public SimpleSpreading(Network n, NetworkColorizer colorizer = null)
{
_network = n;
_colorizer = colorizer;
_infected = new List <Vertex>();
_infectionTime = new Dictionary <Vertex, long>();
}
static void Main(string[] args)
{
// Create a random network
SimpleNetwork net = SimpleNetwork.ReadFromEdgeList("demo.edges");
// We use a custom coloring
NetworkColorizer colors = new NetworkColorizer();
colors.DefaultBackgroundColor = Color.Black;
colors.DefaultEdgeColor = Color.WhiteSmoke;
colors.DefaultVertexColor = Color.SteelBlue;
// Let's use curved edges instead of the default straight ones
Renderer.CurvedEdges = true;
// Fire up the visualizer window
Renderer.Start(net, new NETVisualizer.Layouts.FruchtermanReingold.FRLayout(10), colors);
// Trigger the layout
Renderer.Layout.DoLayoutAsync();
// The rendering and layouting is done asynchronously in parallel,
// so you can modify the network while the visualization and the layout continues
Console.Write("Press ANY KEY to add another edge");
Console.ReadKey();
net.AddEdge("a", "b");
net.AddEdge("b", "c");
// Trigger the layout again. Only changed nodes will be relayouted ...
Renderer.Layout.DoLayoutAsync();
Console.WriteLine("Waiting for rendering window to be closed ...");
}
public SIRSpreading(Network n, NetworkColorizer colorizer = null)
{
_network = n;
_colorizer = colorizer;
_active = new List <Vertex>();
_infected = new List <Vertex>();
_infections = new Dictionary <Vertex, bool>();
}
public CEFPlayer(string cefFile, Network n, NetworkColorizer c = null)
{
filename = cefFile;
network = n;
colorizer = c;
if (cefFile == null || !System.IO.File.Exists(cefFile))
{
Logger.AddMessage(LogEntryType.Error, "Given cef-File does not exist.");
}
}
public static void Main(string[] args)
{
// Basic arg checking
if (args.Length != 2 || !System.IO.File.Exists(args[0]) || !System.IO.File.Exists(args[1]))
{
Console.WriteLine("Usage: CuttleFishPlayer [cxf-File] [cef-File]");
return;
}
// Used to color the network
NetworkColorizer colorizer = new NetworkColorizer();
colorizer.DefaultBackgroundColor = Color.White;
colorizer.DefaultVertexColor = Color.Black;
colorizer.DefaultEdgeColor = Color.Black;
// Load network from cuttlefish CXF-File
Network n = Network.LoadFromCXF(args[0]);
Logger.AddMessage(LogEntryType.AppMsg, string.Format("Initial network: {0} Nodes, {1} Edges", n.VertexCount, n.EdgeCount));
// Start the visualizer with Fruchterman-Reingold layout
NetworkVisualizer.Start(n, new RandomLayout(), colorizer);
// Compute layout and save initial frame
NetworkVisualizer.Layout.DoLayout();
NetworkVisualizer.SaveCurrentImage("frame_0000.bmp");
// Load network evolution from cuttlefish cef file
NETGen.Dynamics.CEF.CEFPlayer player = new NETGen.Dynamics.CEF.CEFPlayer(args[1], n, colorizer);
// On each evolution step, recompute layout and save current image
player.OnStep += new DiscreteDynamics.StepHandler(delegate(long time) {
NetworkVisualizer.Layout.DoLayout();
NetworkVisualizer.SaveCurrentImage(string.Format("frame_{0000}.bmp", time));
Logger.AddMessage(LogEntryType.AppMsg, string.Format("Time {0000}: {1} Nodes, {2} Edges", time, n.VertexCount, n.EdgeCount));
});
// Ready, set, go ...
Logger.AddMessage(LogEntryType.AppMsg, "Press enter to step through network evolution ...");
Console.ReadLine();
player.Run();
Network.SaveToGraphML("mono_network.graphml", n);
}
public VisualizerControl() :
base(Gtk.WindowType.Toplevel)
{
this.Build();
colorizer = new NetworkColorizer();
this.fileChooserNetworkFile.FileSet += HandleFileChooserNetworkFilehandleFileSet;
this.btnComputeLayout.Clicked += HandleBtnComputeLayouthandleClicked;
this.btnChoseDefaultNodeColor.ColorSet += HandleBtnChoseDefaultNodeColorhandleColorSet;
this.btnChoseEdgeColor.ColorSet += HandleBtnChoseEdgeColorhandleColorSet;
this.btnSearch.Clicked += HandleBtnSearchhandleClicked;
this.fileChooserExportPDF.FileSet += HandleFileChooserExportPDFhandleFileSet;
this.fileChooserExportBitmap.FileSet += HandleFileChooserExportBitmaphandleFileSet;
this.fileChooserHighlightNodes.FileSet += HandleFileChooserHighlightNodeshandleFileSet;
this.btnApplyNodeSize.Clicked += HandleBtnApplyNodeSizehandleClicked;
this.btnApplyEdgeWidth.Clicked += HandleBtnApplyEdgeWidthhandleClicked;
this.fileChooserCEFFile.FileSet += HandleFileChooserCEFFilehandleFileSet;
this.btnRunCEF.Clicked += HandlebtnRunCEFhandleClicked;
}
static void Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("\nUsage: Visualize [network-file] [iterations=50]\n");
return;
}
string network_file = args[0];
int iterations = args.Length >= 2 ? int.Parse(args[1]) : 50;
// Load the temporal and aggregate network
Console.Write("Loading temporal network ...");
TemporalNetwork net = TemporalNetwork.ReadFromFile(network_file);
Console.WriteLine("done");
Console.Write("Computing aggregate network ...");
WeightedNetwork agg = net.AggregateNetwork;
Console.WriteLine("done");
// Change the colors
NetworkColorizer colors = new NetworkColorizer();
colors.DefaultBackgroundColor = Color.White;
colors.DefaultVertexColor = Color.DarkBlue;
colors.DefaultEdgeColor = Color.Black;
Renderer.CurvedEdges = true;
RenderableTempNet temp_net = new RenderableTempNet(net);
// Start rendering ...
Renderer.Start(temp_net, new FRLayout(iterations), colors);
// Asynchronously compute the layout ...
Renderer.Layout.DoLayout();
Application.Run(new VisualizationController(temp_net));
}
static void Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("\nUsage: Visualize [network-file] [iterations=50]\n");
return;
}
string network_file = args[0];
int iterations = args.Length >= 2 ? int.Parse(args[1]) : 50;
// Load the temporal and aggregate network
Console.Write("Loading temporal network ...");
TemporalNetwork net = TemporalNetwork.ReadFromFile(network_file);
Console.WriteLine("done");
Console.Write("Computing aggregate network ...");
WeightedNetwork agg = net.AggregateNetwork;
Console.WriteLine("done");
// Change the colors
NetworkColorizer colors = new NetworkColorizer();
colors.DefaultBackgroundColor = Color.White;
colors.DefaultVertexColor = Color.DarkBlue;
colors.DefaultEdgeColor = Color.Black;
Renderer.CurvedEdges = true;
RenderableTempNet temp_net = new RenderableTempNet(net);
// Start rendering ...
Renderer.Start(temp_net, new FRLayout(iterations), colors);
// Asynchronously compute the layout ...
Renderer.Layout.DoLayout();
Application.Run(new VisualizationController(temp_net));
}
static void Main(string[] args)
{
try
{
// The resultfile is given as command line argument
//nodes = Int32.Parse(args[0]);
//edges = Int32.Parse(args[1]);
//clusters = Int32.Parse(args[2]);
resultfile = args[3];
} catch {
Console.WriteLine("Usage: mono Demo.exe [nodes] [edges] [clusters] [resultfile]");
return;
}
// Create a network of the given size and modularity ...
network = new ClusterNetwork(nodes, edges, clusters, 0.63d, true);
System.IO.StreamWriter sw = System.IO.File.CreateText("membership.dat");
int i = 0;
foreach (Vertex v in network.Vertices)
{
v.Label = (i++).ToString();
sw.WriteLine(network.GetClusterForNode(v).ToString());
}
sw.Close();
Network.SaveToEdgeFile(network, "network.edges");
Console.WriteLine("Created network with {0} vertices, {1} edges and modularity {2:0.00}", network.VertexCount, network.EdgeCount, network.NewmanModularityUndirected);
// Run the real-time visualization
NetworkColorizer colorizer = new NetworkColorizer();
//NetworkVisualizer.Start(network, new NETGen.Layouts.FruchtermanReingold.FruchtermanReingoldLayout(15), colorizer);
//NetworkVisualizer.Layout.DoLayoutAsync();
// Distribution of natural frequencies
double mean_frequency = 1d;
Normal normal = new Normal(mean_frequency, mean_frequency / 5d);
sync = new Kuramoto(network,
K,
colorizer,
new Func <Vertex, Vertex[]>(v => { return(new Vertex[] { v.RandomNeighbor }); })
);
foreach (Vertex v in network.Vertices)
{
sync.NaturalFrequencies[v] = normal.Sample();
}
foreach (int g in network.ClusterIDs)
{
pacemaker_mode[g] = false;
}
sync.OnStep += new Kuramoto.StepHandler(recordOrder);
Logger.AddMessage(LogEntryType.AppMsg, "Press enter to start synchronization experiment...");
Console.ReadLine();
// Run the simulation
sync.Run();
// Write the time series to the resultfile
if (resultfile != null)
{
sync.WriteTimeSeries(resultfile);
}
}
/// <summary>
/// Initializes a new synchronization experiment
/// </summary>
/// <param name='n'>
/// The network to run the experiment for
/// </param>
/// <param name='colorizer'>
/// Will be used to color vertices and edges as the experiment runs. Can be null or omitted altogether if no visualization is used.
/// </param>
/// <param name='selectNeighbor'>
/// A lambda expression that will be invoked whenever a neighbor is chosen to couple to. If null or not given, an unbiased random neighbor selection will be used.
/// </param>
public Kuramoto(Network n, double K, NetworkColorizer colorizer = null, Func <Vertex, Vertex[]> couplingSelector = null) : base(0d, new DenseVector((int)n.VertexCount))
{
_network = n;
_colorizer = colorizer;
CouplingStrengths = new Dictionary <Tuple <Vertex, Vertex>, double>();
NaturalFrequencies = new ConcurrentDictionary <Vertex, double>();
foreach (Edge e in _network.Edges)
{
Tuple <Vertex, Vertex> t1 = new Tuple <Vertex, Vertex>(e.Source, e.Target);
Tuple <Vertex, Vertex> t2 = new Tuple <Vertex, Vertex>(e.Target, e.Source);
if (e.EdgeType == EdgeType.Undirected || e.EdgeType == EdgeType.DirectedAB)
{
CouplingStrengths[t1] = K;
}
if (e.EdgeType == EdgeType.Undirected || e.EdgeType == EdgeType.DirectedBA)
{
CouplingStrengths[t2] = K;
}
}
_mapping = new Dictionary <Vertex, int>();
int i = 0;
foreach (Vertex v in _network.Vertices)
{
NaturalFrequencies[v] = 0.1d;
_mapping[v] = i++;
}
// if no neighbor selector is given, just couple to all nearest neighbors
if (couplingSelector == null)
{
CouplingSelector = new Func <Vertex, Vertex[]>(v => {
return(v.Neigbors.ToArray());
});
}
else
{
CouplingSelector = couplingSelector;
}
// Initialize phases, colors and average degree
foreach (Vertex v in _network.Vertices)
{
CurrentValues[_mapping[v]] = _network.NextRandomDouble() * Math.PI * 2d;
if (_colorizer != null)
{
_colorizer[v] = ColorFromPhase(CurrentValues[_mapping[v]]);
}
_avgDeg += v.Degree;
}
_avgDeg /= (double)_network.VertexCount;
Logger.AddMessage(LogEntryType.Info, string.Format("Sychchronization module initialized. Initial global order = {0:0.000}", GetOrder(_network.Vertices.ToArray())));
TimeDelta = Math.PI / 100d;
OnStep += new StepHandler(recolor);
}
