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 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 __build_graph(self, edges, pos, radii):
g = DiGraph()
g.add_edges_from(edges)
for i, p, r in zip(g.GetNodes(), pos, radii):
g.node[i]['pos'] = p
g.node[i]['r'] = r
self.graph = g
flow_in_edges = dict()
for i in currents_in_edges.keys():
flow_in_edges[i] = np.sum([flow[j] for j in currents_in_edges[i]])
# set flow at eache edge
for i in di_g.GetEdges():
if flow_in_edges[i] >= 0:
di_g[i[0]][i[1]]['flow'] = str(flow_in_edges[i])
pass
else:
di_g.ReverseEdge(i)
di_g[i[1]][i[0]]['flow'] = str(-flow_in_edges[i])
# set flow at each node
for i in di_g.GetNodes():
n = di_g.GetSuccessors(i)
if len(n) >= 1:
di_g.node[i]['flow'] = sum([float(di_g[i][j]['flow']) for j in n])
else:
n = di_g.GetPredecessors(i)
di_g.node[i]['flow'] = sum([float(di_g[j][i]['flow']) for j in n])
# set pressure at each edge
flows = [float(di_g[i[0]][i[1]]['flow']) for i in di_g.GetEdges()]
reses = [float(di_g[i[0]][i[1]]['res']) for i in di_g.GetEdges()]
pressures = np.array(flows) * np.array(reses)
for i, p in zip(di_g.GetEdges(), pressures):
di_g[i[0]][i[1]]['pressure'] = str(p)
class GenerateDiGraph(GraphObject):
def __init__(self, Graph=None):
GraphObject.__init__(self, Graph)
def TransferAttributes(self, DiG, G):
attr = ['pos', 'r', 'type', 'branch', 'source', 'sink', 'root']
for att in attr:
for i in DiG.GetNodes():
try:
DiG.node[i][att] = G.node[i][att]
except:
pass
edg = G.GetEdges()[0]
attr_edg = G[edg[0]][edg[1]].keys()
for att in attr_edg:
try:
for i in DiG.GetEdges():
DiG[i[0]][i[1]][att] = G[i[0]][i[1]][att]
except:
print('No edge attribute: \'' + att + '\' assigned to graph!')
############## if attributes are set for some but not all of graph compartments
# ------------ edges ---------#
for i in DiG.GetEdges():
try:
DiG[i[0]][i[1]]['inflow'] = G[i[0]][i[1]]['inflow']
except:
pass
try:
DiG[i[0]][i[1]]['outflow'] = G[i[0]][i[1]]['outflow']
except:
pass
try:
DiG[i[0]][i[1]]['pressure'] = G[i[0]][i[1]]['pressure']
except:
pass
# --------- nodes ------------#
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
try:
DiG.node[i]['sink'] = G.node[i]['sink']
except:
pass
try:
DiG.node[i]['source'] = G.node[i]['source']
except:
pass
def UpdateReducedDiGraphFromGraph(self):
'''
This function generated directed graphs from undirected graph
Note: Sources and Sinks has to be initialized in the object of this class
'''
def flip(s):
return [(i[1], i[0]) for i in s]
def get_traversal(source):
# nodes traversal
non_tree_branches = list(nx.edge_dfs(self.ReducedGraph,
source)) # passes nodes
# edges traversal
tree_branches = list(nx.bfs_edges(self.ReducedGraph,
source)) # passes edges
# to complete cycles (while avoiding self sink)
bi_tree_branches = set(tree_branches).union(
set(flip(tree_branches)))
missing_edges = set(non_tree_branches).difference(bi_tree_branches)
missing_eges = list(missing_edges)
[tree_branches.append(i) for i in missing_edges]
return tree_branches
DirectedBranchesAll = []
for i in self.Sources:
DirectedBranchesAll.append(get_traversal(i))
try:
for i in self.Sinks:
e = get_traversal(i)
e = flip(e)
DirectedBranchesAll.append(e)
except:
'Cannot use sinks to generate Directed edges!'
#----- fix for multiple sources/sinks ----#
nodes = self.ReducedGraph.GetNodes()
visited_edges = set()
composed_edges = zip(*DirectedBranchesAll)
edges = []
for i in composed_edges:
edges_to_add = []
[
edges_to_add.append(k) for k in i
if (k[1], k[0]) not in edges_to_add
]
edges_to_add = list(set(edges_to_add))
# chech if edge not added
not_added = [k not in visited_edges for k in edges_to_add]
edges_to_add = [z for z, k in zip(edges_to_add, not_added) if k]
edges.extend(edges_to_add)
#add edges' nodes to visted nodes
visited_edges = visited_edges.union(set(edges_to_add))
visited_edges = visited_edges.union(set(flip(edges_to_add)))
DirectedBranches = edges
#------ ReducedDiGraph -----#
self.ReducedDiGraph = DiGraph()
self.ReducedDiGraph.add_edges_from(DirectedBranches)
self.TransferAttributes(self.ReducedDiGraph, self.Graph)
def UpdateDirectedBranches(self):
self.DirectedBranches = self.ReducedDiGraph.GetEdges()
def UpdateDictDirectedBranches(self):
Graph = self.Graph
nodes_branches = [
list(
nx.all_shortest_paths(Graph,
source=e[0],
target=e[1],
weight='weight'))
for e in self.DirectedBranches
]
self.DictDirectedBranches = dict(
zip(self.DirectedBranches, nodes_branches))
def UpdateDiGraphFromGraph(self, Sources=[], Sinks=[]):
self.Sources = Sources
self.Sinks = Sinks
if len(self.Sources) == 0:
raise ValueError
return
#------- Init ------#
self.InitGraph()
self.UpdateReducedGraph()
self.UpdateReducedDiGraphFromGraph()
self.UpdateDirectedBranches()
self.UpdateDictDirectedBranches()
#----- DiGraph ------#
self.DiGraph = DiGraph()
nodes_branches = [
self.DictDirectedBranches[i]
for i in self.DictDirectedBranches.keys()
]
#----- Create DiGraph -----#
edges = [self.branch_to_edges(j) for i in nodes_branches for j in i]
edges = [i for j in edges for i in j]
edges = list(set(edges)) # might be not needed
# add edges
self.DiGraph.add_edges_from(edges)
# add attributes
self.TransferAttributes(self.DiGraph, self.Graph)
for i in self.Sources:
self.DiGraph.node[i]['source'] = '1'
for i in self.Sinks:
self.DiGraph.node[i]['sink'] = '1'
def UpdateDiGraphFromGraph2(self, Sources=[], Sinks=[]):
'''
This function generate directed graphs from undirected graph and label di-graph nodes with the branch level
Input:
Source: inflow nodes
Sinks: outflow nodes
Note1: if Source or Sinks are not enterd, they will be
extarcted from the source/sink attributes that are on the input graph (self.Graph)
Note2: This funtion is better and fatser than 'self.UpdateDiGraphFromGraph', which even do not
add branch labels on the di-graph generated
'''
if len(Sources) == 0:
Sources = []
for i in self.DiGraph.GetNodes():
try:
if self.DiGraph.node[i]['source'] == '1':
Sources.append(i)
except:
pass
if len(Sources) == 0:
print('Sources need to be set!')
raise ValueError
self.Sources = Sources
self.Sinks = Sinks
roots = self.Sources
self.InitGraph()
for i in self.Graph.GetNodes():
try:
del (self.Graph.node[i]['branch'])
except:
pass
def flip(ed):
return [(i[1], i[0]) for i in ed]
def get_directed(gg, root):
'''
get directed graph using first breadth search giving one source
'''
edges = list(nx.bfs_edges(gg, root)) # directed edges
old_edges = gg.GetEdges()
g = gg.copy()
self.TransferAttributes(g, gg)
g.remove_edges_from(old_edges)
g = g.to_directed()
g.add_edges_from(edges)
keep_edges = list(set(old_edges).difference(set(edges)))
keep_edges = list(set(keep_edges).difference(set(flip(edges))))
g.add_edges_from(keep_edges)
return g
def propagate(g, n, b):
'''
propagate 1 step from one node forward
'''
cont = 1
g.node[n]['branch'] = b
stat = 0
while cont > 0:
try:
n = g.GetSuccessors(n)
except:
n = g.GetSuccessors(n[0])
if len(n) == 1:
g.node[n[0]]['branch'] = b
stat = 1
else:
cont = 1
break
if len(n) == 0:
return 0, stat
else:
# try:
# dumb=g.node[n[0]]['branch'] # already passed (loopy structure)
# return 0, stat
# except:
return n, stat
def propagate_all(g, roots):
'''
assign branching labeles (brancing level) to a directed graph
'''
nextn = roots
branch = 1
while 1:
nxtn = []
stat = 0
for i in nextn:
n, s = propagate(g, i, branch)
stat += s
if not n == 0:
nxtn.append(n)
branch += 1
nextn = [j for i in nxtn for j in i]
if stat == 0: break
branches = []
no_branches = []
for i in g.GetNodes():
try:
b = g.node[i]['branch']
branches.append(b)
except:
no_branches.append(i)
pass
bmax = np.max(branches)
bmax = bmax + 1
for i in no_branches:
g.node[i]['branch'] = bmax
for e in g.GetEdges():
g[e[0]][e[1]]['branch'] = g.node[e[0]]['branch']
return g
def Transform(gg, roots):
'''
generate directed graphs when multiple sources are defined
'''
# generate seperate di-graphs from each of sources
graphs = []
for r in roots:
g = get_directed(gg, root=r)
g = propagate_all(g, roots=[r])
graphs.append(g)
# egdes
edges = [i.GetEdges() for i in graphs]
# baseline
e0 = edges[0] # edges from baseline di-graph
g0 = graphs[0].copy() # baseline di-graph
self.TransferAttributes(g0, graphs[0])
if len(roots) > 1:
for i, graph in zip(edges[1:], graphs[1:]):
# ------- fix branch level with edges of same orientation between baseline and new graph ---#
ed = np.array(
list(set(i).intersection(set(e0)))
) # edges that have similar orientaion between baseline and new graph
b_baseline = np.array([
graph[k[0]][k[1]]['branch'] for k in ed
]) # branch label on edges from di-g with differetn source
b_new = np.array([
g0[k[0]][k[1]]['branch'] for k in ed
]) # branch label on edges from baseline di-graph
b = np.array([b_baseline, b_new])
ind = np.argmin(b, axis=0)
new_b = b_baseline[ind ==
0] # new branch labels from new graph
new_e = ed[ind ==
0] # edges to bes assigned new branch labels
for ee, bb in zip(new_e, new_b):
g0[ee[0]][ee[1]]['branch'] = bb
g0.node[ee[0]]['branch'] = bb
#-------------- pick right edges( right orientations) and their branch labels between baseline and new graph -------#
ed = np.array(
list(set(i).difference(set(e0)))
) # edges with different orientation between the baseline and new di-graph
ed_flip = np.array(
flip(ed)) # flip edges to match that of from baseline
ed_b = np.array([
graph[k[0]][k[1]]['branch'] for k in ed
]) # branch label on edges from di-g with differetn source
ed_flip_b = np.array([
g0[k[0]][k[1]]['branch'] for k in ed_flip
]) # branch label on edges from baseline di-graph
b = np.array([ed_b, ed_flip_b])
ind = np.argmin(b, axis=0) # look for smaller branch level
new_b = ed_b[ind == 0]
new_e = ed[ind == 0]
remove_e = ed_flip[ind == 0]
g0.remove_edges_from(
remove_e
) # reomve edges with wrong orientation from baseline
g0.add_edges_from(new_e) # add right edge orientation
for ee, bb in zip(new_e, new_b):
g0[ee[0]][ee[1]]['branch'] = bb
g0.node[ee[0]]['branch'] = bb
return g0
g = Transform(self.Graph, roots=roots)
self.DiGraph = g
def UpdateReducedDiGraphFrom(self, DiGraph, ret=False):
ReducedDiGraph = DiGraph.copy()
cont = 1
while cont != 0:
cont = 0
for i in ReducedDiGraph.GetNodes():
p = ReducedDiGraph.GetPredecessors(i)
s = ReducedDiGraph.GetSuccessors(i)
if (len(p) == 1 and len(s) == 1):
ReducedDiGraph.remove_node(i)
ReducedDiGraph.add_edge(p[0], s[0], weight=1)
cont = 1
if ret == True:
return ReducedDiGraph
else:
self.ReducedDiGraph = ReducedDiGraph
def UpdateDirectedBranchesFrom(self, ReducedDiGraph):
return ReducedDiGraph.GetEdges()
def UpdateDictDirectedBranchesFrom(self, Graph, DirectedBranches):
nodes_branches = [
list(
nx.all_shortest_paths(Graph,
source=e[0],
target=e[1],
weight='weight'))
for e in DirectedBranches
]
return dict(zip(DirectedBranches, nodes_branches))
def UpdateReducedTree(self):
try:
self.Tree
except:
print('UpdateTreeFromDiGraph')
return
self.ReducedTree = self.UpdateReducedDiGraphFrom(self.Tree, ret=True)
def UpdateReducedDiGraph(self):
try:
self.DiGraph
except:
print('UpdateDiGraph')
return
self.ReducedDiGraph = self.UpdateReducedDiGraphFrom(self.DiGraph,
ret=True)
def UpdateTreeFromDiGraph(self, root, forest=False):
try:
self.DiGraph
except:
print('Run UpdateDiGraph!')
return
if forest == False:
self.Tree = nx.maximum_spanning_arborescence(self.DiGraph.copy())
# set tree root
self.TreeRoot = root
self.TransferAttributes(self.Tree, self.DiGraph)
self.UpdateReducedTree()
else:
self.Tree = nx.maximum_branching(self.DiGraph.copy())
# set tree root
self.TreeRoot = None
self.TransferAttributes(self.Tree, self.DiGraph)
self.UpdateReducedTree()
self.Tree.node[root]['root'] = '1'
# ----- Setters -------#
def SetDiGraph(self, DiGraph):
self.DiGraph = DiGraph
def SetTree(self, Tree):
self.Tree = Tree
chck = 0
for i in self.Tree.GetNodes():
try:
self.Tree.node[i]['root']
chch + 1
except:
pass
if chck == 0:
for i in self.Tree.GetNodes():
if len(self.Tree.GetPredecessors(i)) == 0:
print('Tree root: ' + str(i))
self.Tree.node[i]['root'] = '1'
if chck > 1:
print('This input is not a tree graph!')
self.Tree = None
#------ Getters -------#
def GetDirectedBranches(self):
try:
return self.DirectedBranches
except:
print('Run UpdateDiGraph!')
def GetDictDirectedBranches(self):
try:
return self.DictDirectedBranches
except:
print('Run UpdateDiGraph!')
def GetDiGraph(self):
try:
return self.DiGraph
except:
print('Run UpdateDiGraph!')
def GetReducedDiGraph(self):
try:
return self.ReducedDiGraph
except:
print('Run UpdateDiGraph!')
def GetReducedTree(self):
try:
return self.ReducedTree
except:
print('Run UpdateTreeFromDiGraph!')
def GetTree(self):
try:
return self.Tree
except:
print('Run UpdateTreeFromDiGraph!')