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-rwxr-xr-xsrc/python/test/test_alpha_complex.py19
-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.py15
-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.py40
-rwxr-xr-xsrc/python/test/test_witness_complex.py4
13 files changed, 117 insertions, 60 deletions
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index 9b27fff2..0d9e9e45 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -1,9 +1,3 @@
-from gudhi import AlphaComplex, SimplexTree
-import math
-import numpy as np
-import itertools
-import pytest
-
""" 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
@@ -14,6 +8,17 @@ import pytest
- 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"
@@ -114,6 +119,6 @@ def test_safe_alpha_persistence_comparison():
diag1 = simplex_tree1.persistence()
diag2 = simplex_tree2.persistence()
- for (first_p, second_p) in itertools.zip_longest(diag1, diag2):
+ 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
index 4ff65f98..dba7f952 100755
--- a/src/python/test/test_representations.py
+++ b/src/python/test/test_representations.py
@@ -1,11 +1,12 @@
import os
import sys
import matplotlib.pyplot as plt
-# 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
-# pytest is unhappy if there are 0 tests
-def test_nothing():
+
+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
index a6bf9901..43dda77e 100755
--- a/src/python/test/test_wasserstein_distance.py
+++ b/src/python/test/test_wasserstein_distance.py
@@ -1,6 +1,3 @@
-from gudhi.wasserstein import wasserstein_distance
-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): Theo Lacombe
@@ -11,6 +8,9 @@ import numpy as np
- 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"
@@ -23,26 +23,26 @@ def test_basic_wasserstein():
diag4 = np.array([[0, 3], [4, 8]])
emptydiag = np.array([[]])
- assert wasserstein_distance(emptydiag, emptydiag, q=2., p=1.) == 0.
- assert wasserstein_distance(emptydiag, emptydiag, q=np.inf, p=1.) == 0.
- assert wasserstein_distance(emptydiag, emptydiag, q=np.inf, p=2.) == 0.
- assert wasserstein_distance(emptydiag, emptydiag, q=2., p=2.) == 0.
+ 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, q=np.inf, p=1.) == 2.
- assert wasserstein_distance(diag3, emptydiag, q=1., p=1.) == 4.
+ 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, q=1., p=2.) == 5. # thank you Pythagorician triplets
- assert wasserstein_distance(diag4, emptydiag, q=np.inf, p=2.) == 2.5
- assert wasserstein_distance(diag4, emptydiag, q=2., p=2.) == 3.5355339059327378
+ 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, q=2., p=1.) == 1.4453593023967701
- assert wasserstein_distance(diag1, diag2, q=2.35, p=1.74) == 0.9772734057168739
+ 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, q=2.35, p=1.7863) == 3.141592214572228
+ assert wasserstein_distance(diag1, emptydiag, internal_p=2.35, order=1.7863) == 3.141592214572228
- assert wasserstein_distance(diag3, diag4, q=1., p=1.) == 3.
- assert wasserstein_distance(diag3, diag4, q=np.inf, p=1.) == 3. # no diag matching here
- assert wasserstein_distance(diag3, diag4, q=np.inf, p=2.) == np.sqrt(5)
- assert wasserstein_distance(diag3, diag4, q=1., p=2.) == np.sqrt(5)
- assert wasserstein_distance(diag3, diag4, q=4.5, p=2.) == np.sqrt(5)
+ 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 2024-07-02 15:19:59 +0000