def test_delinearize_vertex_weights(self):
g = hg.get_4_adjacency_graph((4, 5))
r = hg.delinearize_vertex_weights(np.ones((20, )), g, (4, 5))
self.assertTrue(r.shape == (4, 5))
r = hg.delinearize_vertex_weights(np.ones((4, 5)), g, (4, 5))
self.assertTrue(r.shape == (4, 5))
r = hg.delinearize_vertex_weights(np.ones((4, 5, 10, 12)), g, (4, 5))
self.assertTrue(r.shape == (4, 5, 10, 12))
r = hg.delinearize_vertex_weights(np.ones((20, 4, 5, 2, 3)), g, (4, 5))
self.assertTrue(r.shape == (4, 5, 4, 5, 2, 3))
with self.assertRaises(ValueError):
hg.delinearize_vertex_weights(np.ones((5, 4)), g, (4, 5))
with self.assertRaises(ValueError):
hg.delinearize_vertex_weights(np.ones((25, )), g, (4, 5))
shape = (1, 4)
g = hg.get_4_adjacency_graph(shape)
r = hg.delinearize_vertex_weights(np.ones((4, )), g)
self.assertTrue(r.shape == shape)
r = hg.delinearize_vertex_weights(np.ones(shape), g)
self.assertTrue(r.shape == shape)
r = hg.delinearize_vertex_weights(np.ones((1, 4, 10, 12)), g)
self.assertTrue(r.shape == (1, 4, 10, 12))
r = hg.delinearize_vertex_weights(np.ones((4, 5, 2, 3)), g)
self.assertTrue(r.shape == (1, 4, 5, 2, 3))
with self.assertRaises(ValueError):
hg.delinearize_vertex_weights(np.ones((5, 4)), g)
with self.assertRaises(ValueError):
hg.delinearize_vertex_weights(np.ones((8, )), g)
shape = (4, 1)
g = hg.get_4_adjacency_graph(shape)
r = hg.delinearize_vertex_weights(np.ones((4, )), g)
self.assertTrue(r.shape == shape)
r = hg.delinearize_vertex_weights(np.ones(shape), g)
self.assertTrue(r.shape == shape)
r = hg.delinearize_vertex_weights(np.ones((4, 1, 10, 12)), g)
self.assertTrue(r.shape == (4, 1, 10, 12))
r = hg.delinearize_vertex_weights(np.ones((4, 5, 2, 3)), g)
self.assertTrue(r.shape == (4, 1, 5, 2, 3))
with self.assertRaises(ValueError):
hg.delinearize_vertex_weights(np.ones((5, 4)), g)
with self.assertRaises(ValueError):
hg.delinearize_vertex_weights(np.ones((8, )), g)
def test_assess_fragmentation_curve_BCE_optimal_cut_on_rag(self):
vertex_map = np.asarray((0, 0, 1, 1, 2, 2, 3, 4), dtype=np.int64)
g = hg.get_4_adjacency_graph((1, 8))
hg.CptRegionAdjacencyGraph.link(g, None, vertex_map, np.ones((7, )))
t = hg.Tree((6, 6, 5, 5, 7, 7, 8, 8, 8))
hg.CptHierarchy.link(t, g)
ground_truth = np.asarray((0, 0, 1, 1, 1, 2, 2, 2), dtype=np.int32)
assesser = hg.make_assesser_fragmentation_optimal_cut(
t, ground_truth, hg.OptimalCutMeasure.BCE)
self.assertTrue(assesser.optimal_number_of_regions() == 3)
self.assertTrue(
np.isclose(assesser.optimal_score(),
(2 + 4.0 / 3 + 2.5) / t.num_leaves()))
res = assesser.fragmentation_curve()
res_k = res.num_regions()
res_scores = res.scores()
ref_scores = np.asarray((2.75, 4.5, 2 + 4.0 / 3 + 2.5, 2 + 4.0 / 3 + 2,
2 + 4.0 / 3 + 4.0 / 3))
ref_k = np.asarray((1, 2, 3, 4, 5), dtype=np.int32)
self.assertTrue(np.allclose(res_scores, (ref_scores / t.num_leaves())))
self.assertTrue(np.all(res_k == ref_k))
def test_graph_4_adjacency_2_khalimsky(self):
g = hg.get_4_adjacency_graph((2, 3))
data = np.asarray((1, 0, 2, 1, 1, 1, 2))
ref = np.asarray(((0, 1, 0, 2, 0), (0, 1, 1, 2, 1), (0, 1, 0, 2, 0)))
r = hg.graph_4_adjacency_2_khalimsky(g, data)
self.assertTrue(np.allclose(ref, r))
def test_hierarchy_alignement(self):
g = hg.get_4_adjacency_graph((3, 3))
fine_labels = np.asarray((0, 1, 2, 3, 4, 2, 3, 4, 2), dtype=np.int32)
aligner = hg.HierarchyAligner.from_labelisation(g, fine_labels)
t = hg.Tree(np.asarray((9, 10, 10, 9, 11, 11, 9, 11, 11, 13, 12, 12, 13, 13), dtype=np.int64))
altitudes = np.asarray((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2), dtype=np.int32)
sm = aligner.align_hierarchy(t, altitudes)
sm_k = hg.graph_4_adjacency_2_khalimsky(g, sm, (3, 3))
sm_coarse = np.asarray((2, 0, 0, 1, 1, 2, 0, 0, 0, 0, 2, 0), dtype=np.int32)
sm2 = aligner.align_hierarchy(g, sm_coarse)
sm2_k = hg.graph_4_adjacency_2_khalimsky(g, sm2, (3, 3))
sm_k_ref = np.asarray(((0, 2, 0, 1, 0),
(0, 2, 1, 1, 0),
(0, 2, 0, 0, 0),
(0, 2, 0, 0, 0),
(0, 2, 0, 0, 0)), dtype=np.int32)
self.assertTrue(np.all(sm_k == sm_k_ref))
self.assertTrue(np.all(sm2_k == sm_k_ref))
def test_vertex_perimeter2(self):
g = hg.get_4_adjacency_graph((2, 3))
hg.set_attribute(g, "no_border_vertex_out_degree", None)
ref = np.asarray(((2, 3, 2),
(2, 3, 2)))
res = hg.attribute_vertex_perimeter(g)
self.assertTrue(np.allclose(ref, res))
def test_weighting_graph(self):
g = hg.get_4_adjacency_graph((2, 2))
data = np.asarray((0, 1, 2, 3))
ref = (0.5, 1, 2, 2.5)
r = hg.weight_graph(g, data, hg.WeightFunction.mean)
self.assertTrue(np.allclose(ref, r))
ref = (0, 0, 1, 2)
r = hg.weight_graph(g, data, hg.WeightFunction.min)
self.assertTrue(np.allclose(ref, r))
ref = (1, 2, 3, 3)
r = hg.weight_graph(g, data, hg.WeightFunction.max)
self.assertTrue(np.allclose(ref, r))
ref = (1, 2, 2, 1)
r = hg.weight_graph(g, data, hg.WeightFunction.L1)
self.assertTrue(np.allclose(ref, r))
ref = (math.sqrt(1), 2, 2, math.sqrt(1))
r = hg.weight_graph(g, data, hg.WeightFunction.L2)
self.assertTrue(np.allclose(ref, r))
ref = (1, 2, 2, 1)
r = hg.weight_graph(g, data, hg.WeightFunction.L_infinity)
self.assertTrue(np.allclose(ref, r))
ref = (1, 4, 4, 1)
r = hg.weight_graph(g, data, hg.WeightFunction.L2_squared)
self.assertTrue(np.allclose(ref, r))
def test_watershed_hierarchy_by_minima_ordering(self):
g = hg.get_4_adjacency_graph((1, 7))
edge_weights = np.asarray((1, 4, 1, 0, 10, 8))
# same as dynamics
minima_ranking = np.asarray((2, 2, 0, 3, 3, 1, 1), dtype=np.uint64)
minima_altitudes = np.asarray((0, 2, 3, 10), dtype=np.float64)
t, altitudes = hg.watershed_hierarchy_by_minima_ordering(
g, edge_weights, minima_ranking, minima_altitudes)
ref_parents = np.asarray((7, 7, 8, 8, 8, 9, 9, 11, 10, 10, 11, 11))
ref_tree = hg.Tree(ref_parents)
ref_altitudes = np.asarray((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 3))
self.assertTrue(hg.CptHierarchy.validate(t))
self.assertTrue(hg.test_tree_isomorphism(t, ref_tree))
self.assertTrue(np.allclose(altitudes, ref_altitudes))
# binary watershed hierarchy
t, altitudes = hg.watershed_hierarchy_by_minima_ordering(
g,
edge_weights,
minima_ranking,
minima_altitudes=None,
canonize_tree=False)
ref_parents = np.asarray(
(8, 8, 9, 7, 7, 10, 10, 9, 12, 11, 11, 12, 12))
ref_tree = hg.Tree(ref_parents)
ref_altitudes = np.asarray((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2))
self.assertTrue(hg.CptBinaryHierarchy.validate(t))
self.assertTrue(hg.test_tree_isomorphism(t, ref_tree))
self.assertTrue(np.allclose(altitudes, ref_altitudes))
def test_binary_partition_tree_exponential_linkage_equiv(self):
np.random.seed(10)
g = hg.get_4_adjacency_graph((10, 10))
edge_weights = np.random.rand(g.num_edges())
edge_weight_weights = np.random.randint(1, 10, g.num_edges())
tree, altitudes = hg.binary_partition_tree_exponential_linkage(
g, edge_weights, 0, edge_weight_weights)
t_ref, alt_ref = hg.binary_partition_tree_average_linkage(
g, edge_weights, edge_weight_weights)
self.assertTrue(np.all(tree.parents() == t_ref.parents()))
self.assertTrue(np.allclose(altitudes, alt_ref))
tree, altitudes = hg.binary_partition_tree_exponential_linkage(
g, edge_weights, float('inf'), edge_weight_weights)
t_ref, alt_ref = hg.binary_partition_tree_complete_linkage(
g, edge_weights)
self.assertTrue(np.all(tree.parents() == t_ref.parents()))
self.assertTrue(np.allclose(altitudes, alt_ref))
tree, altitudes = hg.binary_partition_tree_exponential_linkage(
g, edge_weights, float('-inf'), edge_weight_weights)
t_ref, alt_ref = hg.binary_partition_tree_single_linkage(
g, edge_weights)
self.assertTrue(np.all(tree.parents() == t_ref.parents()))
self.assertTrue(np.allclose(altitudes, alt_ref))
def test_labelisation_horizontal_cut_num_regions(self):
g = hg.get_4_adjacency_graph((1, 11))
tree = hg.Tree((11, 11, 11, 12, 12, 16, 13, 13, 13, 14, 14, 17, 16, 15,
15, 18, 17, 18, 18))
hg.CptHierarchy.link(tree, g)
altitudes = np.asarray(
(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 3, 1, 2, 3))
ref_labels = (np.asarray((1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)),
np.asarray((1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3)),
np.asarray((0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3)),
np.asarray((0, 1, 2, 3, 4, 5, 6, 6, 6, 7, 8)))
k_cuts = (1, 3, 4, 9)
for i in range(4):
labels = hg.labelisation_horizontal_cut_from_num_regions(
tree, altitudes, k_cuts[i])
self.assertTrue(hg.is_in_bijection(labels, ref_labels[i]))
# cuts with at least the given number of regions
k_cuts = (1, 2, 4, 5)
for i in range(4):
labels = hg.labelisation_horizontal_cut_from_num_regions(
tree, altitudes, k_cuts[i])
self.assertTrue(hg.is_in_bijection(labels, ref_labels[i]))
# cuts with at most the given number of regions
k_cuts = (2, 3, 8, 20)
for i in range(4):
labels = hg.labelisation_horizontal_cut_from_num_regions(
tree, altitudes, k_cuts[i], "at_most")
self.assertTrue(hg.is_in_bijection(labels, ref_labels[i]))
def test_bpt_canonical_vectorial(self):
graph = hg.get_4_adjacency_graph((2, 3))
edge_weights = np.asarray(
((1, 0, 2, 1, 1, 1, 2), (0, 2, 0, 0, 1, 1, 0), (0, 5, 5, 1, 0, 1,
1))).T
sorted_edge_indices = np.asarray((1, 0, 3, 4, 5, 6, 2))
ref_parents = np.asarray((6, 7, 9, 6, 8, 9, 7, 8, 10, 10, 10))
ref_mst_edge_map = np.asarray((1, 0, 3, 4, 6))
ref_altitudes = np.asarray(((0, 0, 0, 0, 0, 0, 0, 1, 1, 1,
2), (0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0),
(0, 0, 0, 0, 0, 0, 5, 0, 1, 0, 1))).T
ref_altitudes_no_weights = np.asarray(
(0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 5))
tree, altitudes = hg.bpt_canonical(graph, edge_weights)
self.assertTrue(np.all(tree.parents() == ref_parents))
self.assertTrue(np.all(altitudes == ref_altitudes))
self.assertTrue(np.all(tree.mst_edge_map == ref_mst_edge_map))
tree, altitudes = hg.bpt_canonical(graph, edge_weights,
sorted_edge_indices)
self.assertTrue(np.all(tree.parents() == ref_parents))
self.assertTrue(np.all(altitudes == ref_altitudes))
self.assertTrue(np.all(tree.mst_edge_map == ref_mst_edge_map))
tree, altitudes = hg.bpt_canonical(
graph, sorted_edge_indices=sorted_edge_indices)
self.assertTrue(np.all(tree.parents() == ref_parents))
self.assertTrue(np.all(altitudes == ref_altitudes_no_weights))
self.assertTrue(np.all(tree.mst_edge_map == ref_mst_edge_map))
def test_seeded_watershed(self):
g = hg.get_4_adjacency_graph((4, 4))
edge_weights = np.asarray((1, 2, 5, 5, 4, 8, 1, 4, 3, 4, 4, 1, 5, 2, 6,
2, 5, 2, 0, 7, 0, 3, 4, 0))
seeds = np.asarray(
((1, 1, 0, 0), (1, 0, 0, 0), (0, 0, 0, 0), (1, 1, 2, 2)))
labels = hg.labelisation_seeded_watershed(g, edge_weights, seeds)
expected = np.asarray(
((1, 1, 2, 2), (1, 1, 2, 2), (1, 1, 2, 2), (1, 1, 2, 2)))
self.assertTrue(np.all(labels == expected))
seeds = np.asarray(
((1, 1, 9, 9), (1, 9, 9, 9), (9, 9, 9, 9), (2, 2, 3, 3)))
labels = hg.labelisation_seeded_watershed(g,
edge_weights,
seeds,
background_label=9)
expected = np.asarray(
((1, 1, 3, 3), (1, 1, 3, 3), (2, 2, 3, 3), (2, 2, 3, 3)))
self.assertTrue(np.all(labels == expected))
def test_contour_accumulator_partition_tree(self):
graph = hg.get_4_adjacency_graph((3, 3))
tree = hg.Tree(
(9, 9, 10, 11, 11, 13, 12, 12, 13, 10, 14, 14, 15, 14, 15, 15))
hg.CptHierarchy.link(tree, graph)
node_saliency = np.asarray(
(0, 0, 0, 0, 0, 0, 20, 0, 0, 5, 2, 7, 3, 8, 1, 50))
result = hg.accumulate_on_contours(tree, node_saliency,
hg.Accumulators.max)
expected = np.asarray((0, 7, 5, 7, 8, 0, 20, 8, 7, 0, 20, 8))
self.assertTrue(np.allclose(result, expected))
node_saliency = np.asarray(
((0, 0), (1, 0), (2, 0), (3, 0), (4, 0), (5, 0), (6, 20), (7, 0),
(8, 0), (9, 5), (10, 2), (11, 7), (12, 3), (13, 8), (14, 1),
(15, 50)))
result = hg.accumulate_on_contours(tree, node_saliency,
hg.Accumulators.sum)
expected = np.asarray(
((1, 0), (33, 14), (12, 5), (35, 14), (30, 10), (7, 0), (46, 31),
(33, 15), (48, 11), (13, 0), (13, 20), (54, 12)))
self.assertTrue(np.allclose(result, expected))
def test_horizontal_cut_nodes(self):
g = hg.get_4_adjacency_graph((1, 11))
tree = hg.Tree((11, 11, 11, 12, 12, 16, 13, 13, 13, 14, 14, 17, 16, 15, 15, 18, 17, 18, 18))
hg.CptHierarchy.link(tree, g)
altitudes = np.asarray((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 3, 1, 2, 3))
hch = hg.HorizontalCutExplorer(tree, altitudes)
cut_nodes = (
(18,),
(17, 13, 14),
(11, 16, 13, 14),
(0, 1, 2, 3, 4, 5, 13, 9, 10)
)
c = hch.horizontal_cut_from_num_regions(3)
lbls = c.labelisation_leaves(tree)
ref_lbls = (17, 17, 17, 17, 17, 17, 13, 13, 13, 14, 14)
self.assertTrue(np.all(lbls == ref_lbls))
rec = c.reconstruct_leaf_data(tree, altitudes)
ref_rec = (2, 2, 2, 2, 2, 2, 0, 0, 0, 1, 1)
self.assertTrue(np.all(rec == ref_rec))
cut = c.graph_cut(tree)
ref_cut = (0, 0, 0, 0, 0, 1, 0, 0, 1, 0)
self.assertTrue(np.all(cut == ref_cut))
def test_hierarchy_to_optimal_MumfordShah_energy_cut_hierarchy(self):
# Test strategy:
# 1) start from a random hierarchy
# 2) construct the corresponding optimal Mumford-Shah energy cut hierarchy
# 3) verify that the horizontal cuts of the new hierarchy corresponds to the
# optimal energy cuts of the first hierarchy obtained from the explicit MF energy
# and the function labelisation_optimal_cut_from_energy
shape = (10, 10)
g = hg.get_4_adjacency_graph(shape)
np.random.seed(2)
vertex_weights = np.random.rand(*shape)
edge_weights = hg.weight_graph(g, vertex_weights, hg.WeightFunction.L1)
tree1, altitudes1 = hg.watershed_hierarchy_by_area(g, edge_weights)
tree, altitudes = hg.hierarchy_to_optimal_MumfordShah_energy_cut_hierarchy(
tree1,
vertex_weights,
approximation_piecewise_linear_function=999999)
for a in altitudes:
if a != 0:
res = False
cut1 = hg.labelisation_horizontal_cut_from_threshold(
tree, altitudes, a)
# du to numerical issues, and especially as we test critical scale level lambda,
# we test several very close scale levels
for margin in [-1e-8, 0, 1e-8]:
mfs_energy = hg.attribute_piecewise_constant_Mumford_Shah_energy(
tree1, vertex_weights, a + margin)
cut2 = hg.labelisation_optimal_cut_from_energy(
tree1, mfs_energy)
res = res or hg.is_in_bijection(cut1, cut2)
self.assertTrue(res)
def test_perimeter_length_component_tree(self):
g = hg.get_4_adjacency_graph((4, 4))
# for reference, tree is a max tree on the following image
# 0, 1, 4, 4,
# 7, 5, 6, 8,
# 2, 3, 4, 1,
# 9, 8, 6, 7
t = hg.Tree((28, 27, 24, 24,
20, 23, 22, 18,
26, 25, 24, 27,
16, 17, 21, 19,
17, 21, 22, 21, 23, 24, 23, 24, 25, 26, 27, 28, 28),
hg.TreeCategory.ComponentTree)
res = hg.attribute_perimeter_length(t, leaf_graph=g)
ref = np.asarray((4, 4, 4, 4,
4, 4, 4, 4,
4, 4, 4, 4,
4, 4, 4, 4,
4, 6, 4, 4, 4, 10, 6, 10, 22, 20, 18, 16, 16), dtype=np.float64)
self.assertTrue(np.all(res == ref))
def test_make_rag_from_graph_cut(self):
g = hg.get_4_adjacency_graph((4, 4))
edge_weights = np.asarray((0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0,
0, 1, 0, 0, 1, 1, 0, 1, 0))
rag = hg.make_region_adjacency_graph_from_graph_cut(g, edge_weights)
detail = hg.CptRegionAdjacencyGraph.construct(rag)
vertex_map = detail["vertex_map"]
edge_map = detail["edge_map"]
self.assertTrue(rag.num_vertices() == 4)
self.assertTrue(rag.num_edges() == 5)
expected_edges = ((0, 1), (1, 2), (0, 2), (2, 3), (0, 3))
i = 0
for e in rag.edges():
self.assertTrue((e[0], e[1]) == expected_edges[i])
i += 1
expected_vertex_map = np.asarray(
(0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 2, 2, 0, 0, 3, 3))
self.assertTrue(np.allclose(vertex_map, expected_vertex_map))
iv = -1
expected_edge_map = np.asarray(
(iv, iv, 0, iv, iv, iv, iv, iv, iv, 0, iv, iv, 1, 1, iv, iv, 2, iv,
iv, 3, 3, iv, 4, iv))
self.assertTrue(np.allclose(edge_map, expected_edge_map))
def get_rag():
g = hg.get_4_adjacency_graph((4, 4))
vertex_labels = np.asarray(
(1, 1, 5, 5, 1, 1, 5, 5, 1, 1, 3, 3, 1, 1, 10, 10))
return hg.make_region_adjacency_graph_from_labelisation(
g, vertex_labels)
def test_filter_non_relevant_node_from_tree(self):
g = hg.get_4_adjacency_graph((1, 8))
edge_weights = np.asarray((0, 2, 0, 0, 1, 0, 0))
tree, altitudes = hg.bpt_canonical(g, edge_weights)
def functor(tree, altitudes):
area = hg.attribute_area(tree)
area_min_children = hg.accumulate_parallel(tree, area, hg.Accumulators.min)
return area_min_children < 3
res_tree, res_altitudes = hg.filter_non_relevant_node_from_tree(tree, altitudes, functor, canonize_tree=False)
sm = hg.saliency(res_tree, res_altitudes)
sm_ref = np.asarray((0, 0, 0, 0, 1, 0, 0))
self.assertTrue(np.all(sm == sm_ref))
ref_parents = (8, 8, 9, 9, 10, 11, 11, 12, 13, 10, 13, 12, 14, 14, 14)
ref_altitudes = (0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1)
self.assertTrue(hg.CptBinaryHierarchy.validate(res_tree))
self.assertTrue(np.all(ref_parents == res_tree.parents()))
self.assertTrue(np.all(res_altitudes == ref_altitudes))
res_tree, res_altitudes = hg.filter_non_relevant_node_from_tree(tree, altitudes, functor, canonize_tree=True)
sm = hg.saliency(res_tree, res_altitudes)
sm_ref = np.asarray((0, 0, 0, 0, 1, 0, 0))
self.assertTrue(np.all(sm == sm_ref))
ref_parents = (8, 8, 8, 8, 8, 9, 9, 9, 10, 10, 10)
ref_tree = hg.Tree(ref_parents)
ref_altitudes = (0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1)
self.assertFalse(hg.CptBinaryHierarchy.validate(res_tree))
self.assertTrue(hg.test_tree_isomorphism(res_tree, ref_tree))
self.assertTrue(np.all(res_altitudes == ref_altitudes))
def test_BPT(self):
graph = hg.get_4_adjacency_graph((2, 3))
edge_weights = np.asarray((1, 0, 2, 1, 1, 1, 2))
tree, altitudes = hg.bpt_canonical(graph, edge_weights)
mst = hg.CptBinaryHierarchy.construct(tree)["mst"]
mst_edge_map = hg.get_attribute(mst, "mst_edge_map")
self.assertTrue(tree.num_vertices() == 11)
self.assertTrue(tree.num_edges() == 10)
self.assertTrue(
np.allclose(tree.parents(), (6, 7, 9, 6, 8, 9, 7, 8, 10, 10, 10)))
self.assertTrue(
np.allclose(altitudes, (0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 2)))
self.assertTrue(mst.num_vertices() == 6)
self.assertTrue(mst.num_edges() == 5)
ref = [(0, 3), (0, 1), (1, 4), (2, 5), (1, 2)]
test = []
for e in mst.edges():
test.append((e[0], e[1]))
self.assertTrue(ref == test)
self.assertTrue(np.all(mst_edge_map == (1, 0, 3, 4, 2)))
def test_contour_strength_component_tree(self):
g = hg.get_4_adjacency_graph((4, 4))
edge_weights = np.arange(g.num_edges(), dtype=np.float64)
# for reference, tree is a max tree on the following image
# 0, 1, 4, 4,
# 7, 5, 6, 8,
# 2, 3, 4, 1,
# 9, 8, 6, 7
t = hg.Tree(
(28, 27, 24, 24, 20, 23, 22, 18, 26, 25, 24, 27, 16, 17, 21, 19,
17, 21, 22, 21, 23, 24, 23, 24, 25, 26, 27, 28, 28),
hg.TreeCategory.ComponentTree)
hg.CptHierarchy.link(t, g)
res = hg.attribute_contour_strength(t, edge_weights)
ref_perimeter = np.asarray(
(4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 4, 4, 4, 10,
6, 10, 22, 20, 18, 16, 16),
dtype=np.float64)
ref_weights = np.asarray(
(1, 5, 11, 10, 16, 29, 37, 30, 37, 57, 65, 51, 36, 60, 64, 43, 36,
54, 30, 43, 16, 71, 45, 58, 123, 94, 57, 1, 0),
dtype=np.float64)
self.assertTrue(np.allclose(ref_weights / ref_perimeter, res))
def test_LCAFastV(self):
g = hg.get_4_adjacency_graph((2, 2))
t = hg.Tree((4, 4, 5, 5, 6, 6, 6))
lca = hg.LCAFast(t)
ref = (4, 6, 6, 5)
res = lca.lca(g)
self.assertTrue(np.all(ref == res))
def test_watershed(self):
g = hg.get_4_adjacency_graph((4, 4))
edge_weights = np.asarray((1, 2, 5, 5, 5, 8, 1, 4, 3, 4, 4, 1, 5, 2, 6,
3, 5, 4, 0, 7, 0, 3, 4, 0))
labels = hg.labelisation_watershed(g, edge_weights)
expected = ((1, 1, 1, 2), (1, 1, 2, 2), (1, 1, 3, 3), (1, 1, 3, 3))
self.assertTrue(np.allclose(labels, expected))
def test_graph_cut_2_labelisation(self):
graph = hg.get_4_adjacency_graph((3, 3))
edge_weights = np.asarray((1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0), dtype=np.int32)
labels = hg.graph_cut_2_labelisation(graph, edge_weights)
ref_labels = np.asarray((1, 2, 2, 1, 1, 3, 1, 3, 3), dtype=np.int32)
self.assertTrue(hg.is_in_bijection(labels, ref_labels))
def test_vertex_perimeter_rag(self):
g = hg.get_4_adjacency_graph((2, 3))
vertex_labels = np.asarray(((1, 2, 2), (3, 3, 3)))
rag = hg.make_region_adjacency_graph_from_labelisation(
g, vertex_labels)
ref = np.asarray((2, 3, 3))
res = hg.attribute_vertex_perimeter(rag)
self.assertTrue(np.allclose(ref, res))
def rebuild_mean_pb_hierarchy(self, rag, vertex_map, edge_map, tree,
altitudes, shape):
shape = hg.normalize_shape(shape)
graph = hg.get_4_adjacency_graph(shape)
hg.CptRegionAdjacencyGraph.link(rag, graph, vertex_map, edge_map)
hg.CptHierarchy.link(tree, rag)
return tree, altitudes
def ultrametric_open(self):
graph = hg.get_4_adjacency_graph((3, 3))
edge_weights = np.asarray((2, 3, 9, 5, 10, 1, 5, 8, 2, 2, 4, 3), dtype=np.int32)
subd_ultrametric = hg.ultrametric_open(graph, edge_weights)
ref_subd_ultrametric = np.asarray((2, 3, 9, 3, 9, 1, 4, 3, 2, 2, 4, 3), dtype=np.int32)
self.assertTrue(hg.is_in_bijection(subd_ultrametric, ref_subd_ultrametric))
def test_dasgupta_cost(self):
g = hg.get_4_adjacency_graph((3, 3))
edge_weights = np.asarray((1, 7, 3, 7, 1, 1, 6, 5, 6, 4, 1, 2))
tree, _ = hg.bpt_canonical(g, edge_weights)
cost = hg.dasgupta_cost(tree, edge_weights)
ref_cost = 2 / 1 + 4 / 3 + 9 / 7 + 9 / 7 + 2 / 1 + 2 / 1 + 9 / 5 + 9 / 6 + 9 / 6 + 7 / 4 + 2 / 1 + 3 / 2
self.assertTrue(np.isclose(cost, ref_cost))
def test_filter_non_relevant_node_from_tree(self):
g = hg.get_4_adjacency_graph((1, 8))
edge_weights = np.asarray((0, 2, 0, 0, 1, 0, 0))
tree, altitudes = hg.quasi_flat_zone_hierarchy(g, edge_weights)
res_tree, res_altitudes = hg.filter_small_nodes_from_tree(tree, altitudes, 3)
sm = hg.saliency(res_tree, res_altitudes)
sm_ref = np.asarray((0, 0, 0, 0, 1, 0, 0))
self.assertTrue(np.all(sm == sm_ref))
def test_filter_weak_frontier_nodes_from_tree(self):
g = hg.get_4_adjacency_graph((1, 8))
edge_weights = np.asarray((0, 2, 0, 0, 1, 0, 0))
tree, altitudes = hg.bpt_canonical(g, edge_weights)
res_tree, res_altitudes = hg.filter_weak_frontier_nodes_from_tree(tree, altitudes, edge_weights, 2)
sm = hg.saliency(res_tree, res_altitudes)
sm_ref = np.asarray((0, 2, 0, 0, 0, 0, 0))
self.assertTrue(np.all(sm == sm_ref))
def test_dendrogram_purity_random(self):
g = hg.get_4_adjacency_graph((10, 10))
np.random.seed(42)
for i in range(5):
ew = np.random.randint(0, 20, g.num_edges())
tree, _ = hg.quasi_flat_zone_hierarchy(g, ew)
labels = np.random.randint(0, 10, (100, ))
v1 = hg.dendrogram_purity(tree, labels)
v2 = dendrogram_purity_naif(tree, labels)
self.assertTrue(np.allclose(v1, v2))