def BuildGraph(self):
'''
1 Build graph based on info from 'path_net'
2 Set attributes to graph nodes based on info from 'path_attr'
'''
def setatt(g, e, v, name):
for i, j in zip(e, v):
try:
if j > G.node[i[0]][name]:
G.node[i[0]][name] = j
except:
G.node[i[0]][name] = j
try:
if j > G.node[i[1]][name]:
G.node[i[1]][name] = j
except:
G.node[i[1]][name] = j
return g
p, e = self.ReadNet()
if self.path_attr is not None:
self.attr = self.ReadAttr()
if self.mode == 'di':
G = DiGraph()
else:
G = Graph()
G.add_nodes_from(range(len(p)))
for i, j in zip(G.GetNodes(), p):
G.node[i]['pos'] = j
e = np.array(e) - 1
G.add_edges_from(e.tolist())
# set diameter/radius
try:
d = np.array(self.attr['Dia']).ravel().astype(float)
G = setatt(G, e, d, 'd')
G = setatt(G, e, d / 2, 'r')
except:
print('--Cannot set diam!')
# set flow
try:
flow = np.array(self.attr['flow']).ravel().astype(float)
G = setatt(G, e, flow, 'flow')
except:
print('--Cannot set flow!')
# set po2
try:
po2 = np.array(self.attr['ppO2']).ravel().astype(float)
G = setatt(G, e, po2, 'po2')
except:
print('--Cannot set po2!')
self.G = fixG(G)
def BuildGraph(self):
'''
read nodes with their pos and diameter, read edges
'''
d, p, e, f = self.ReadLines()
G=DiGraph()
G.add_nodes_from(range(len(p)))
for i, j in zip(G.GetNodes(), p):
G.node[i]['pos']=j
e=np.array(e)-1
G.add_edges_from(e.tolist())
for i, j in zip(e, d):
try:
if j>G.node[i[0]]['d']:
G.node[i[0]]['d']=j
except:
G.node[i[0]]['d']=j
try:
if j>G.node[i[1]]['d']:
G.node[i[1]]['d']=j
except:
G.node[i[1]]['d']=j
self.G=fixG(G)
def fix_indexing(g_old, root):
bfs=list(nx.bfs_predecessors(treegraph, root))
old_indices=[root]
old_indices.extend([i[0] for i in bfs])
new_indices=range(len(old_indices))
mapping={old_indices[i]:new_indices[i] for i in new_indices}
g=DiGraph()
g.add_nodes_from(new_indices)
for i in old_indices:
g.node[mapping[i]]['pos']=g_old.node[i]['pos']
g.node[mapping[i]]['r']=g_old.node[i]['r']
edges_old=g_old.GetEdges()
edges_new=[[mapping[e[0]], mapping[e[1]]] for e in edges_old]
g.add_edges_from(edges_new)
return g
except:
pass
for i in DiG.GetNodes():
try:
DiG.node[i]['inflow'] = G.node[i]['inflow']
except:
pass
try:
DiG.node[i]['outflow'] = G.node[i]['outflow']
except:
pass
print('Build directed graph ...')
di_g = DiGraph()
di_g.add_nodes_from(g.GetNodes())
di_g.add_edges_from(di_edges)
TransferAttributes(di_g, g)
# ---------------------------------------------#
# ------ build A from cycles ---------#
print('Build A matrix ...')
# assigne currents contibuting to each edge
currents_in_edges = dict()
for ed in di_g.GetEdges():
cyc = []
for idx, c in enumerate(cycles):
if ed in c:
cyc.append(idx)