def test_chain():
periodic = True
# periodic = False
graph = gt_gen.lattice([1, 200], periodic=periodic)
if periodic:
figure_title = 'line_periodic'
else:
figure_title = 'line_non-periodic'
n = graph.num_vertices()
location1 = 0.2 * n
location2 = n - location1
jump = 1e-3
weight = graph.new_edge_property('double', vals=1)
e1 = graph.edge(location1, location1 + 1)
weight[e1] = jump
e2 = graph.edge(location2 - 1, location2)
weight[e2] = jump
pos_x = np.arange(n)
pos_y = np.zeros((n,))
v_pos = graph.new_vertex_property('vector<double>',
vals=np.vstack((pos_x, pos_y)).T)
v_text = graph.new_vertex_property('string')
for v in graph.vertices():
v_text[v] = pos_x[graph.vertex_index[v]]
palette = sns.color_palette('Set1', n_colors=2)
cmap = colors.ListedColormap(palette)
gt_draw.graph_draw(graph, pos=v_pos, edge_color=weight, ecmap=cmap,
edge_pen_width=.5, vertex_fill_color='w', vertex_size=2,
vertex_text=v_text, vertex_font_size=1,
output=figure_title + '_graph.pdf')
x_signal1 = np.cos(np.linspace(0, 4 * np.pi, location1))
x_signal2 = np.cos(np.linspace(0, 50 * np.pi, n - 2 * location1))
x_signal3 = np.cos(np.linspace(0, 8 * np.pi, location1))
x_signal = np.hstack([x_signal1, x_signal2, x_signal3])
palette = sns.color_palette('Set1', n_colors=3)
plt.figure()
markerline, stemlines, baseline = plt.stem(x_signal, markerfmt=' ')
plt.setp(stemlines, color=palette[1], linewidth=1.5)
plt.setp(baseline, color='k')
plt.savefig(figure_title + '_signal.pdf', dpi=300)
n_eigs = graph.num_vertices() - 1
tau = 200
alpha = -1e-4
factories = [spec.ConvolutionSGFT(graph, n_eigs, tau, weight=weight),
spec.PageRankSGFT(graph, n_eigs, alpha, weight=weight),
spec.ConvolutionSGFT(graph, n_eigs, tau, weight=None),
spec.PageRankSGFT(graph, n_eigs, alpha, weight=None)]
sgft.comparison.compare_spectrograms(factories, x_signal, graph, v_pos,
file_name=figure_title)
sgft.comparison.compare_localization(factories, location1, graph, v_pos,
file_name=figure_title)
def test_main():
g = lattice((5, 5))
for n, c in [(0, 1), (10, 5), (g.num_vertices(), 1)]:
for _ in range(c):
obs = np.random.choice(np.arange(g.num_vertices()),
g.num_vertices(),
replace=False)
t = min_steiner_tree(g, obs)
assert is_tree(t)
assert set(obs).issubset(set(map(int, t.vertices())))
def test_unweighted():
g = lattice((5, 5))
for n, c in [(10, 5), (g.num_vertices(), 1)]:
# repeat `c` rounds, using `n` terminals
for _ in range(c):
obs = np.random.choice(np.arange(g.num_vertices()), n,
replace=False)
t = min_steiner_tree(g, obs)
assert is_tree(t)
assert set(obs).issubset(set(map(int, t.vertices())))
def g():
graph = remove_filters(lattice((10, 10)))
graph.set_directed(True)
edges_iter = list(graph.edges())
for e in edges_iter:
graph.add_edge(e.target(), e.source())
ew = graph.new_edge_property('float')
ew.a = np.random.random(graph.num_edges()) * 0.2 + 0.8
graph.edge_properties['weights'] = ew
return preprocess(graph)
def load_graph_by_name(name, weighted=False, suffix=''):
suffix = suffix.strip()
if name == 'lattice':
shape = (10, 10)
g = lattice(shape)
else:
if weighted:
path = 'data/{}/graph_weighted{}.gt'.format(name, suffix)
else:
path = 'data/{}/graph{}.gt'.format(name, suffix)
print('load graph from {}'.format(path))
g = load_graph(path)
# assert not g.is_directed()
return remove_filters(g) # add shell
def test_chain():
graph = gt_gen.lattice([1, 1000], periodic=False)
# gt_draw.graph_draw(graph)
jump = 1e-3
weight = graph.new_edge_property('double', vals=1)
e1 = graph.edge(300, 301)
weight[e1] = jump
e1 = graph.edge(699, 700)
weight[e1] = jump# + 0.01
for e in graph.edges():
# weight[e] += min(abs(0.3 * np.random.randn()), 1)
if e.source() == 300 or e.source() == 699:
print e, weight[e]
n_eigs = 100
alpha = -1e-10
factory_weighted = ppr.PersonalizedPageRank(graph, n_eigs, weight=weight)
factory_unweighted = ppr.PersonalizedPageRank(graph, n_eigs, weight=None)
spectrogram_weighted = np.zeros((graph.num_vertices(), n_eigs))
spectrogram_unweighted = np.zeros((graph.num_vertices(), n_eigs))
t = timeit.default_timer()
for v in range(graph.num_vertices()):
_, loadings_weighted = factory_weighted.vector([graph.vertex(v)], alpha)
_, loadings_unweighted = factory_unweighted.vector([graph.vertex(v)],
alpha)
spectrogram_weighted[v, :] = loadings_weighted
spectrogram_unweighted[v, :] = loadings_unweighted
print timeit.default_timer() - t
spectrogram_weighted = np.abs(spectrogram_weighted)
spectrogram_unweighted = np.abs(spectrogram_unweighted)
spectrogram_weighted /= np.atleast_2d(np.sum(spectrogram_weighted, axis=1)).T
spectrogram_unweighted /= np.atleast_2d(np.sum(spectrogram_unweighted, axis=1)).T
palette = sns.color_palette('RdBu_r', n_colors=256)
cmap = colors.ListedColormap(palette, N=256)
plt.figure()
plt.subplot(121)
plt.imshow(spectrogram_weighted, interpolation='none', cmap=cmap)
plt.title('Weighted')
plt.axis('tight')
plt.subplot(122)
plt.imshow(spectrogram_unweighted, interpolation='none', cmap=cmap)
plt.title('Unweighted')
plt.axis('tight')
def batonGraph(drawGraph=False):
'''
A graph with NO symmetries.
'''
g = generation.lattice((9, 1))
v = g.add_vertex()
g.add_edge(v, g.vertex(6))
if drawGraph == True:
draw.graph_draw(g,
vertex_text=g.vertex_index,
edge_color="black",
output="batton.pdf")
return g
def lattice(n1: int, n2: int):
"""
Build 2D lattice graph
Parameters
----------
n1: int
Number of nodes in dimension 1
n2: int
Number of nodes in dimension 2
Returns
-------
Graph
Lattice graph
"""
return generation.lattice((n1, n2))
def test_weighted():
g = lattice((5, 5))
# assign some random weight
p = g.new_edge_property('float')
weights = np.random.random(g.num_edges())
p.a = (-np.log(weights))
for n, c in [(10, 5), (g.num_vertices(), 1)]:
# repeat `c` rounds, using `n` terminals
for _ in range(c):
obs = np.random.choice(np.arange(g.num_vertices()), n,
replace=False)
t = min_steiner_tree(g, obs, p)
# print(t)
assert is_tree(t)
assert set(obs).issubset(set(map(int, t.vertices())))
def test_contract_graph_by_nodes():
def get_weight_by_edges(g, weights, edges):
return [weights[g.edge(u, v)] for u, v in edges]
# weighted graph
g = lattice((2, 2))
weights = g.new_edge_property('float')
for e in g.edges():
weights[e] = int(e.target())
# contract 0 and 1
cg, new_weights = contract_graph_by_nodes(g, [0, 1], weights)
assert set(extract_nodes(cg)) == set(range(3))
edges = [(0, 0), (0, 1), (0, 2), (1, 2)]
assert set(extract_edges(cg)) == set(edges)
assert_almost_equal(get_weight_by_edges(cg, new_weights, edges),
[1, 2, 3, 3])
# contract 0, 1 and 2
cg, new_weights = contract_graph_by_nodes(g, [0, 1, 2], weights)
assert set(extract_nodes(cg)) == set(range(2))
edges = [(0, 0), (0, 1)]
assert set(extract_edges(cg)) == set(edges)
assert_almost_equal(get_weight_by_edges(cg, new_weights, edges),
[3, 6])
# contract all nodes
cg, new_weights = contract_graph_by_nodes(g, [0, 1, 2, 3], weights)
assert set(extract_nodes(cg)) == {0}
assert set(extract_edges(cg)) == {(0, 0)}
assert_almost_equal(new_weights.a, [9])
# contract just 1
cg, new_weights = contract_graph_by_nodes(g, [0], weights)
assert set(extract_nodes(cg)) == set(extract_nodes(g))
assert set(extract_edges(cg)) == set(extract_edges(g))
assert_almost_equal(new_weights.a, weights.a)
def main(filename, f_seeds, b_seeds):
# Load image
print("Reading", filename, flush=True, end="...")
img = cv3.imread(filename, cv3.IMREAD_COLOR)[:, :, ::-1]
rows, cols, _ = img.shape
print("Done")
# Init graph
print("Initializing graph", flush=True, end="...")
g = gt.lattice((rows, cols))
v_r = g.new_vertex_property('int')
v_g = g.new_vertex_property('int')
v_b = g.new_vertex_property('int')
e_w = g.new_edge_property('float')
print("Done")
# Make a row,col map of the indices for easy access
dex = np.zeros((rows, cols), dtype='int')
np.ravel(dex)[:] = range(rows * cols)
# Load vertex property arrays with pixel values
print("Loading pixel values", flush=True, end="...")
v_r.a = np.ravel(img[:, :, 0])
v_g.a = np.ravel(img[:, :, 1])
v_b.a = np.ravel(img[:, :, 2])
print("Done")
# Weight n-link edges
print("Setting n-link weights", flush=True, end="...")
def n_weight(s_r, s_g, s_b, t_r, t_g, t_b):
return 1.0 - 3.0**-0.5 * ((v_r[s] - v_r[t])**2 + (v_g[s] - v_g[t])**2 +
(v_b[s] - v_b[t])**2) / 65536.0 # Scale to 1
for e in g.edges():
s, t = e.source(), e.target()
e_w[e] = 0.13 * n_weight(v_r[s], v_g[s], v_b[s], v_r[t], v_g[t],
v_b[t])
print("Done")
# Double up and make directed
print("Converting to directed graph", flush=True, end="...")
g.set_directed(True)
g.add_edge_list([(e.target(), e.source(), e_w[e]) for e in g.edges()],
eprops=(e_w, ))
print("Done")
# Make t-link edges
print("Making t-link edges", flush=True, end="...")
f, b = g.add_vertex(2)
for n in range(rows * cols):
g.add_edge(f, n)
g.add_edge(n, b)
print("Done")
# Seeds
kde = KernalDensityEstimator([img[c] for c in f_seeds],
[img[c] for c in b_seeds])
# Weight t-link edges
print("Setting t-link weights", flush=True, end="...")
for row, col in product(range(rows), range(cols)):
if (row, col) in f_seeds:
e_w[g.edge(f, g.vertex(dex[row, col]))] = 1e9
e_w[g.edge(g.vertex(dex[row, col]), b)] = 0.0
elif (row, col) in b_seeds:
e_w[g.edge(f, g.vertex(dex[row, col]))] = 0.0
e_w[g.edge(g.vertex(dex[row, col]), b)] = 1e9
else:
(e_w[g.edge(f, g.vertex(dex[row, col]))],
e_w[g.edge(g.vertex(dex[row, col]), b)]) = kde.probs(img[row,
col])
print("Done")
# Perform the cut
print("Making the cut", flush=True, end="...")
res = gt.flow.boykov_kolmogorov_max_flow(g, f, b, e_w)
cut = gt.flow.min_st_cut(g, f, e_w, res)
print("Done")
# Display the result
print("Highlighting", flush=True, end="...")
highlight = np.array((0.2, 0.8, 0.8))
for row, col in product(range(rows), range(cols)):
if not cut[g.vertex(dex[row, col])]:
img[row, col] = 255 - highlight * (255 - img[row, col])
# img[row, col] = (0, 0, 128)
print("Done")
display_image(img)
return g, e_w, v_r, cut
sample_steiner_trees(g,
obs,
method,
n_samples=1,
gi=gi,
return_tree_nodes=return_tree_nodes)
te = time.time()
return te - ts
def run(g, N, method, return_tree_nodes):
t_sum = 0
gi = util.from_gt(g, None)
for i in tqdm(range(N), total=N):
obs = np.random.choice(np.arange(g.num_vertices()), 10, replace=False)
t_sum += wrapper_for_sampling_procedure(g, obs, method, gi,
return_tree_nodes)
print('{} took {:.2f} sec on average'.format(method, t_sum / N))
# return_tree_nodes plays a big difference here
# construting the GraphView is very time consuming
g_dim = 100
return_tree_nodes = True
g = lattice((g_dim, g_dim))
run(g, N, 'cut_naive', return_tree_nodes)
run(g, N, 'cut', return_tree_nodes)
run(g, N, 'loop_erased', return_tree_nodes)
import line_profiler
import numpy as np
from sample_pool import TreeSamplePool
from random_steiner_tree.util import from_gt
from graph_helpers import remove_filters
from core1 import query_score, prediction_error, matching_trees_cython
from core1_python import query_score as query_score_py, prediction_error as prediction_error_py, matching_trees
from graph_tool.generation import lattice
g = lattice((10, 10))
gv = remove_filters(g)
gi = from_gt(g)
pool = TreeSamplePool(gv,
n_samples=20,
method='cut',
gi=gi,
return_tree_nodes=True # using tree nodes
)
n_obs = 10
obs = np.random.permutation(g.num_vertices())[:n_obs]
print(obs)
pool.fill(obs)
q = 0
hidden_nodes = set(map(int, g.vertices())) - {q}- set(obs)
def test_circle():
size = 50
periodic = True
# periodic = False
graph = gt_gen.lattice([size, size], periodic=periodic)
if periodic:
figure_title = 'grid_periodic'
else:
figure_title = 'grid_non-periodic'
indices = np.arange(size * size)
rows = np.mod(indices, size)
cols = np.floor(indices / size)
v_pos = graph.new_vertex_property('vector<double>',
vals=np.vstack((rows, cols)).T)
radius = 10
center = (size + 1) * (size / 2)
vertex_w = set([])
for i in range(-radius, radius):
for j in range(-radius, radius):
if i ** 2 + j ** 2 < radius ** 2:
idx = j * size + i + center
vertex_w.add(idx)
jump = 1e-5
weight = graph.new_edge_property('double', vals=1)
for idx in vertex_w:
u = graph.vertex(idx)
for e in u.out_edges():
if e.target() not in vertex_w:
weight[e] = jump
v_color = graph.new_vertex_property('vector<double>')
for u in graph.vertices():
if graph.vertex_index[u] in vertex_w:
v_color[u] = [1, 0, 0, 1]
else:
v_color[u] = [0, 0, 1, 1]
vertex_w = list(vertex_w)
x = np.linspace(-np.pi, np.pi, size)
y = np.linspace(-np.pi, np.pi, size)
xx, yy = np.meshgrid(x, y)
z1 = np.sin(np.pi * xx).flatten()
z2 = np.sin(2 * np.pi * yy).flatten()
x_signal = z1
x_signal[vertex_w] = z2[vertex_w]
palette = sns.color_palette('RdBu', n_colors=256, desat=.7)
cmap = colors.ListedColormap(palette, N=256)
plt.figure()
plt.imshow(np.reshape(x_signal, (size, size)), interpolation='nearest',
cmap=cmap)
plt.savefig(figure_title + '_signal.pdf', dpi=300)
n_eigs = 500 # graph.num_vertices() - 1
alpha = -1e-4
factories = [spec.ConvolutionSGFT(graph, n_eigs, tau=200, weight=weight),
spec.PageRankSGFT(graph, n_eigs, alpha, weight=weight),
spec.ConvolutionSGFT(graph, n_eigs, tau=5, weight=None),
spec.PageRankSGFT(graph, n_eigs, alpha, weight=None)]
sgft.comparison.compare_spectrograms(factories, x_signal,
graph, v_pos,
file_name=figure_title,
show_ncomps=300)
spec.show_window(factories[0], center, weight=weight, pos=v_pos,
vertex_size=20,
file_name=figure_title + '_w_window.png')
spec.show_window(factories[1], center, weight=weight, pos=v_pos,
vertex_size=20,
file_name=figure_title + '_w_window_ppr.png')
spec.show_window(factories[2], center, weight=None, pos=v_pos,
vertex_size=20,
file_name=figure_title + '_u_window.png')
spec.show_window(factories[3], center, weight=None, pos=v_pos,
vertex_size=20,
file_name=figure_title + '_u_window_ppr.png')
def test_circle():
size = 100
graph = gt_gen.lattice([size, size], periodic=False)
indices = np.arange(size * size)
rows = np.mod(indices, size)
cols = np.floor(indices / size)
v_pos = graph.new_vertex_property('vector<double>',
vals=np.vstack((rows, cols)).T)
center = size * (size / 2) + size / 2 - 20
radius = 20
vertex_w = set([])
for i in range(-radius, radius):
for j in range(-radius, radius):
if i ** 2 + j ** 2 < radius ** 2:
idx = j * size + i + center
vertex_w.add(idx)
idx = j * size + i + center + 35
vertex_w.add(idx)
print len(vertex_w)
jump = 1e-5
weight = graph.new_edge_property('double', vals=1)
for idx in vertex_w:
u = graph.vertex(idx)
for e in u.out_edges():
if e.target() not in vertex_w:
weight[e] = jump
# for e in graph.edges():
# weight[e] += min(abs(0.01 * np.random.randn()), 1)
v_color = graph.new_vertex_property('vector<double>')
for u in graph.vertices():
if graph.vertex_index[u] in vertex_w:
v_color[u] = [1, 0, 0, 1]
else:
v_color[u] = [0, 0, 1, 1]
# gt_draw.graph_draw(graph, pos=v_pos, vertex_fill_color=v_color,
# vertex_size=3)
alpha = -1e-5
n_eigs = 50
factory_weighted = ppr.PersonalizedPageRank(graph, n_eigs, weight=weight)
factory_unweighted = ppr.PersonalizedPageRank(graph, n_eigs, weight=None)
spectrogram_weighted = np.zeros((graph.num_vertices(), n_eigs - 1))
spectrogram_unweighted = np.zeros((graph.num_vertices(), n_eigs - 1))
t = timeit.default_timer()
for v in range(graph.num_vertices()):
_, loadings_weighted = factory_weighted.vector([graph.vertex(v)], alpha)
_, loadings_unweighted = factory_unweighted.vector([graph.vertex(v)],
alpha)
spectrogram_weighted[v, :] = loadings_weighted
spectrogram_unweighted[v, :] = loadings_unweighted
print timeit.default_timer() - t
spectrogram_weighted = np.abs(spectrogram_weighted)
spectrogram_unweighted = np.abs(spectrogram_unweighted)
spectrogram_weighted /= np.atleast_2d(np.sum(spectrogram_weighted, axis=1)).T
spectrogram_unweighted /= np.atleast_2d(np.sum(spectrogram_unweighted, axis=1)).T
plt.figure()
plt.subplot(121)
plt.imshow(spectrogram_weighted, interpolation='none')
plt.title('Weighted')
plt.axis('tight')
plt.subplot(122)
plt.imshow(spectrogram_unweighted, interpolation='none')
plt.title('Unweighted')
plt.axis('tight')