| public static PromptExistingFile ( string out_file ) : bool | ||
| out_file | string | The file that shall be overwritten |
| return | bool | |
/// <summary>
/// Parallely computes the betweenness preference distribution of a given temporal network
/// </summary>
/// <param name="args"></param>
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet T2 [temporal_network_file] [output_file] [aggregationWndow=1] [undirected=false]");
return;
}
string out_file = args[2];
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
bool undirected = false;
int aggregationWindow = 1;
if (args.Length >= 4)
{
aggregationWindow = int.Parse(args[3]);
}
if (args.Length >= 5)
{
undirected = Boolean.Parse(args[4]);
}
Console.Write("Reading temporal network as {0} network...", undirected ? "undirected" : "directed");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[1], undirected: undirected);
Console.WriteLine(" done.");
Console.WriteLine("Applying aggregation window, length = {0}, time steps before = {1}", aggregationWindow, temp_net.Length);
temp_net.AggregateTime(aggregationWindow);
Console.WriteLine("done, time steps after = {0}", temp_net.Length);
Console.Write("Building aggregate networks ...");
temp_net.ReduceToTwoPaths();
Console.WriteLine(" done.");
Console.Write("Writing transition matrix ...");
WriteTwopathTransitionMatrix(temp_net, out_file);
Console.WriteLine("done.");
}
/// <summary>
/// Runs an SI spreading process on a temporal network and outputs the dynamics of the infection size
/// </summary>
/// <param name="args"></param>
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet spreading [temporal_network_file] [output_file]");
return;
}
string out_file = args[2];
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
Console.Write("Reading temporal network as directed...");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[1]);
// Prevent the network from being reduced to two paths
temp_net.StripEdgesToTwoPaths = false;
Console.WriteLine("done.");
Console.Write("Running SI spreading on temporal network with {0} time steps ...", temp_net.Length);
string times = null;
string output = SISpreading.RunSpreading(temp_net, out times, 1d);
Console.WriteLine(" done.");
if (output != null)
{
Console.Write("Finished path discovery. Writing path length matrix");
System.IO.File.WriteAllText(out_file, output);
System.IO.File.WriteAllText(out_file + ".times", times);
Console.WriteLine("done.");
}
}
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet tikz [temporal_network_file] [output_file]");
return;
}
string out_file = args[2];
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
Console.Write("Reading temporal network ...");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[1]);
Console.WriteLine("done.");
Console.Write("Exporting to tikz...");
TikzExporter.CreateTikzUnfolding(out_file, null, temp_net);
Console.WriteLine(" done.");
}
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet visualize [temporal_network_file] [output_png] [square=TRUE] [border=5]");
return;
}
string out_file = args[2];
bool square = true;
int border = 5;
if (args.Length >= 4)
{
square = bool.Parse(args[3]);
}
if (args.Length >= 5)
{
border = int.Parse(args[4]);
}
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
Console.Write("Reading temporal network ...");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[1]);
Console.WriteLine("done.");
CreateBitmap(temp_net, out_file, square, border);
Console.WriteLine(" done.");
}
/// <summary>
/// Runs a random walk process on an aggregate networks and outputs the dynamics of the infection size
/// </summary>
/// <param name="args"></param>
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet rw [network_file] [output_file] [RWMode=static_first] [aggregationWindow=1] [steps=1000]");
Console.WriteLine("\t where RWMode can be ... ");
Console.WriteLine("\t static_first\t Performs a random walk on the aggregate network that considers betweenness preferences computed from the temporal network");
Console.WriteLine("\t static_second\t ...");
return;
}
string out_file = args[2];
RandomWalkMode mode = RandomWalkMode.StaticFirstOrder;
int runs = 1;
int length = 1000;
int aggregationWindow = 1;
if (args.Length >= 4)
{
if (args[3] == "static_second")
{
mode = RandomWalkMode.StaticSecondOrder;
}
else
{
Console.WriteLine("Unknown walk mode '{0}'", args[3]);
}
}
if (args.Length >= 5)
{
aggregationWindow = int.Parse(args[4]);
}
if (args.Length >= 6)
{
runs = int.Parse(args[5]);
}
if (args.Length >= 7)
{
length = int.Parse(args[6]);
}
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
Console.Write("Reading temporal network as undirected network...");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[1], true);
Console.WriteLine("done.");
if (aggregationWindow != 1)
{
Console.WriteLine("Applying aggregation window, length = {0}, time steps before = {1}", aggregationWindow, temp_net.Length);
temp_net.AggregateTime(aggregationWindow);
Console.WriteLine("done, time steps after = {0}", temp_net.Length);
}
Console.Write("Building aggregate network...");
WeightedNetwork aggregateNet = temp_net.AggregateNetwork;
Console.WriteLine("done.");
Console.WriteLine("Starting random walk ...");
Dictionary <int, double> tvd = new Dictionary <int, double>();
RandomWalk walk = new RandomWalk(temp_net, mode);
for (int t = 0; t < length; t++)
{
walk.Step();
tvd[t] = walk.TVD;
Console.WriteLine("Node = {0}, step = {1}, tvd={2:0.000}", walk.CurrentNode, t, tvd[t]);
}
Console.Write("Writing time series of total variation distance ...");
StringBuilder sb = new StringBuilder();
foreach (var step in tvd)
{
sb.AppendLine(string.Format(System.Globalization.CultureInfo.GetCultureInfo("en-US").NumberFormat, "{0} {1}", step.Key, step.Value));
}
System.IO.File.WriteAllText(out_file + ".dat", sb.ToString());
Console.WriteLine(" done.");
}
/// <summary>
/// Creates the simple example network with betweenness preference that can be seen in the paper in Figure 2 (right)
/// </summary>
/// <param name="args"></param>
public static void Run(string[] args)
{
if (args.Length < 2)
{
Console.WriteLine("Usage: TempNet example [output_file]");
return;
}
string out_file = args[1];
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
TemporalNetwork temporal_net = new TemporalNetwork();
int k = 0;
for (int i = 0; i < 1; i++)
{
// Add edges according to two paths
temporal_net.AddTemporalEdge(k++, "c", "e");
temporal_net.AddTemporalEdge(k++, "e", "f");
temporal_net.AddTemporalEdge(k++, "a", "e");
temporal_net.AddTemporalEdge(k++, "e", "g");
temporal_net.AddTemporalEdge(k++, "c", "e");
temporal_net.AddTemporalEdge(k++, "e", "f");
temporal_net.AddTemporalEdge(k++, "a", "e");
temporal_net.AddTemporalEdge(k++, "e", "g");
temporal_net.AddTemporalEdge(k++, "c", "e");
temporal_net.AddTemporalEdge(k++, "e", "f");
// Note that the next added edge additionally continues a two-path e -> f -> e
temporal_net.AddTemporalEdge(k++, "f", "e");
temporal_net.AddTemporalEdge(k++, "e", "b");
// An additional edge that will be filtered during preprocessing
temporal_net.AddTemporalEdge(k++, "e", "b");
temporal_net.AddTemporalEdge(k++, "c", "e");
temporal_net.AddTemporalEdge(k++, "e", "f");
temporal_net.AddTemporalEdge(k++, "b", "e");
temporal_net.AddTemporalEdge(k++, "e", "g");
temporal_net.AddTemporalEdge(k++, "c", "e");
temporal_net.AddTemporalEdge(k++, "e", "f");
temporal_net.AddTemporalEdge(k++, "c", "e");
temporal_net.AddTemporalEdge(k++, "e", "f");
}
Console.Write("Saving to file ...");
TemporalNetwork.SaveToFile(out_file, temporal_net);
Console.WriteLine(" done.");
}
/// <summary>
/// Parallely computes the betweenness preference distribution of a given temporal network
/// </summary>
/// <param name="args"></param>
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet distribution [temporal_network_file] [output_file] [aggregationWndow=1] [undirected=false]");
return;
}
string out_file = args[2];
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
bool undirected = false;
int aggregationWindow = 1;
if (args.Length >= 4)
aggregationWindow = int.Parse(args[3]);
if (args.Length >= 5)
undirected = Boolean.Parse(args[4]);
Console.Write("Reading temporal network as {0} network...", undirected ? "undirected" : "directed");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[1], undirected:undirected);
Console.WriteLine(" done.");
Console.WriteLine("Applying aggregation window, length = {0}, time steps before = {1}", aggregationWindow, temp_net.Length);
temp_net.AggregateTime(aggregationWindow);
Console.WriteLine("done, time steps after = {0}", temp_net.Length);
Console.Write("Preparing temporal network ...");
temp_net.ReduceToTwoPaths();
Console.WriteLine(" done.");
double nodeNum = temp_net.AggregateNetwork.VertexCount;
double current = 0d;
double last_perc = 0d;
Console.WriteLine("Computing betweenness preference for {0} nodes ...", nodeNum);
// Parallely compute betweenness preference for all nodes
#if DEBUG
foreach(string v in temp_net.AggregateNetwork.Vertices)
#else
Parallel.ForEach<string>(temp_net.AggregateNetwork.Vertices, v =>
#endif
{
double betweennessPref = BetweennessPref.GetBetweennessPref(temp_net, v);
// Synchronized access to file and to counters ...
if(temp_net.AggregateNetwork.GetIndeg(v)>0 && temp_net.AggregateNetwork.GetOutdeg(v)>0)
lock (out_file)
{
System.IO.File.AppendAllText(out_file, v + " " + string.Format(System.Globalization.CultureInfo.GetCultureInfo("en-US").NumberFormat, "{0:0.000000}\n", betweennessPref));
current++;
if (100 * current / nodeNum >= last_perc + 5d)
{
last_perc = 100 * current / nodeNum;
Console.WriteLine("Completed for {0} nodes [{1:0.0} %]", current, last_perc);
}
}
}
#if !DEBUG
);
#endif
Console.WriteLine("done.");
}
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet G2_null [weighted_edge_list.agg.1.edges] [output_file]");
return;
}
string out_file = args[2];
string input_file = args[1];
if (!CmdlTools.PromptExistingFile(out_file))
{
return;
}
Console.Write("Reading edge list...");
string[] agg1 = System.IO.File.ReadAllLines(input_file);
Console.WriteLine("done.");
// Prepare output file
StringBuilder output = new StringBuilder();
output.AppendLine("source target weight");
Console.Write("Computing cumulative edge weights...");
// Compute the cumulative weight of all outgoing edges for all nodes
Dictionary <string, float> sum_out_w = new Dictionary <string, float>();
for (int i = 1; i < agg1.Length; i++)
{
string[] fields = agg1[i].Split(' ');
if (!sum_out_w.ContainsKey(fields[0]))
{
sum_out_w[fields[0]] = float.Parse(fields[2], nf);
}
else
{
sum_out_w[fields[0]] += float.Parse(fields[2], nf);
}
}
Console.WriteLine("done.");
Console.Write("Computing null model edge weights...");
// Compute the null model second-order edge weights for all second-order edges (i.e. two-paths)
for (int i = 1; i < agg1.Length; i++)
{
for (int j = 1; j < agg1.Length; j++)
{
string[] fields1 = agg1[i].Split(' ');
string[] fields2 = agg1[j].Split(' ');
// This is a two-path candidate
string a = fields1[0];
string b = fields1[1];
string c = fields2[0];
string d = fields2[1];
// It is a possible two-path if b==c
if (b == c)
{
float w_ab = float.Parse(fields1[2], nf);
float w_cd = float.Parse(fields2[2], nf);
float null_model_weight = 0.5f * w_ab * w_cd / (sum_out_w[c]);
output.AppendLine(string.Format(nf, "({0};{1}) ({1};{2}) {3:0.0000}", a, b, d, null_model_weight));
}
}
}
Console.WriteLine("done.");
// Write to file
Console.Write("Writing output file...");
System.IO.File.WriteAllText(out_file, output.ToString());
Console.WriteLine("done.");
}
/// <summary>
/// Runs a random walk process on an aggregate networks and outputs the dynamics of the infection size
/// </summary>
/// <param name="args"></param>
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet rw [network_file] [output_file] [WalkType=random] [aggregationWindow=1] [runs=1] [length=100000]");
Console.WriteLine("\t where WalkType can be ... ");
Console.WriteLine("\t bwp_pres\t Performs a random walk on the aggregate network that considers betweenness preferences computed from the temporal network");
Console.WriteLine("\t bwp_null\t ...");
return;
}
string out_file = args[2];
string type = "bwp_pres";
int runs = 1;
int length = 100000;
int aggregationWindow = 1;
if (args.Length >= 4)
{
type = args[3];
}
if (args.Length >= 5)
{
aggregationWindow = int.Parse(args[4]);
}
if (args.Length >= 6)
{
runs = int.Parse(args[5]);
}
if (args.Length >= 7)
{
length = int.Parse(args[6]);
}
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
Console.Write("Reading temporal network as undirected network...");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[1], true);
Console.WriteLine("done.");
if (aggregationWindow != 1)
{
Console.WriteLine("Applying aggregation window, length = {0}, time steps before = {1}", aggregationWindow, temp_net.Length);
temp_net.AggregateTime(aggregationWindow);
Console.WriteLine("done, time steps after = {0}", temp_net.Length);
}
Console.Write("Building aggregate network...");
WeightedNetwork aggregateNet = temp_net.AggregateNetwork;
Console.WriteLine("done.");
for (int r = 2000; r <= 2000 + runs; r++)
{
Console.WriteLine("Running Random walk [{0}] in mode [{1}] ...", r, type);
IDictionary <int, double> tvd = null;
if (type == "bwp_pres")
{
tvd = RandomWalk.RunRW_BWP(temp_net, length, null_model: false);
}
else if (type == "bwp_null")
{
tvd = RandomWalk.RunRW_BWP(temp_net, length, null_model: true);
}
else
{
Console.WriteLine("\nError: RWType {0} unknown", type);
return;
}
Console.Write("Writing time series of total variation distance ...");
StringBuilder sb = new StringBuilder();
foreach (var step in tvd)
{
sb.AppendLine(string.Format(System.Globalization.CultureInfo.GetCultureInfo("en-US").NumberFormat, "{0} {1}", step.Key, step.Value));
}
System.IO.File.WriteAllText(out_file + "_r_" + r + ".dat", sb.ToString());
Console.WriteLine(" done.");
}
}
/// <summary>
/// Outputs a simple example temporal network
/// </summary>
/// <param name="args"></param>
public static void Run(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: TempNet aggregate [temporal_network_file] [output_file] [aggregationWindow=1] [weighted_aggregate_networks=false]");
return;
}
string out_file = args[2];
bool two_path = false;
int aggregationWindow = 1;
if (args.Length >= 4)
{
aggregationWindow = int.Parse(args[3]);
}
if (args.Length >= 5)
{
two_path = bool.Parse(args[4]);
}
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
Console.Write("Reading temporal network as undirected...");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[1], undirected: true);
Console.WriteLine(" done.");
Console.WriteLine(temp_net.Length);
Console.Write("Applying agggregation window [{0}] ...", aggregationWindow);
temp_net.AggregateTime(aggregationWindow);
Console.WriteLine("done.");
Console.WriteLine(temp_net.Length);
Console.Write("Reducing to two path networks ...");
temp_net.ReduceToTwoPaths();
Console.WriteLine("done.");
if (!two_path)
{
Console.Write("Saving temporal network ...");
TemporalNetwork.SaveToFile(out_file, temp_net);
Console.WriteLine(" done.");
}
else
{
//WeightedNetwork net = new WeightedNetwork();
//foreach(string tp in temp_net.TwoPathWeights.Keys)
//{
// string[] comps = tp.Split(',');
// net.AddEdge(comps[0], comps[2], EdgeType.Directed, temp_net.TwoPathWeights[tp]);
//}
Console.Write("Saving weighted first-order aggregate network ...");
WeightedNetwork.SaveToFile(out_file + ".1.edges", temp_net.AggregateNetwork);
Console.WriteLine(" done.");
Console.Write("Saving weighted second-order aggregate network ...");
WeightedNetwork.SaveToFile(out_file + ".2.edges", temp_net.SecondOrderAggregateNetwork);
Console.WriteLine(" done.");
}
}
/// <summary>
/// Creates randomized temporal networks based on a shuffling of edges or two-paths
/// </summary>
/// <param name="args"></param>
public static void Run(string[] args)
{
if (args.Length < 4)
{
Console.WriteLine("Usage: TempNet shuffle [what] [original_net_file] [output_file] [undirected=false] [length=0]");
Console.WriteLine("... where [what] is ...");
Console.WriteLine("\t 'twopaths' \t Shuffle the two-paths in the original network. Preserves the aggregate network and the betweenness preference distribution.");
Console.WriteLine("\t 'edges' \t Shuffles the edges in the original network. Preserves the aggregate network only.");
Console.WriteLine("");
return;
}
string shuffling = args[1];
string out_file = args[3];
if (!CmdlTools.PromptExistingFile(out_file))
{
Console.WriteLine("User opted to exit.");
return;
}
bool undirected = false;
if (args.Length >= 5)
{
undirected = bool.Parse(args[4]);
}
int length = 0;
if (args.Length == 6)
{
length = int.Parse(args[5]);
}
TemporalNetwork output = null;
Console.Write("Reading temporal network as {0} network...", undirected ? "undirected" : "directed");
TemporalNetwork temp_net = TemporalNetwork.ReadFromFile(args[2], undirected: undirected);
Console.WriteLine(" done.");
Console.Write("Extracting two paths and building aggregate network...");
temp_net.ReduceToTwoPaths();
Console.WriteLine(" done.");
if (shuffling == "twopaths")
{
Console.Write("Shuffling two paths ...");
output = TemporalNetworkEnsemble.ShuffleTwoPaths(temp_net, length);
Console.WriteLine(" done.");
}
else if (shuffling == "edges")
{
Console.Write("Shuffling edges ...");
output = TemporalNetworkEnsemble.ShuffleEdges(temp_net, length);
Console.WriteLine(" done.");
}
else
{
Console.WriteLine("{0} is not a valid parameter!", shuffling);
}
if (output != null)
{
Console.Write("Saving temporal network to {0}...", out_file);
TemporalNetwork.SaveToFile(out_file, output);
Console.WriteLine(" done.");
}
}