- a/src/python/test/test_reader_utils.py
+++ b/src/python/test/test_reader_utils.py
@@ -1,6 +1,3 @@
-import gudhi
-import numpy as np
-
""" 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
@@ -11,6 +8,9 @@ import numpy as np
- YYYY/MM Author: Description of the modification
"""
+import gudhi
+import numpy as np
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2017 Inria"
__license__ = "MIT"
diff --git a/src/python/test/test_representations.py b/src/python/test/test_representations.py
new file mode 100755
index 00000000..dba7f952
--- /dev/null
+++ b/src/python/test/test_representations.py
@@ -0,0 +1,12 @@
+import os
+import sys
+import matplotlib.pyplot as plt
+
+def test_representations_examples():
+ # Disable graphics for testing purposes
+ plt.show = lambda:None
+ here = os.path.dirname(os.path.realpath(__file__))
+ sys.path.append(here + "/../example")
+ import diagram_vectorizations_distances_kernels
+
+ return None
diff --git a/src/python/test/test_rips_complex.py b/src/python/test/test_rips_complex.py
index d55ae22f..b02a68e1 100755
--- a/src/python/test/test_rips_complex.py
+++ b/src/python/test/test_rips_complex.py
@@ -1,6 +1,3 @@
-from gudhi import RipsComplex
-from math import sqrt
-
""" 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
@@ -11,6 +8,9 @@ from math import sqrt
- YYYY/MM Author: Description of the modification
"""
+from gudhi import RipsComplex
+from math import sqrt
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 8d8971c1..1822c43b 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -1,5 +1,3 @@
-from gudhi import SimplexTree
-
""" 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
@@ -10,6 +8,8 @@ from gudhi import SimplexTree
- YYYY/MM Author: Description of the modification
"""
+from gudhi import SimplexTree
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py
index c816e203..fe0985fa 100755
--- a/src/python/test/test_subsampling.py
+++ b/src/python/test/test_subsampling.py
@@ -1,5 +1,3 @@
-import gudhi
-
""" 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
@@ -10,6 +8,8 @@ import gudhi
- YYYY/MM Author: Description of the modification
"""
+import gudhi
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
diff --git a/src/python/test/test_tangential_complex.py b/src/python/test/test_tangential_complex.py
index 0f828d8e..e650e99c 100755
--- a/src/python/test/test_tangential_complex.py
+++ b/src/python/test/test_tangential_complex.py
@@ -1,5 +1,3 @@
-from gudhi import TangentialComplex, SimplexTree
-
""" 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
@@ -10,6 +8,8 @@ from gudhi import TangentialComplex, SimplexTree
- YYYY/MM Author: Description of the modification
"""
+from gudhi import TangentialComplex, SimplexTree
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
diff --git a/src/python/test/test_wasserstein_distance.py b/src/python/test/test_wasserstein_distance.py
new file mode 100755
index 00000000..43dda77e
--- /dev/null
+++ b/src/python/test/test_wasserstein_distance.py
@@ -0,0 +1,48 @@
+""" 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): Theo Lacombe
+
+ Copyright (C) 2019 Inria
+
+ Modification(s):
+ - YYYY/MM Author: Description of the modification
+"""
+
+from gudhi.wasserstein import wasserstein_distance
+import numpy as np
+
+__author__ = "Theo Lacombe"
+__copyright__ = "Copyright (C) 2019 Inria"
+__license__ = "MIT"
+
+
+def test_basic_wasserstein():
+ diag1 = np.array([[2.7, 3.7], [9.6, 14.0], [34.2, 34.974]])
+ diag2 = np.array([[2.8, 4.45], [9.5, 14.1]])
+ diag3 = np.array([[0, 2], [4, 6]])
+ diag4 = np.array([[0, 3], [4, 8]])
+ emptydiag = np.array([[]])
+
+ assert wasserstein_distance(emptydiag, emptydiag, internal_p=2., order=1.) == 0.
+ assert wasserstein_distance(emptydiag, emptydiag, internal_p=np.inf, order=1.) == 0.
+ assert wasserstein_distance(emptydiag, emptydiag, internal_p=np.inf, order=2.) == 0.
+ assert wasserstein_distance(emptydiag, emptydiag, internal_p=2., order=2.) == 0.
+
+ assert wasserstein_distance(diag3, emptydiag, internal_p=np.inf, order=1.) == 2.
+ assert wasserstein_distance(diag3, emptydiag, internal_p=1., order=1.) == 4.
+
+ assert wasserstein_distance(diag4, emptydiag, internal_p=1., order=2.) == 5. # thank you Pythagorician triplets
+ assert wasserstein_distance(diag4, emptydiag, internal_p=np.inf, order=2.) == 2.5
+ assert wasserstein_distance(diag4, emptydiag, internal_p=2., order=2.) == 3.5355339059327378
+
+ assert wasserstein_distance(diag1, diag2, internal_p=2., order=1.) == 1.4453593023967701
+ assert wasserstein_distance(diag1, diag2, internal_p=2.35, order=1.74) == 0.9772734057168739
+
+ assert wasserstein_distance(diag1, emptydiag, internal_p=2.35, order=1.7863) == 3.141592214572228
+
+ assert wasserstein_distance(diag3, diag4, internal_p=1., order=1.) == 3.
+ assert wasserstein_distance(diag3, diag4, internal_p=np.inf, order=1.) == 3. # no diag matching here
+ assert wasserstein_distance(diag3, diag4, internal_p=np.inf, order=2.) == np.sqrt(5)
+ assert wasserstein_distance(diag3, diag4, internal_p=1., order=2.) == np.sqrt(5)
+ assert wasserstein_distance(diag3, diag4, internal_p=4.5, order=2.) == np.sqrt(5)
+
diff --git a/src/python/test/test_witness_complex.py b/src/python/test/test_witness_complex.py
index 36ced635..7baf18c9 100755
--- a/src/python/test/test_witness_complex.py
+++ b/src/python/test/test_witness_complex.py
@@ -1,5 +1,3 @@
-from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree
-
""" 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
@@ -10,6 +8,8 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree
- YYYY/MM Author: Description of the modification
"""
+from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree
+
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-29 01:01:41 +0000