def test_reduction(triangle):
X, f = triangle
e = Extended(X, f)
bm, _ = e._up_down_boundary_matrix(X, f)
pairs = e._compute_persistence_pairs(bm)
assert pairs == [(0, 7), (1, 2), (3, 4), (5, 6), (8, 9), (10, 11),
(12, 13)]
def test_from_nx_map(self):
g = nx.tutte_graph()
vals = {n: np.random.random() for n in g.nodes}
e = Extended.from_nx(g, vals)
assert len(e.simplices) == len(g.nodes) + len(g.edges)
assert set(vals.values()) == set(e.f.values())
def test_from_nx_weights(self):
g = nx.tutte_graph()
vals = {n: np.random.random() for n in g.nodes}
nx.set_node_attributes(g, vals, "weight_str")
e = Extended.from_nx(g, "weight_str")
assert len(e.simplices) == len(g.nodes) + len(g.edges)
assert set(vals.values()) == set(e.f.values())
def test_lower_boundary_matrix(triangle):
X, f = triangle
bm, _ = Extended(X, f)._up_down_boundary_matrix(X, f)
assert bm == [ # this was manually computed by @sauln
(0, []), (0, []), (1, [0, 1]), (0, []), (1, [1, 3]), (1, [0, 3]),
(2, [2, 4, 5]), (1, [3]), (1, [1]), (2, [4, 7, 8]), (1, [0]),
(2, [2, 8, 10]), (2, [5, 7, 10]), (3, [6, 9, 11, 12])
]
def test_from_kmapper_mapping_nodes(self):
km = kmapper.KeplerMapper()
np.random.seed(0)
data = np.random.random((300, 5))
lens = km.project(data)
graph = km.map(lens, data)
f = {k: np.random.random() for k in graph['nodes']}
e = Extended.from_kmapper(graph, f)
assert len(f) == len(e.f)
assert set(e.f.values()) == set(f.values())
def test_from_kmapper_mapping_lens(self):
km = kmapper.KeplerMapper()
np.random.seed(0)
data = np.random.random((300, 5))
lens = km.project(data)
graph = km.map(lens, data)
e = Extended.from_kmapper(graph, lens)
assert len(graph['nodes']) == len(e.f)
assert set(e.f.values()) == set(
np.mean(lens[v]) for v in graph['nodes'].values())
def test_from_kmapper_simplices(self):
km = kmapper.KeplerMapper()
data = np.random.random((300, 5))
lens = km.project(data)
graph = km.map(lens, data)
e = Extended.from_kmapper(graph, lens)
vs = [s for s in e.simplices if len(s) == 1]
ls = [s for s in e.simplices if len(s) == 2]
assert len(vs) == len(graph['nodes'])
assert len(ls) == sum(len(v) for v in graph['links'].values())
assert len(e.simplices) == len(graph['simplices'])
def test_reeb_known(reeb):
X, f, expected = reeb
diagrams = Extended(X, f).diagrams()
assert expected == diagrams