def saveGraphs():
g = snap.LoadEdgeList(snap.PUNGraph, sys.argv[1],0,1)
Graphs = []
a = snap.TIntV()
for file in sys.argv[2:]:
Graphs.append(snap.LoadEdgeList(snap.PUNGraph, file, 0, 1))
folder = str(file).split("/")[0]
if folder != "data":
sys.exit("comparison should be made with file in 'data' folder")
data = sys.argv[2].split("/")[1]
path = "/"
if "DCS_LP" in sys.argv[1]:
path = "results/snap/"+data+"DCS_LP/"
else :# DCS_GREEDY
path = "results/snap/"+data+"DCS_GREEDY/"
if not os.path.exists(path) :
os.makedirs(path)
for i in g.Nodes() :
a.Add(i.GetId())
for i in range(0,len(Graphs)):
Graphs[i] = snap.GetSubGraph(Graphs[i],a)
filename = raw_input('Enter a snapgraph name: ')
print "saving graphs in: " + path +" under names "+filename+"i.txt"
for i in range(0,len(Graphs)):
snap.SaveEdgeList(Graphs[i],path+filename+str(i+1)+".txt","Minimal graph from" + sys.argv[1])
def main(argv):
asUnDir = False
oneGraph = False
if (len(argv) < 2):
sys.exit("usage: python lp.py [-d] <file1> ... <fileN>")
if (len(argv) == 2):
if argv[1] == "-d":
sys.exit("no input.")
oneGraph = True
if (len(argv) == 3 and argv[1] == "-d"):
asUnDir = True
oneGraph = True
if (len(argv) > 3 and argv[1] == "-d"):
asUnDir = True
if (oneGraph):
if (asUnDir):
Graph = snap.LoadEdgeList(snap.PNGraph, argv[2], 0, 1)
snap.MakeUnDir(Graph)
else:
Graph = snap.LoadEdgeList(snap.PUNGraph, argv[1], 0, 1)
printSingleGraph(Graph)
else:
Graphs = []
if (asUnDir):
for file in argv[2:]:
g = snap.LoadEdgeList(snap.PNGraph, file, 0, 1)
snap.MakeUnDir(g)
Graphs.append(g)
else:
for file in argv[1:]:
Graphs.append(snap.LoadEdgeList(snap.PUNGraph, file, 0, 1))
printMoreGraphs(Graphs)
dense = cplex.Cplex("dense.lp")
os.remove("dense.lp")
alg = dense.parameters.lpmethod.values
dense.parameters.lpmethod.set(alg.barrier)
# include the below line to not do the crossover and get a close
# but not exact solution that can be extracted with filterLpSolution
dense.parameters.barrier.crossover.set(-1)
startTime = time.clock()
#dense.parameters.lpmethod.set(5) # sifting algorithm
dense.solve()
printResults.save(dense)
print("time taken: " + str(time.clock() - startTime))
print "The solution is", dense.solution.get_status_string()
print "Density:", dense.solution.get_objective_value()
def loadGraph():
print("using graph " + sys.argv[1])
graph = snap.LoadEdgeList(snap.PUNGraph, sys.argv[1], 0, 1)
print(
str(graph.GetNodes()) + " nodes and " + str(graph.GetEdges()) +
" edges.")
return graph
def printStats(): g = snap.LoadEdgeList(snap.PUNGraph, sys.argv[1],0,1) for i in range(2,len(sys.argv)): cName,cExt = os.path.splitext(sys.argv[i]) a = snap.TIntV() gi = snap.LoadEdgeList(snap.PUNGraph, sys.argv[i], 0, 1) print "Printing stats..." for n in g.Nodes(): a.Add(n.GetId()) g0 = snap.GetSubGraph(gi,a) n = g0.GetNodes() e = g0.GetEdges() print "---" print "Stats from : " + str(cName) print "Nodes : "+str(n) print "Edges : "+str(e) print "Density : "+ str( e / float(n))
def findSmallestGraph(): g = snap.LoadEdgeList(snap.PUNGraph, sys.argv[1],0,1) Graphs = [] names = [] for file in sys.argv[2:]: Graphs.append(snap.LoadEdgeList(snap.PUNGraph, file, 0, 1)) lpName,lpExt = os.path.splitext(file) names.append(lpName) a = snap.TIntV() for i in g.Nodes() : a.Add(i.GetId()) density = 500 for i in range(0,len(Graphs)): Graphs[i] = snap.GetSubGraph(Graphs[i],a) newD = Graphs[i].GetEdges() / float(Graphs[i].GetNodes()) if newD < density : density = newD g = i print "Smallest graph was: "+ str(names[i]) print "Density: "+str(density) return (names[i],Graphs[g])
def fsg(nodes):
g = -1
Graphs = []
names = []
for file in sys.argv[1:]:
Graphs.append(snap.LoadEdgeList(snap.PUNGraph, file, 0, 1))
lpName, lpExt = os.path.splitext(file)
names.append(lpName)
a = snap.TIntV()
for i in nodes:
a.Add(i)
density = sys.maxint
for i in range(0, len(Graphs)):
Graphs[i] = snap.GetSubGraph(Graphs[i], a)
newD = Graphs[i].GetEdges() / float(Graphs[i].GetNodes())
if newD < density:
density = newD
g = i
print "Smallest graph was: " + str(names[g])
print "Density: " + str(density)
return (names[g], Graphs[g], density)
return a
# returns the induced subgraph of the nodes from graph over the graph target_graph
def getSubgraph(target_graph, graph):
a = snap.TIntV()
for i in graph.Nodes():
a.Add(i.GetId())
return snap.GetSubGraph(target_graph, a)
# Start of main program
if (len(sys.argv) < 3):
usage()
pG = snap.LoadEdgeList(snap.PUNGraph, sys.argv[1], 0, 1)
gG = snap.LoadEdgeList(snap.PUNGraph, sys.argv[2], 0, 1)
if "minLP" not in sys.argv[1]:
usage()
if "minGREEDY" not in sys.argv[2]:
usage()
print "What would you like to do?"
print "1) print common nodes"
print "2) print structural properties"
i = ""
while i not in ["1", "2"]:
i = raw_input(">")
if i == "1":
# calc similarities between node sets...
lpN = getNodes(lpG)
def loadGraphs(locations):
graphs = []
for arg in locations:
graphs.append(snap.LoadEdgeList(snap.PUNGraph, arg, 0, 1))
return graphs
def main(argv):
if len(argv) < 1:
usage()
gs = []
for file in argv[1:]:
gs.append(snap.LoadEdgeList(snap.PUNGraph, file, 0, 1))
# Load and solve LP
usr_in = ""
print "Program: minimize..."
print "use the following input"
print "data/oregonFAULT-2/oregon2_010421.txt data/oregonFAULT-2/oregon2_010428.txt data/oregonFAULT-2/oregon2_010407.txt"
print "1) minimize nodes wrt sys.argv[1:]"
print "2) Does this input fail (sys.argv[1:]) yes/no"
print "3) Run this: Example nodes"
while usr_in not in ["1", "2", "3"]:
usr_in = raw_input(">")
print "You have Choosen " + usr_in + "!"
if usr_in == "1":
lp.printMoreGraphs(gs)
dense = cplex.Cplex("dense.lp")
os.remove("dense.lp")
alg = dense.parameters.lpmethod.values
dense.parameters.lpmethod.set(alg.barrier)
dense.solve()
# get the nodes for the LP
nodes = getNodes(getNonZero(dense))
print "size nodes:" + str(nodes)
# minimize the nodes and respective graphs
n, gs = ddmin(2, nodes, gs)
gs0 = []
for g in gs:
gs0.append(getSubgraph(g, n))
lp.printMoreGraphs(gs)
dense = cplex.Cplex("dense.lp")
os.remove("dense.lp")
alg = dense.parameters.lpmethod.values
dense.parameters.lpmethod.set(alg.barrier)
dense.solve()
t = getSolution(getNonZero(dense))
(name, graph, density) = findSmallestGraph(n, gs)
print "t* = " + str(t)
print "density = " + str(density)
print "t* =? density : " + str(abs(t - density) < 0.000005)
print "Local minimal nodes: " + str(n)
print "---"
print "Would you like to save the fault inducing minimized graphs? y/n"
while usr_in not in ["y", "n"]:
usr_in = raw_input(">")
if usr_in == "y":
data = sys.argv[1].split("/")[1]
path = "results/snap/minimal/"
if not os.path.exists(path):
os.makedirs(path)
filename = raw_input('Enter a snapgraph name: ')
print "saving graphs in: " + path + " under names " + filename + "i.txt"
for i in range(0, len(gs)):
snap.SaveEdgeList(gs[i], path + filename + str(i + 1) + ".txt",
"Minimal graph from" + data)
else:
print "exiting..."
if usr_in == "2":
if testGraphs(gs, True):
print "No, input does not fail, e.g t* = density"
else:
print "Yes, input does fail, e.g t* != density"
if usr_in == "3":
nodes = [5388, 6659, 13237, 5466, 9019, 9013, 5611]
for g in gs:
g = getSubgraph(g, nodes)
lp.printMoreGraphs(gs)
dense = cplex.Cplex("dense.lp")
os.remove("dense.lp")
alg = dense.parameters.lpmethod.values
dense.parameters.lpmethod.set(alg.barrier)
dense.solve()
t = getSolution(getNonZero(dense))
(name, graph, density) = fsg(nodes)
print "t* = " + str(t)
print "density = " + str(density)
print "t* =? density : " + str(abs(t - density) < 0.000005)
print "Local minimal nodes: " + str(nodes)
# remove duplicates
nodes = list(set(nodes))
print "maximize t"
print "\nsubject to"
print(" +\n".join(nodes)) + " <= 1" # sum yi <= 1
for e in allEdges:
print(" +\n".join(e)) + " - t >= 0" # sum xij >= t
for c in allEdgeCons:
print " \n".join(c) # xij <= yi and xij <= yj
print "\nend"
if (oneGraph):
if (asUnDir):
Graph = snap.LoadEdgeList(snap.PNGraph, sys.argv[2], 0, 1)
snap.MakeUnDir(Graph)
else:
Graph = snap.LoadEdgeList(snap.PUNGraph, sys.argv[1], 0, 1)
printSingleGraph(Graph)
else:
Graphs = []
if (asUnDir):
for file in sys.argv[2:]:
g = snap.LoadEdgeList(snap.PNGraph, file, 0, 1)
snap.MakeUnDir(g)
Graphs.append(g)
else:
for file in sys.argv[1:]:
Graphs.append(snap.LoadEdgeList(snap.PUNGraph, file, 0, 1))
printMoreGraphs(Graphs)
xijm = [e for es in allEdges for e in es]
with open("dense.lp", "w") as f:
print >> f, "maximize "+tobj+" +"
print >> f, " +\n".join(xijm)
print >> f, "\nsubject to"
print >> f, (" +\n".join(nodes))+" <= 1" # sum yi <= 1
for c in allEdgeCons:
print >> f, " \n".join(c) # xij <= yi and xij <= yj
print >> f, "\nend"
Graphs = []
for file in sys.argv[1:]:
Graphs.append(snap.LoadEdgeList(snap.PUNGraph, file, 0, 1))
printGraphs(Graphs)
# index for all x's are 1-len(xijm), in cplex.
print "Warning: This file assumes already preprocessed files,"
print " meaning the input should be undirected and"
print " all node-sets should be equal, see preprocess.py.\n"
print "Warning: Only does " + str(5) + " iterations.\n"
print "Info: total number of edges:" + str(len(xijm))
dense0 = cplex.Cplex("dense.lp")
#dense0.set_results_stream(None)
alg = dense0.parameters.lpmethod.values
dense0.parameters.lpmethod.set(alg.barrier)
dense0.parameters.barrier.crossover.set(-1)
from lib import snap
import os
import sys
def usage():
sys.exit("usage: python pic.py <inputGraph.txt>")
if len(sys.argv) < 2:
usage()
g = snap.LoadEdgeList(snap.PUNGraph, sys.argv[1], 0, 1)
labels = snap.TIntStrH()
for NI in g.Nodes():
labels[NI.GetId()] = str(NI.GetId())
name = ""
while name == "":
name = raw_input("save file as: ")
print ">"
snap.DrawGViz(g, snap.gvlDot, name + ".png", " ", labels)
