def grid_ville():
'''
Type: Graph
Number of nodes: 1200
Number of edges: 1320
Average degree: 2.2000
Gridville summed lengths: 24200.000000000062
'''
grid_ville = nx.Graph()
# divisor and extents
div = 12
ext = 1100
# add nodes
for x_id in range(div):
for y_id in range(div):
grid_ville.add_node(f'{x_id}_{y_id}',
x=ext / div * x_id,
y=ext / div * y_id)
# add edges
sum_lengths = 0
for x_id in range(div):
for y_id in range(div):
node_set = []
# last row and column do not have a next row / column
# add edge in the x direction
if y_id < div - 1:
a_nd_start = f'{x_id}_{y_id}'
a_nd_end = f'{x_id}_{y_id + 1}'
node_set.append((a_nd_start, a_nd_end))
# add edge in the y direction
if x_id < div - 1:
b_nd_start = f'{x_id}_{y_id}'
b_nd_end = f'{x_id + 1}_{y_id}'
node_set.append((b_nd_start, b_nd_end))
# for x direction and y direction node sets, add edges and edge geoms
for start, end in node_set:
start_x = grid_ville.nodes[start]['x']
start_y = grid_ville.nodes[start]['y']
end_x = grid_ville.nodes[end]['x']
end_y = grid_ville.nodes[end]['y']
geom = geometry.LineString([(start_x, start_y),
(end_x, end_y)])
grid_ville.add_edge(start, end, geom=geom)
sum_lengths += geom.length
# decompose new edges
grid_ville = graphs.nX_decompose(grid_ville, 20)
# print info
print(nx.info(grid_ville))
# report sum
print(f'Gridville summed lengths: {sum_lengths}')
# ready
return grid_ville
def test_to_networkX(primal_graph):
# also see test_graphs.test_networkX_from_graph_maps for underlying graph maps version
# check round trip to and from graph maps results in same graph
# explicitly set live and weight params for equality checks
# graph_maps_from_networkX generates these implicitly if missing
G = graphs.nX_decompose(primal_graph, decompose_max=20)
for n in G.nodes():
G.nodes[n]['live'] = bool(np.random.randint(0, 1))
for s, e, k in G.edges(keys=True):
G[s][e][k]['imp_factor'] = np.random.randint(0, 2)
# add random data to check persistence at other end
baa_node = None
for n in G.nodes():
baa_node = n
G.nodes[n]['boo'] = 'baa'
break
boo_edge = None
for s, e, k in G.edges(keys=True):
boo_edge = (s, e)
G[s][e][k]['baa'] = 'boo'
break
# test with metrics
N = networks.NetworkLayerFromNX(G, distances=[500])
N.node_centrality(measures=['node_harmonic'])
metrics_dict = N.metrics_to_dict()
G_round_trip = N.to_networkX()
for n, d in G.nodes(data=True):
assert G_round_trip.nodes[n]['x'] == d['x']
assert G_round_trip.nodes[n]['y'] == d['y']
assert G_round_trip.nodes[n]['live'] == d['live']
for s, e, k, d in G.edges(keys=True, data=True):
assert G_round_trip[s][e][k]['geom'] == d['geom']
assert G_round_trip[s][e][k]['imp_factor'] == d['imp_factor']
# check that metrics came through
for uid, metrics in metrics_dict.items():
assert G_round_trip.nodes[uid]['metrics'] == metrics
# check data persistence
assert G_round_trip.nodes[baa_node]['boo'] == 'baa'
assert G_round_trip[boo_edge[0]][boo_edge[1]][0]['baa'] == 'boo'
from shapely import geometry
from cityseer.metrics import networks, layers
from cityseer.tools import mock, graphs, plot
base_path = os.getcwd()
plt.style.use('matplotlibrc')
###
# INTRO PLOT
G = mock.mock_graph()
plot.plot_nX(G, labels=True, node_size=80, path='images/graph.png', dpi=150)
# INTRO EXAMPLE PLOTS
G = graphs.nX_simple_geoms(G)
G = graphs.nX_decompose(G, 20)
N = networks.NetworkLayerFromNX(G, distances=[400, 800])
N.segment_centrality(measures=['segment_harmonic'])
data_dict = mock.mock_data_dict(G, random_seed=25)
D = layers.DataLayerFromDict(data_dict)
D.assign_to_network(N, max_dist=400)
landuse_labels = mock.mock_categorical_data(len(data_dict), random_seed=25)
D.hill_branch_wt_diversity(landuse_labels, qs=[0])
G_metrics = N.to_networkX()
segment_harmonic_vals = []
mixed_uses_vals = []
for node, data in G_metrics.nodes(data=True):
segment_harmonic_vals.append(
def test_nX_from_graph_maps(primal_graph):
# also see test_networks.test_to_networkX for tests on implementation via Network layer
# check round trip to and from graph maps results in same graph
# explicitly set live params for equality checks
# graph_maps_from_networkX generates these implicitly if missing
for n in primal_graph.nodes():
primal_graph.nodes[n]['live'] = bool(np.random.randint(0, 1))
# test directly from and to graph maps
node_uids, node_data, edge_data, node_edge_map = graphs.graph_maps_from_nX(primal_graph)
G_round_trip = graphs.nX_from_graph_maps(node_uids, node_data, edge_data, node_edge_map)
assert list(G_round_trip.nodes) == list(primal_graph.nodes)
assert list(G_round_trip.edges) == list(primal_graph.edges)
# check with metrics dictionary
N = networks.NetworkLayerFromNX(primal_graph, distances=[500, 1000])
N.node_centrality(measures=['node_harmonic'])
data_dict = mock.mock_data_dict(primal_graph)
landuse_labels = mock.mock_categorical_data(len(data_dict))
D = layers.DataLayerFromDict(data_dict)
D.assign_to_network(N, max_dist=400)
D.compute_landuses(landuse_labels,
mixed_use_keys=['hill', 'shannon'],
accessibility_keys=['a', 'c'],
qs=[0, 1])
metrics_dict = N.metrics_to_dict()
# without backbone
G_round_trip_data = graphs.nX_from_graph_maps(node_uids,
node_data,
edge_data,
node_edge_map,
metrics_dict=metrics_dict)
for uid, metrics in metrics_dict.items():
assert G_round_trip_data.nodes[uid]['metrics'] == metrics
# with backbone
G_round_trip_data = graphs.nX_from_graph_maps(node_uids,
node_data,
edge_data,
node_edge_map,
networkX_multigraph=primal_graph,
metrics_dict=metrics_dict)
for uid, metrics in metrics_dict.items():
assert G_round_trip_data.nodes[uid]['metrics'] == metrics
# test with decomposed
G_decomposed = graphs.nX_decompose(primal_graph, decompose_max=20)
# set live explicitly
for n in G_decomposed.nodes():
G_decomposed.nodes[n]['live'] = bool(np.random.randint(0, 1))
node_uids_d, node_data_d, edge_data_d, node_edge_map_d = graphs.graph_maps_from_nX(G_decomposed)
G_round_trip_d = graphs.nX_from_graph_maps(node_uids_d, node_data_d, edge_data_d, node_edge_map_d)
assert list(G_round_trip_d.nodes) == list(G_decomposed.nodes)
for n, iter_node_data in G_round_trip.nodes(data=True):
assert n in G_decomposed
assert iter_node_data['live'] == G_decomposed.nodes[n]['live']
assert iter_node_data['x'] == G_decomposed.nodes[n]['x']
assert iter_node_data['y'] == G_decomposed.nodes[n]['y']
assert G_round_trip_d.edges == G_decomposed.edges
# error checks for when using backbone graph:
# mismatching numbers of nodes
corrupt_G = primal_graph.copy()
corrupt_G.remove_node(0)
with pytest.raises(ValueError):
graphs.nX_from_graph_maps(node_uids,
node_data,
edge_data,
node_edge_map,
networkX_multigraph=corrupt_G)
# mismatching node uid
with pytest.raises(KeyError):
corrupt_node_uids = list(node_uids)
corrupt_node_uids[0] = 'boo'
graphs.nX_from_graph_maps(corrupt_node_uids,
node_data,
edge_data,
node_edge_map,
networkX_multigraph=primal_graph)
# missing edge
with pytest.raises(KeyError):
corrupt_primal_graph = primal_graph.copy()
corrupt_primal_graph.remove_edge(0, 1)
graphs.nX_from_graph_maps(node_uids,
node_data,
edge_data,
node_edge_map,
networkX_multigraph=corrupt_primal_graph)
def test_nX_decompose(primal_graph):
# check that missing geoms throw an error
G = primal_graph.copy()
del G[0][1][0]['geom']
with pytest.raises(KeyError):
graphs.nX_decompose(G, 20)
# check that non-LineString geoms throw an error
G = primal_graph.copy()
for s, e, k in G.edges(keys=True):
G[s][e][k]['geom'] = geometry.Point([G.nodes[s]['x'], G.nodes[s]['y']])
break
with pytest.raises(TypeError):
graphs.nX_decompose(G, 20)
# test decomposition
G = primal_graph.copy()
# first clean the graph to strip disconnected looping component
# this gives a start == end node situation for testing
G_simple = graphs.nX_remove_filler_nodes(G)
G_decompose = graphs.nX_decompose(G_simple, 50)
# from cityseer.tools import plot
# plot.plot_nX(G_simple, labels=True, node_size=80, plot_geoms=True)
# plot.plot_nX(G_decompose, plot_geoms=True)
assert nx.number_of_nodes(G_decompose) == 292
assert nx.number_of_edges(G_decompose) == 314
for s, e in G_decompose.edges():
assert G_decompose.number_of_edges(s, e) == 1
# check that total lengths are the same
G_lens = 0
for s, e, e_data in G_simple.edges(data=True):
G_lens += e_data['geom'].length
G_d_lens = 0
for s, e, e_data in G_decompose.edges(data=True):
G_d_lens += e_data['geom'].length
assert np.allclose(G_lens, G_d_lens, atol=0.001, rtol=0)
# check that geoms are correctly flipped
G_forward = primal_graph.copy()
G_forward_decompose = graphs.nX_decompose(G_forward, 20)
G_backward = primal_graph.copy()
for i, (s, e, k, d) in enumerate(G_backward.edges(data=True, keys=True)):
# flip each third geom
if i % 3 == 0:
G[s][e][k]['geom'] = geometry.LineString(d['geom'].coords[::-1])
G_backward_decompose = graphs.nX_decompose(G_backward, 20)
for n, d in G_forward_decompose.nodes(data=True):
assert d['x'] == G_backward_decompose.nodes[n]['x']
assert d['y'] == G_backward_decompose.nodes[n]['y']
# test that geom coordinate mismatch throws an error
G = primal_graph.copy()
for k in ['x', 'y']:
for n in G.nodes():
G.nodes[n][k] = G.nodes[n][k] + 1
break
with pytest.raises(ValueError):
graphs.nX_decompose(G, 20)
def test_assign_to_network(primal_graph):
# create additional dead-end scenario
primal_graph.remove_edge(14, 15)
primal_graph.remove_edge(15, 28)
# G = graphs.nX_auto_edge_params(G)
G = graphs.nX_decompose(primal_graph, 50)
node_uids, node_data, edge_data, node_edge_map = graphs.graph_maps_from_nX(G)
# generate data
data_dict = mock.mock_data_dict(G, random_seed=25)
data_uids, data_map = layers.data_map_from_dict(data_dict)
# override data point locations for test cases vis-a-vis isolated nodes and isolated edges
data_map[18, :2] = [701200, 5719400]
data_map[39, :2] = [700750, 5720025]
data_map[26, :2] = [700400, 5719525]
# 500m visually confirmed in plots
data_map_1600 = data_map.copy()
data_map_1600 = data.assign_to_network(data_map_1600,
node_data,
edge_data,
node_edge_map,
max_dist=1600)
targets = np.array([
[0, 164, 163],
[1, 42, 241],
[2, 236, 235],
[3, 48, 262],
[4, 211, 212],
[5, 236, 235],
[6, 58, 57],
[7, 72, 5],
[8, 75, 76],
[9, 92, 9],
[10, 61, 62],
[11, 96, 13],
[12, 0, 59],
[13, 98, 99],
[14, 203, 202],
[15, 121, 120],
[16, 48, 262],
[17, 2, 70],
[18, 182, 183],
[19, 158, 157],
[20, 83, 84],
[21, 2, np.nan],
[22, 171, 170],
[23, 266, 52],
[24, 83, 84],
[25, 88, 11],
[26, 49, np.nan],
[27, 19, 138],
[28, 134, 135],
[29, 262, 46],
[30, 78, 9],
[31, 188, 189],
[32, 180, 181],
[33, 95, 94],
[34, 226, 225],
[35, 110, 111],
[36, 39, 228],
[37, 158, 25],
[38, 88, 87],
[39, 263, np.nan],
[40, 120, 121],
[41, 146, 21],
[42, 10, 97],
[43, 119, 118],
[44, 82, 5],
[45, 11, 88],
[46, 100, 99],
[47, 138, 19],
[48, 14, np.nan],
[49, 106, 105]
])
# for debugging
# from cityseer.tools import plot
# plot.plot_graph_maps(node_data, edge_data, data_map)
# assignment map includes data x, data y, nearest assigned, next nearest assigned
assert np.allclose(data_map_1600[:, 2:],
targets[:, 1:],
equal_nan=True,
atol=0,
rtol=0)
# max distance of 0 should return all NaN
data_map_test_0 = data_map.copy()
data_map_test_0 = data.assign_to_network(data_map_test_0,
node_data,
edge_data,
node_edge_map,
max_dist=0)
assert np.all(np.isnan(data_map_test_0[:, 2]))
assert np.all(np.isnan(data_map_test_0[:, 3]))
# max distance of 2000 should return no NaN for nearest
# there will be some NaN for next nearest
data_map_test_2000 = data_map.copy()
data_map_test_2000 = data.assign_to_network(data_map_test_2000,
node_data,
edge_data,
node_edge_map,
max_dist=2000)
assert not np.any(np.isnan(data_map_test_2000[:, 2]))
def york_burb():
'''
NX graph summary before pruning
Name:
Type: Graph
Number of nodes: 42590
Number of edges: 43728
Average degree: 2.0534
NX graph summary after pruning
Name:
Type: Graph
Number of nodes: 1298
Number of edges: 1361
Average degree: 2.0971
Yorkburb summed lengths: 23704.85033655231
'''
db_config = {
'host': 'localhost',
'port': 5433,
'user': '******',
'database': 'gareth',
'password': ''
}
# use process loaders to load graph
york_burb = asyncio.run(inner_york_burb(db_config))
# sum lengths for reference
sum_lengths = 0
for s, e, d in york_burb.edges(data=True):
sum_lengths += geometry.LineString(d['geom']).length
print(f'Yorkburb summed lengths: {sum_lengths}')
# adjust x / y values to smaller coordinate system
# first pass - find minimums
min_x = min_y = np.inf
for n, d in york_burb.nodes(data=True):
x, y = (d['x'], d['y'])
if x < min_x:
min_x = x
if y < min_y:
min_y = y
# second pass - adjust coordinates
for n in york_burb.nodes():
old_x = york_burb.nodes[n]['x']
york_burb.nodes[n]['x'] = old_x - min_x
old_y = york_burb.nodes[n]['y']
york_burb.nodes[n]['y'] = old_y - min_y
# likewise adjust and check geoms
for s, e, d in york_burb.edges(data=True):
old_geom = d['geom']
new_geom = []
for x, y in old_geom.coords:
new_geom.append((x - min_x, y - min_y))
new_geom = geometry.LineString(new_geom)
d['geom'] = new_geom
assert old_geom.length == new_geom.length
# check that total lengths haven't changed
post_sum_lengths = 0
for s, e, d in york_burb.edges(data=True):
post_sum_lengths += geometry.LineString(d['geom']).length
assert post_sum_lengths == sum_lengths
# relabel nodes
rl = {}
rl_counter = 0
for n in york_burb.nodes():
rl[n] = rl_counter
rl_counter += 1
york_burb = nx.relabel_nodes(york_burb, rl, copy=True)
# remove link (shorten dead-end to simplify adding new routes)
york_burb.remove_edge(1283, 1074)
# remove node (make way for adjacent edge)
york_burb.remove_nodes_from([157, 1089, 1144, 1163, 998, 503])
# add nodes where necessary
for x, y in [(460379.79, 451844.15), (460402.13, 451866.82),
(460429.81, 451876.83), (460462.79, 451626.64),
(460160.19, 451843.77), (460147.19, 451864.79),
(460140.00, 451826.62), (460107.08, 451863.13),
(460160.19, 451797.30), (460104.04, 451788.73),
(460188.12, 451423.61), (459840.70, 451434.38),
(459913.19, 451389.30)]:
adj_x = x - min_x
adj_y = y - min_y
york_burb.add_node(rl_counter, x=adj_x, y=adj_y)
rl_counter += 1
# add missing footpaths
for start_nd, end_nd in [
(238, 865), (1117, 43), (797, 67), (918, 797), (795, 653), (365, 797),
(705, 673), (230, 362), (1068, 1085), (666, 1041), (869, 426),
(116, 991), (1097, 991), (99, 312), (771, 1113), (1069, 1218),
(223, 447), (1167, 1186), (643, 1049), (1034, 185), (1189, 886),
(4, 671), (60, 78), (359, 1188), (540, 1283), (1283, 770), (770, 817),
(82, 889), (223, 306), (874, 304), (969, 478), (159, 1298),
(1298, 1299), (1299, 1300), (1300, 1246), (659, 1300), (1028, 1299),
(624, 1298), (1298, 616), (628, 1303), (1303, 1302), (1302, 160),
(1302, 1304), (1305, 1304), (1304, 1306), (945, 1307), (1307, 620),
(1307, 1275), (478, 1301), (1301, 493), (1301, 492), (1180, 1308),
(1308, 856), (871, 1308), (870, 1309), (1309, 1310), (1310, 1172),
(1310, 429), (1017, 778)
]:
x_start = (york_burb.nodes[start_nd]['x'])
y_start = (york_burb.nodes[start_nd]['y'])
x_end = (york_burb.nodes[end_nd]['x'])
y_end = (york_burb.nodes[end_nd]['y'])
geom = geometry.LineString([(x_start, y_start), (x_end, y_end)])
york_burb.add_edge(start_nd, end_nd, geom=geom)
# decompose new edges
york_burb = graphs.nX_decompose(york_burb, 20)
# ready
return york_burb
def suburb():
'''
Number of nodes: 1349
Number of edges: 1348
Average degree: 1.9985
Gridville summed lengths: 23550.0. Last length 14.0625
'''
suburb = nx.Graph()
# set params
recursions = 7
distance = 1200
# set the seed centroid
node_id = 1
suburb.add_node(node_id, x=distance / 2, y=distance / 2)
centroids = [node_id]
node_id += 1
# sum geom lengths
sum_lengths = 0
last_length = np.inf
# recursively add centroids and edges
for i in range(recursions):
# alternate directions
x_direction = True
if i % 2 == 0:
x_direction = False
# distance only updated every second cycle
distance = distance / 2 - 25
# new centroids - keep separate and then replace at end of loop
new_centroids = []
# for each centroid
for start_id in centroids:
x_start = suburb.nodes[start_id]['x']
y_start = suburb.nodes[start_id]['y']
# add the new nodes and geoms in either direction
for dist in [distance, -distance]:
# create the end coordinates
if x_direction:
x_centroid = x_start + dist / 2
y_centroid = y_start
x_end = x_start + dist
y_end = y_start
else:
x_centroid = x_start
y_centroid = y_start + dist / 2
x_end = x_start
y_end = y_start + dist
# calculate the new centroids and end nodes
centroid_id = node_id
node_id += 1
new_centroids.append(centroid_id) # add to new centroids
suburb.add_node(centroid_id, x=x_centroid, y=y_centroid)
end_id = node_id
node_id += 1
suburb.add_node(end_id, x=x_end, y=y_end)
# create the new geoms and edges
geom_a = geometry.LineString([(x_start, y_start),
(x_centroid, y_centroid)])
suburb.add_edge(start_id, centroid_id, geom=geom_a)
sum_lengths += geom_a.length
geom_b = geometry.LineString([(x_centroid, y_centroid),
(x_end, y_end)])
suburb.add_edge(centroid_id, end_id, geom=geom_b)
sum_lengths += geom_b.length
# keep track of least length
last_length = geom_a.length
centroids = new_centroids
# decompose new edges
suburb = graphs.nX_decompose(suburb, 20)
# print info
print(nx.info(suburb))
# report sum
print(f'Suburb summed lengths: {sum_lengths}. Last length {last_length}')
return suburb
def test_decomposed_local_centrality(primal_graph):
# centralities on the original nodes within the decomposed network should equal non-decomposed workflow
betas = np.array([0.02, 0.01, 0.005, 0.0008, 0.0])
distances = networks.distance_from_beta(betas)
node_measure_keys = ('node_density', 'node_farness', 'node_cycles',
'node_harmonic', 'node_beta', 'node_betweenness',
'node_betweenness_beta')
segment_measure_keys = ('segment_density', 'segment_harmonic',
'segment_beta', 'segment_betweenness')
# test a decomposed graph
G_decomposed = graphs.nX_decompose(primal_graph, 20)
# graph maps
node_uids, node_data, edge_data, node_edge_map = graphs.graph_maps_from_nX(
primal_graph) # generate node and edge maps
node_uids_decomp, node_data_decomp, edge_data_decomp, node_edge_map_decomp = graphs.graph_maps_from_nX(
G_decomposed)
# non-decomposed case
node_measures_data = centrality.local_node_centrality(node_data,
edge_data,
node_edge_map,
distances,
betas,
node_measure_keys,
angular=False)
# decomposed case
node_measures_data_decomposed = centrality.local_node_centrality(
node_data_decomp,
edge_data_decomp,
node_edge_map_decomp,
distances,
betas,
node_measure_keys,
angular=False)
# node
d_range = len(distances)
m_range = len(node_measure_keys)
assert node_measures_data.shape == (m_range, d_range, len(primal_graph))
assert node_measures_data_decomposed.shape == (m_range, d_range,
len(G_decomposed))
# with increasing decomposition:
# - node based measures will not match
# - closeness segment measures will match - these measure to the cut endpoints per thresholds
# - betweenness segment measures won't match - don't measure to cut endpoints
# segment versions
segment_measures_data = centrality.local_segment_centrality(
node_data,
edge_data,
node_edge_map,
distances,
betas,
segment_measure_keys,
angular=False)
segment_measures_data_decomposed = centrality.local_segment_centrality(
node_data_decomp,
edge_data_decomp,
node_edge_map_decomp,
distances,
betas,
segment_measure_keys,
angular=False)
m_range = len(segment_measure_keys)
assert segment_measures_data.shape == (m_range, d_range, len(primal_graph))
assert segment_measures_data_decomposed.shape == (m_range, d_range,
len(G_decomposed))
for m_idx in range(m_range):
for d_idx in range(d_range):
match = np.allclose(
segment_measures_data[m_idx][d_idx],
# compare against the original 56 elements (prior to adding decomposed)
segment_measures_data_decomposed[m_idx][d_idx][:57],
atol=0.1,
rtol=0) # relax precision
if m_range in (0, 1, 2):
assert match
