Merge remote-tracking branch 'origin/master' into tomato2

2 files changed, 90 insertions, 0 deletions

diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py
index fce4875c..d0e4e9e8 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -147,3 +147,30 @@ def test_connected_sublevel_sets():
                                  periodic_dimensions = periodic_dimensions)
     assert cub.persistence() == [(0, (2.0, float("inf")))]
     assert cub.betti_numbers() == [1, 0, 0]
+
+def test_cubical_generators():
+    cub = CubicalComplex(top_dimensional_cells = [[0, 0, 0], [0, 1, 0], [0, 0, 0]])
+    cub.persistence()
+    g = cub.cofaces_of_persistence_pairs()
+    assert len(g[0]) == 2
+    assert len(g[1]) == 1
+    assert np.array_equal(g[0][0], np.empty(shape=[0,2]))
+    assert np.array_equal(g[0][1], np.array([[7, 4]]))
+    assert np.array_equal(g[1][0], np.array([8]))
+
+def test_cubical_cofaces_of_persistence_pairs_when_pd_has_no_paired_birth_and_death():
+    cubCpx = CubicalComplex(dimensions=[1,2], top_dimensional_cells=[0.0, 1.0])
+    Diag = cubCpx.persistence(homology_coeff_field=2, min_persistence=0)
+    pairs = cubCpx.cofaces_of_persistence_pairs()
+    assert pairs[0] == []
+    assert np.array_equal(pairs[1][0], np.array([0]))
+
+def test_periodic_cofaces_of_persistence_pairs_when_pd_has_no_paired_birth_and_death():
+    perCubCpx = PeriodicCubicalComplex(dimensions=[1,2], top_dimensional_cells=[0.0, 1.0],
+                                       periodic_dimensions=[True, True])
+    Diag = perCubCpx.persistence(homology_coeff_field=2, min_persistence=0)
+    pairs = perCubCpx.cofaces_of_persistence_pairs()
+    assert pairs[0] == []
+    assert np.array_equal(pairs[1][0], np.array([0]))
+    assert np.array_equal(pairs[1][1], np.array([0, 1]))
+    assert np.array_equal(pairs[1][2], np.array([1]))
diff --git a/src/python/test/test_weighted_rips.py b/src/python/test/test_weighted_rips.py
new file mode 100644
index 00000000..7ef48333
--- /dev/null
+++ b/src/python/test/test_weighted_rips.py
@@ -0,0 +1,63 @@
+""" 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):       Yuichi Ike and Masatoshi Takenouchi
+
+    Copyright (C) 2020 Inria
+
+    Modification(s):
+      - YYYY/MM Author: Description of the modification
+"""
+
+from gudhi.weighted_rips_complex import WeightedRipsComplex
+from gudhi.point_cloud.dtm import DistanceToMeasure
+import numpy as np
+from math import sqrt
+from scipy.spatial.distance import cdist
+import pytest
+
+def test_non_dtm_rips_complex():
+    dist = [[], [1]]
+    weights = [1, 100]
+    w_rips = WeightedRipsComplex(distance_matrix=dist, weights=weights)
+    st = w_rips.create_simplex_tree(max_dimension=2)
+    assert st.filtration([0,1]) == pytest.approx(200.0)
+
+def test_compatibility_with_rips():
+    distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]]
+    w_rips = WeightedRipsComplex(distance_matrix=distance_matrix,max_filtration=42)
+    st = w_rips.create_simplex_tree(max_dimension=1)
+    assert list(st.get_filtration()) == [
+        ([0], 0.0),
+        ([1], 0.0),
+        ([2], 0.0),
+        ([3], 0.0),
+        ([0, 1], 1.0),
+        ([0, 2], 1.0),
+        ([1, 3], 1.0),
+        ([2, 3], 1.0),
+        ([1, 2], sqrt(2)),
+        ([0, 3], sqrt(2)),
+    ]
+
+def test_compatibility_with_filtered_rips():
+    distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]]
+    w_rips = WeightedRipsComplex(distance_matrix=distance_matrix,max_filtration=1.0)
+    st = w_rips.create_simplex_tree(max_dimension=1)
+    
+    assert st.__is_defined() == True
+    assert st.__is_persistence_defined() == False
+
+    assert st.num_simplices() == 8
+    assert st.num_vertices() == 4
+
+def test_dtm_rips_complex():
+    pts = np.array([[2.0, 2.0], [0.0, 1.0], [3.0, 4.0]])
+    dist = cdist(pts,pts)
+    dtm = DistanceToMeasure(2, q=2, metric="precomputed")
+    r = dtm.fit_transform(dist)
+    w_rips = WeightedRipsComplex(distance_matrix=dist, weights=r)
+    st = w_rips.create_simplex_tree(max_dimension=2)
+    st.persistence()
+    persistence_intervals0 = st.persistence_intervals_in_dimension(0)
+    assert persistence_intervals0 == pytest.approx(np.array([[3.16227766, 5.39834564],[3.16227766, 5.39834564], [3.16227766, float("inf")]]))
+