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fix initializer for kamada_kawai_layout (networkx networkx#3658) (net…
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…workx#3782)

* fixed high-dimensional initializer for kamada_kawai_layout (networkx networkx#3658)

* added tests for kamada_kawai 3d

* increased test coverage of kamada_kawai_layout

* fixed empty-graph oversight in kamada_kawai_layout

* removed unused variable vpos from smoke tests

Fixes networkx#3658
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@boothby @dschult
boothby authored and dschult committed Jan 20, 2020
1 parent e2e147b commit 15e17c0
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Showing 2 changed files with 76 additions and 46 deletions.
6 changes: 5 additions & 1 deletion networkx/drawing/layout.py
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Original file line number Diff line number Diff line change
Expand Up @@ -687,6 +687,8 @@ def kamada_kawai_layout(G, dist=None,

G, center = _process_params(G, center, dim)
nNodes = len(G)
if nNodes == 0:
return {}

if dist is None:
dist = dict(nx.shortest_path_length(G, weight=weight))
Expand All @@ -701,7 +703,9 @@ def kamada_kawai_layout(G, dist=None,
dist_mtx[row][col] = rdist[nc]

if pos is None:
if dim >= 2:
if dim >= 3:
pos = random_layout(G, dim=dim)
elif dim == 2:
pos = circular_layout(G, dim=dim)
else:
pos = {n: pt for n, pt in zip(G, np.linspace(0, 1, len(G)))}
Expand Down
116 changes: 71 additions & 45 deletions networkx/drawing/tests/test_layout.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,46 +48,48 @@ def test_spring_init_pos(self):

def test_smoke_empty_graph(self):
G = []
vpos = nx.random_layout(G)
vpos = nx.circular_layout(G)
vpos = nx.planar_layout(G)
vpos = nx.spring_layout(G)
vpos = nx.fruchterman_reingold_layout(G)
vpos = nx.spectral_layout(G)
vpos = nx.shell_layout(G)
vpos = nx.bipartite_layout(G, G)
vpos = nx.spiral_layout(G)
# FIXME vpos = nx.kamada_kawai_layout(G)
nx.random_layout(G)
nx.circular_layout(G)
nx.planar_layout(G)
nx.spring_layout(G)
nx.fruchterman_reingold_layout(G)
nx.spectral_layout(G)
nx.shell_layout(G)
nx.bipartite_layout(G, G)
nx.spiral_layout(G)
nx.kamada_kawai_layout(G)

def test_smoke_int(self):
G = self.Gi
vpos = nx.random_layout(G)
vpos = nx.circular_layout(G)
vpos = nx.planar_layout(G)
vpos = nx.spring_layout(G)
vpos = nx.fruchterman_reingold_layout(G)
vpos = nx.fruchterman_reingold_layout(self.bigG)
vpos = nx.spectral_layout(G)
vpos = nx.spectral_layout(G.to_directed())
vpos = nx.spectral_layout(self.bigG)
vpos = nx.spectral_layout(self.bigG.to_directed())
vpos = nx.shell_layout(G)
vpos = nx.spiral_layout(G)
vpos = nx.kamada_kawai_layout(G)
vpos = nx.kamada_kawai_layout(G, dim=1)
nx.random_layout(G)
nx.circular_layout(G)
nx.planar_layout(G)
nx.spring_layout(G)
nx.fruchterman_reingold_layout(G)
nx.fruchterman_reingold_layout(self.bigG)
nx.spectral_layout(G)
nx.spectral_layout(G.to_directed())
nx.spectral_layout(self.bigG)
nx.spectral_layout(self.bigG.to_directed())
nx.shell_layout(G)
nx.spiral_layout(G)
nx.kamada_kawai_layout(G)
nx.kamada_kawai_layout(G, dim=1)
nx.kamada_kawai_layout(G, dim=3)

def test_smoke_string(self):
G = self.Gs
vpos = nx.random_layout(G)
vpos = nx.circular_layout(G)
vpos = nx.planar_layout(G)
vpos = nx.spring_layout(G)
vpos = nx.fruchterman_reingold_layout(G)
vpos = nx.spectral_layout(G)
vpos = nx.shell_layout(G)
vpos = nx.spiral_layout(G)
vpos = nx.kamada_kawai_layout(G)
vpos = nx.kamada_kawai_layout(G, dim=1)
nx.random_layout(G)
nx.circular_layout(G)
nx.planar_layout(G)
nx.spring_layout(G)
nx.fruchterman_reingold_layout(G)
nx.spectral_layout(G)
nx.shell_layout(G)
nx.spiral_layout(G)
nx.kamada_kawai_layout(G)
nx.kamada_kawai_layout(G, dim=1)
nx.kamada_kawai_layout(G, dim=3)

def check_scale_and_center(self, pos, scale, center):
center = numpy.array(center)
Expand All @@ -113,6 +115,10 @@ def test_scale_and_center_arg(self):
sc(nx.spiral_layout(G, scale=2, center=c), scale=2, center=c)
sc(nx.kamada_kawai_layout(G, scale=2, center=c), scale=2, center=c)

c = (2, 3, 5)
sc(nx.kamada_kawai_layout(G, dim=3, scale=2, center=c), scale=2, center=c)


def test_planar_layout_non_planar_input(self):
G = nx.complete_graph(9)
pytest.raises(nx.NetworkXException, nx.planar_layout, G)
Expand All @@ -135,6 +141,10 @@ def test_default_scale_and_center(self):
sc(nx.spiral_layout(G), scale=1, center=c)
sc(nx.kamada_kawai_layout(G), scale=1, center=c)

c = (0, 0, 0)
sc(nx.kamada_kawai_layout(G, dim=3), scale=1, center=c)


def test_circular_planar_and_shell_dim_error(self):
G = nx.path_graph(4)
pytest.raises(ValueError, nx.circular_layout, G, dim=1)
Expand Down Expand Up @@ -190,7 +200,7 @@ def test_fixed_node_fruchterman_reingold(self):

def test_center_parameter(self):
G = nx.path_graph(1)
vpos = nx.random_layout(G, center=(1, 1))
nx.random_layout(G, center=(1, 1))
vpos = nx.circular_layout(G, center=(1, 1))
assert tuple(vpos[0]) == (1, 1)
vpos = nx.planar_layout(G, center=(1, 1))
Expand Down Expand Up @@ -218,6 +228,7 @@ def test_center_wrong_dimensions(self):
pytest.raises(ValueError, nx.spectral_layout, G, dim=3, center=(1, 1))
pytest.raises(ValueError, nx.shell_layout, G, center=(1, 1, 1))
pytest.raises(ValueError, nx.spiral_layout, G, center=(1, 1, 1))
pytest.raises(ValueError, nx.kamada_kawai_layout, G, center=(1, 1, 1))

def test_empty_graph(self):
G = nx.empty_graph()
Expand All @@ -239,6 +250,8 @@ def test_empty_graph(self):
assert vpos == {}
vpos = nx.spiral_layout(G, center=(1, 1))
assert vpos == {}
vpos = nx.kamada_kawai_layout(G, center=(1, 1))
assert vpos == {}

def test_bipartite_layout(self):
G = nx.complete_bipartite_graph(3, 5)
Expand Down Expand Up @@ -282,19 +295,11 @@ def test_kamada_kawai_costfn_1d(self):
assert almost_equal(grad[0], -0.5)
assert almost_equal(grad[1], 0.5)

def test_kamada_kawai_costfn_2d(self):
def check_kamada_kawai_costfn(self, pos, invdist, meanwt, dim):
costfn = nx.drawing.layout._kamada_kawai_costfn

pos = numpy.array([[1.3, -3.2],
[2.7, -0.3],
[5.1, 2.5]])
invdist = 1 / numpy.array([[0.1, 2.1, 1.7],
[2.1, 0.2, 0.6],
[1.7, 0.6, 0.3]])
meanwt = 0.3

cost, grad = costfn(pos.ravel(), numpy, invdist,
meanweight=meanwt, dim=2)
meanweight=meanwt, dim=dim)

expected_cost = 0.5 * meanwt * numpy.sum(numpy.sum(pos, axis=0) ** 2)
for i in range(pos.shape[0]):
Expand All @@ -321,6 +326,27 @@ def test_kamada_kawai_costfn_2d(self):
assert almost_equal(grad[idx], (cplus - cminus) / (2 * dx),
places=5)

def test_kamada_kawai_costfn(self):
invdist = 1 / numpy.array([[0.1, 2.1, 1.7],
[2.1, 0.2, 0.6],
[1.7, 0.6, 0.3]])
meanwt = 0.3

# 2d
pos = numpy.array([[1.3, -3.2],
[2.7, -0.3],
[5.1, 2.5]])

self.check_kamada_kawai_costfn(pos, invdist, meanwt, 2)

# 3d
pos = numpy.array([[0.9, 8.6, -8.7],
[-10, -0.5, -7.1],
[9.1, -8.1, 1.6]])

self.check_kamada_kawai_costfn(pos, invdist, meanwt, 3)


def test_spiral_layout(self):

G = self.Gs
Expand Down

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