def test_detect_corners(self):
path = PointSet(3)
path.append(10, 2, 0)
path.append(11, 3, 0)
path.append(12, 4, 0)
path.append(13, 5, 0)
path.append(14, 6, 0)
path.append(15, 7, 0) # top
path.append(16, 6, 0)
path.append(17, 5, 0)
path.append(18, 4, 0)
path.append(19, 3, 0)
path.append(20, 2, 0) # bottom
path.append(21, 3, 0)
path.append(22, 4, 0)
path.append(23, 5, 0)
path.append(24, 6, 0)
path.append(25, 7, 0) # top
path.append(26, 6, 0)
path.append(27, 5, 0)
path.append(28, 4, 0)
path.append(29, 3, 0)
path0 = path
for i in range(3):
path = path0.copy()
path[:, 2] = path[:, i]
path[:, i] = 0
# Test that _detect_corners detects the indices correctly
I = _detect_corners(path, smoothFactor=1)
assert I == [5, 10, 15]
# Test that _add_corner_to_edge constructs the graph and splits
# the path in the correct way
graph = StentGraph()
n1, n5 = tuple(path[0].flat), tuple(path[-1].flat)
n2, n3, n4 = tuple(path[5].flat), tuple(path[10].flat), tuple(
path[15].flat)
graph.add_edge(n1, n5, path=path, cost=0, ctvalue=0)
_add_corner_to_edge(graph, n1, n5, smoothFactor=1)
assert graph.number_of_nodes() == 5
assert graph.number_of_edges() == 4
for n in [n1, n2, n3, n4, n5]:
assert n in graph.nodes()
path12, path23, path34, path45 = path[0:6], path[5:11], path[
10:16], path[15:20]
if n1 > n2: path12 = np.flipud(path12)
if n2 > n3: path23 = np.flipud(path23)
if n3 > n4: path34 = np.flipud(path34)
if n4 > n5: path45 = np.flipud(path45)
assert np.all(graph.edge[n1][n2]['path'] == path12)
assert np.all(graph.edge[n2][n3]['path'] == path23)
assert np.all(graph.edge[n3][n4]['path'] == path34)
assert np.all(graph.edge[n4][n5]['path'] == path45)
def test_very_weak(self):
# Create simple graph
graph = StentGraph()
graph.add_edge(1, 4, ctvalue=50)
graph.add_edge(1, 5, ctvalue=40)
graph.add_edge(1, 2, ctvalue=30)
graph.add_edge(1, 3, ctvalue=20)
# Remove weak edges
th = 35
prune_very_weak(graph, th)
# Check result
assert graph.number_of_edges() == 2
for (n1, n2) in graph.edges_iter():
assert graph[n1][n2]['ctvalue'] > th
def test_prune_redundant2(self):
""" Test removing redundant edges on a graph with two triangles
that are connected by a two edges, twice.
"""
# Create two triangles that are connected with a single edge
graph = StentGraph()
graph.add_edge(11, 12, cost=1, ctvalue=50)
graph.add_edge(12, 13, cost=3, ctvalue=50)
graph.add_edge(13, 11, cost=2, ctvalue=50)
#
graph.add_edge(21, 22, cost=2, ctvalue=60)
graph.add_edge(22, 23, cost=3, ctvalue=60)
graph.add_edge(23, 21, cost=1, ctvalue=60)
#
graph.add_edge(21, 1, cost=4, ctvalue=10)
graph.add_edge(1, 11, cost=4, ctvalue=10)
#
graph.add_edge(22, 2, cost=4, ctvalue=10)
graph.add_edge(2, 12, cost=4, ctvalue=10)
assert graph.number_of_nodes() == 8
assert graph.number_of_edges() == 10
prune_redundant(graph, 55)
assert graph.number_of_nodes() == 8
assert graph.number_of_edges() == 10 - 1
prune_redundant(graph, 55)
assert graph.number_of_nodes() == 8
assert graph.number_of_edges() == 10 - 1
prune_redundant(graph, 65)
assert graph.number_of_nodes() == 8
assert graph.number_of_edges() == 10 - 2
prune_tails(graph, 2)
assert graph.number_of_nodes() == 8 - 2
assert graph.number_of_edges() == 10 - 2 - 2
def test_pop_nodes(self):
# Create dummy paths
path1 = PointSet(2)
path1.append(1, 11)
path1.append(1, 12)
# create 4 nodes (6-7-8-9), remove 8
graph = StentGraph()
graph.add_edge(6, 7, cost=4, ctvalue=70, path=path1)
graph.add_edge(7, 8, cost=2, ctvalue=50, path=path1)
graph.add_edge(8, 9, cost=3, ctvalue=60, path=path1)
graph0 = graph.copy()
# Pop straight line
graph = graph0.copy()
pop_nodes(graph)
assert graph.number_of_nodes() == 2
assert graph.number_of_edges() == 1
assert graph.edge[6][9]['path'].shape[0] == 3 + 1
# Pop cycle
graph = graph0.copy()
graph.add_edge(9, 6, cost=3, ctvalue=60, path=path1)
pop_nodes(graph)
assert graph.number_of_nodes() == 1
assert graph.number_of_edges() == 1
n = graph.nodes()[0]
assert graph.edge[n][n]['path'].shape[0] == 4 + 1 + 1 # cycle
# arbitrary what node stayed around
# Pop with one side branch popping
graph = graph0.copy()
graph.add_edge(7, 2, cost=3, ctvalue=60, path=path1)
pop_nodes(graph)
assert graph.number_of_nodes() == 4
assert graph.number_of_edges() == 3
assert graph.edge[7][9]['path'].shape[0] == 2 + 1
# Pop with one prevent popping
graph = graph0.copy()
graph.node[7]['nopop'] = True
pop_nodes(graph)
assert graph.number_of_nodes() == 3
assert graph.number_of_edges() == 2
assert graph.edge[7][9]['path'].shape[0] == 2 + 1
def test_pop_node(self):
# Create paths
path1 = PointSet(2)
path1.append(1, 11)
path1.append(1, 12)
path2 = PointSet(2)
path2.append(1, 12)
path2.append(1, 13)
#
path12 = PointSet(2)
path12.append(1, 11)
path12.append(1, 12)
path12.append(1, 13)
# create 4 nodes (6-7-8-9), remove 8
graph = StentGraph()
graph.add_edge(6, 7, cost=4, ctvalue=70)
graph.add_edge(7, 8, cost=2, ctvalue=50, path=path1)
graph.add_edge(8, 9, cost=3, ctvalue=60, path=path2)
# Pop
_pop_node(graph, 8)
# Check
assert graph.number_of_nodes() == 3
assert 8 not in graph.nodes()
assert graph.edge[7][9]['ctvalue'] == 50
assert graph.edge[7][9]['cost'] == 5
assert np.all(graph.edge[7][9]['path'] == path12)
# create 4 nodes (6-8-7-9), remove 7
graph = StentGraph()
graph.add_edge(6, 8, cost=4, ctvalue=70)
graph.add_edge(8, 7, cost=2, ctvalue=50, path=np.flipud(path1))
graph.add_edge(7, 9, cost=3, ctvalue=60, path=path2)
# Pop
_pop_node(graph, 7)
# Check
assert graph.number_of_nodes() == 3
assert 7 not in graph.nodes()
assert graph.edge[8][9]['ctvalue'] == 50
assert graph.edge[8][9]['cost'] == 5
assert np.all(graph.edge[8][9]['path'] == path12)
# create 4 nodes (7-8-6-9), remove 8
graph = StentGraph()
graph.add_edge(7, 8, cost=4, ctvalue=70, path=np.flipud(path2))
graph.add_edge(8, 6, cost=2, ctvalue=50, path=path1)
graph.add_edge(6, 9, cost=3, ctvalue=60)
# Pop
_pop_node(graph, 8)
# Check
assert graph.number_of_nodes() == 3
assert 8 not in graph.nodes()
assert graph.edge[6][7]['ctvalue'] == 50
assert graph.edge[6][7]['cost'] == 6
assert np.all(graph.edge[6][7]['path'] == path12)
# create 3 nodes in a cycle. It should remove all but one
graph = StentGraph()
graph.add_edge(7, 8, cost=4, ctvalue=70, path=path1)
graph.add_edge(8, 9, cost=2, ctvalue=50, path=path2)
graph.add_edge(9, 7, cost=3, ctvalue=60, path=path2)
# Pop
_pop_node(graph, 8)
# Check
assert graph.number_of_nodes() == 1
assert graph.number_of_edges() == 1
assert 8 not in graph.nodes()
n = graph.nodes()[0]
assert len(graph.edge[n][n]['path']) == 6 - 1
# create 3 nodes in a cycle, with one subbranch
graph = StentGraph()
graph.add_edge(7, 8, cost=4, ctvalue=70, path=path1)
graph.add_edge(8, 9, cost=2, ctvalue=50, path=path2)
graph.add_edge(9, 7, cost=3, ctvalue=60, path=path2)
graph.add_edge(7, 4, cost=3, ctvalue=60, path=path2)
# Pop
_pop_node(graph, 8)
# Check
assert graph.number_of_nodes() == 2
assert graph.number_of_edges() == 2
assert 8 not in graph.nodes()
assert len(graph.edge[7][7]['path']) == 6 - 1
def test_pack2(self):
# Auto generate
import random
n = 500
p = dict(
(i, (random.gauss(0, 2), random.gauss(0, 2))) for i in range(n))
g_ = nx.random_geometric_graph(n, 0.1, dim=3, pos=p)
g = StentGraph(summary='dit is een stent!', lala=3)
g.add_nodes_from(g_.nodes_iter())
g.add_edges_from(g_.edges_iter())
fname = '/home/almar/test.ssdf'
ssdf.save(fname, g.pack())
g2 = StentGraph()
g2.unpack(ssdf.load(fname))
#print(nx.is_isomorphic(g, g2))
assert nx.is_isomorphic(g, g2)
def test_pack1(self):
# Custom stent
g = StentGraph(summary='dit is een stent!', lala=3)
g.add_node((10, 20), foo=3)
g.add_node((30, 40), foo=5)
g.add_edge((1, 1), (2, 2), bar=10)
g.add_edge((10, 20), (1, 1), bar=20)
fname = '/home/almar/test.ssdf'
ssdf.save(fname, g.pack())
g2 = StentGraph()
g2.unpack(ssdf.load(fname))
#print(nx.is_isomorphic(g, g2))
assert nx.is_isomorphic(g, g2)
def test_weak3(self):
""" 2 456
/ | |
3 - 1 - 0 - 789
"""
# Test that indeed only weakest are removed
graph = StentGraph()
graph.add_edge(1, 2, cost=2, ctvalue=50)
graph.add_edge(2, 3, cost=2, ctvalue=50)
graph.add_edge(3, 1, cost=2, ctvalue=50)
#
graph.add_edge(4, 5, cost=2, ctvalue=50)
graph.add_edge(5, 6, cost=2, ctvalue=50)
graph.add_edge(6, 4, cost=2, ctvalue=50)
#
graph.add_edge(7, 8, cost=2, ctvalue=50)
graph.add_edge(8, 9, cost=2, ctvalue=50)
graph.add_edge(9, 7, cost=2, ctvalue=50)
# Connect three subgraphs
graph.add_edge(0, 1, cost=2, ctvalue=50)
graph.add_edge(0, 4, cost=3, ctvalue=50) # gets removed
graph.add_edge(0, 7, cost=2, ctvalue=50)
# Prune
prune_weak(graph, 2, 80)
# Check result
assert graph.number_of_edges() == 9 + 2
for e in graph.edges_iter():
assert e not in [(0, 4)]
# Connect three subgraphs
graph.add_edge(0, 1, cost=1, ctvalue=50)
graph.add_edge(0, 4, cost=1, ctvalue=50)
graph.add_edge(0, 7, cost=2, ctvalue=50) # gets removed
# Prune
prune_weak(graph, 2, 80)
# Check result
assert graph.number_of_edges() == 9 + 2
for e in graph.edges_iter():
assert e not in [(0, 7)]
# Connect three subgraphs
graph.add_edge(0, 1, cost=3, ctvalue=50)
graph.add_edge(0, 4, cost=4, ctvalue=90) # None gets removed
graph.add_edge(0, 7, cost=3, ctvalue=50)
# Prune
prune_weak(graph, 2, 80)
# Check result
assert graph.number_of_edges() == 9 + 3
def test_weak2(self):
""" 2 5
/ | | \
3 - 1 - 4 - 6
"""
# Test that indeed only weakest are removed
graph = StentGraph()
graph.add_edge(1, 2, cost=2, ctvalue=50)
graph.add_edge(2, 3, cost=2, ctvalue=50)
graph.add_edge(3, 1, cost=2, ctvalue=50)
#
graph.add_edge(4, 5, cost=2, ctvalue=50)
graph.add_edge(5, 6, cost=2, ctvalue=50)
graph.add_edge(6, 4, cost=2, ctvalue=50)
# Connect two subgraphs with weaker connection
graph.add_edge(1, 4, cost=3, ctvalue=50)
# Prune
prune_weak(graph, 2, 80)
# Check result
assert graph.number_of_edges() == 6
for e in graph.edges_iter():
assert e not in [(1, 4)]
# Again, now with lower cost (stronger connection)
graph.add_edge(1, 4, cost=1, ctvalue=50)
# Prune
prune_weak(graph, 2, 80)
# Check result
assert graph.number_of_edges() == 7
# Again, now with high ct value
graph.add_edge(1, 4, cost=3, ctvalue=90)
# Prune
prune_weak(graph, 2, 80)
# Check result
assert graph.number_of_edges() == 7
def test_weak1(self):
""" 2
/ | \
5 - 1 - 3
\ | /
4
"""
# Test that indeed only weakest are removed
graph = StentGraph()
graph.add_edge(1, 2, cost=2, ctvalue=50)
graph.add_edge(1, 3, cost=3, ctvalue=50) # gets removed
graph.add_edge(1, 4, cost=4, ctvalue=50) # gets removed
graph.add_edge(1, 5, cost=1, ctvalue=50)
#
graph.add_edge(2, 3, cost=1, ctvalue=50)
graph.add_edge(3, 4, cost=1, ctvalue=50)
graph.add_edge(4, 5, cost=1, ctvalue=50)
graph.add_edge(5, 2, cost=1, ctvalue=50)
prune_weak(graph, 2, 80)
# Check result
assert graph.number_of_edges() == 6
for e in graph.edges_iter():
assert e not in [(1, 3), (1, 4)]
def test_prune_clusters(self):
# Create two small cliques
graph = StentGraph()
graph.add_edge(1, 2, cost=2, ctvalue=50)
graph.add_edge(2, 3, cost=2, ctvalue=50)
graph.add_edge(3, 1, cost=2, ctvalue=50)
#
graph.add_edge(4, 5, cost=2, ctvalue=50)
graph.add_edge(5, 6, cost=2, ctvalue=50)
graph.add_edge(6, 7, cost=2, ctvalue=50)
graph.add_edge(7, 4, cost=2, ctvalue=50)
# Connect them
graph.add_edge(1, 4, cost=3, ctvalue=50)
# Also add loose node
graph.add_nodes_from([101, 102])
# Remove cliques and check that nothing happened
prune_clusters(graph, 4)
assert graph.number_of_edges() == 8
assert graph.number_of_nodes() == 7
# Remove connection
graph.remove_edge(1, 4)
# Remove cliques and check that one clique is removed
prune_clusters(graph, 4)
assert graph.number_of_edges() == 4
assert graph.number_of_nodes() == 4
# Remove cliques and check that one clique is removed
prune_clusters(graph, 5)
assert graph.number_of_edges() == 0
assert graph.number_of_nodes() == 0
def test_prune_tails(self):
graph = StentGraph()
graph.add_edge(1, 2, cost=2, ctvalue=50)
graph.add_edge(2, 3, cost=2, ctvalue=50)
graph.add_edge(3, 1, cost=2, ctvalue=50)
# Tail from 1
graph.add_edge(1, 11, cost=3, ctvalue=50)
graph.add_edge(11, 12, cost=3, ctvalue=50)
graph.add_edge(12, 13, cost=3, ctvalue=50)
graph.add_edge(13, 14, cost=3, ctvalue=50)
# Tail from 2
graph.add_edge(2, 21, cost=3, ctvalue=50)
graph.add_edge(21, 22, cost=3, ctvalue=50)
graph.add_edge(22, 23, cost=3, ctvalue=50)
assert graph.number_of_nodes() == 3 + 4 + 3
assert graph.number_of_edges() == 3 + 4 + 3
prune_tails(graph, 3)
assert graph.number_of_nodes() == 3 + 4
assert graph.number_of_edges() == 3 + 4
prune_tails(graph, 9)
assert graph.number_of_nodes() == 3
assert graph.number_of_edges() == 3
added_node1 = 10, 5, 0
added_node2 = 10, 7, 0
for n in (n1, n2, n3, n4, n5, added_node1, added_node2):
assert n in graph.nodes()
if __name__ == "__main__":
# Run test. Nose is acting weird. So wrote a little test runner myself:
test = TestStentGraph()
for m in dir(test):
if m.startswith('test_'):
print('Running %s ... ' % m, end='')
try:
getattr(test, m)()
except AssertionError as err:
print('Fail')
raise
except Exception:
print('Error')
raise
else:
print("Ok")
# Create simple graph
graph = StentGraph()
graph.add_edge(1, 4, cost=5)
graph.add_edge(1, 5, cost=4)
graph.add_edge(1, 2, cost=3)
graph.add_edge(1, 3, cost=2)