public void EpidemicSyncTest()
{
Network n = new Network();
Vertex a = n.CreateVertex();
Vertex b = n.CreateVertex();
n.CreateEdge(a, b);
Kuramoto sync = new Kuramoto(n, 2d);
sync.WriteTimeSeries(null);
sync.Stop();
}
/// <summary>
/// Loads a network from a textfile in which each edge is given by a line of whitespace- or comma-seperated strings representing two nodes
/// </summary>
/// <param name="path">
/// The path of the textfile
/// </param>
/// <returns>
/// The network
/// </returns>
public static Network LoadFromEdgeFile(string path)
{
// First read all lines
string[] lines = System.IO.File.ReadAllLines(path);
Network net = new Network();
// Then process them in parallel
System.Threading.Tasks.Parallel.ForEach(lines, s =>
{
string[] vertices = s.Split(' ', '\t');
if (vertices.Length >= 2)
{
Vertex v1 = net.SearchVertex(vertices[0]);
Vertex v2 = net.SearchVertex(vertices[1]);
// this needs to be atomic
lock (net)
{
if (v1 == null)
{
v1 = net.CreateVertex(vertices[0]);
}
if (v2 == null)
{
v2 = net.CreateVertex(vertices[1]);
}
}
Edge e = net.CreateEdge(v1, v2, EdgeType.Undirected);
if (vertices.Length == 3)
{
try {
e.Weight = float.Parse(vertices[2]);
}
catch
{
Logger.AddMessage(LogEntryType.Warning, "Could not parse edge weight.");
}
}
}
});
return(net);
}
public static Network LoadFromCXF(string filename)
{
string[] cxf = System.IO.File.ReadAllLines(filename);
Network n = new Network();
foreach (string s in cxf)
{
string type = s.Substring(0, s.IndexOf(":"));
if (type == "node")
{
string label = ExtractNodeLabel(s);
n.CreateVertex(label);
// if(colorizer!= null && extractColor(s)!=Color.Empty)
// colorizer[v] = extractColor(s);
}
else if (type == "edge")
{
string sourceLabel = ExtractSourceLabel(s);
string targetLabel = ExtractTargetLabel(s);
n.CreateEdge(n.SearchVertex(sourceLabel), n.SearchVertex(targetLabel));
}
}
return(n);
}
/// <summary>
/// The entry point of the program, where the program control starts and ends.
/// </summary>
/// <param name='args'>
/// The command-line arguments.
/// </param>
public static void Main(string[] args)
{
int limit = 0;
// Print usage information
if (args.Length<3)
{
Console.WriteLine("Usage: MonoParser [class_number] [scan_path] [output_file]");
Console.WriteLine("\t path: \tPath of the directory to scan for assemblies");
Console.WriteLine("\t output_file: \tPath of the graphML file to produce for the resulting network");
return;
}
// Some error handling
if (!System.IO.Directory.Exists(args[1]))
{
Console.WriteLine("Error: The given scan_path '{0}' is not a valid directory", args[1]);
return;
}
limit = Int32.Parse(args[0]);
try
{
System.IO.File.CreateText(args[2]);
}
catch(System.IO.IOException)
{
Console.WriteLine("Error: Cannot write to the specified output_file");
return;
}
// The network
Network n = new Network();
// Scan the assemblies
List<Assembly> assemblies = new List<Assembly>();
foreach(string s in System.IO.Directory.GetFiles(args[1], "*.dll", System.IO.SearchOption.AllDirectories))
{
Assembly a = Assembly.LoadFile(s);
assemblies.Add(a);
}
Console.WriteLine("Found {0} assemblies", assemblies.Count);
// Scan for classes
foreach(Assembly a in assemblies)
foreach(Type t in a.GetTypes())
if(t.FullName!="System.Object")
if((t.IsClass || t.IsInterface || t.IsAbstract) && n.VertexCount < limit)
n.CreateVertex(t.FullName);
Console.WriteLine("Found {0} classes", n.VertexCount);
// Scan for class relations
foreach(Assembly a in assemblies)
foreach(Type t in a.GetTypes())
if(t.IsClass || t.IsInterface || t.IsAbstract)
{
Type baseType = t.BaseType;
TryAddTypeRelation(n, baseType, t);
foreach(Type i in t.GetInterfaces())
TryAddTypeRelation(n, i, t);
}
/*
foreach(PropertyInfo p in t.GetProperties())
TryAddTypeRelation(n, t, p.PropertyType);
foreach(FieldInfo f in t.GetFields())
TryAddTypeRelation(n, t, f.FieldType);
foreach(MethodInfo m in t.GetMethods())
{
ParameterInfo[] info = m.GetParameters();
MethodBody mb = m.GetMethodBody();
mb.
if(mb != null)
foreach(LocalVariableInfo i in m.GetMethodBody().LocalVariables)
TryAddTypeRelation(n, t, i.LocalType);
}
*/
//}
Console.WriteLine("Found {0} types and {1} connections", n.VertexCount, n.EdgeCount);
// n.ReduceToLargestConnectedComponent();
int maxDegree = int.MinValue;
Vertex maxVertex = null;
foreach(Vertex v in n.Vertices)
{
if(v.Degree > maxDegree)
{
maxDegree = v.Degree;
maxVertex = v;
}
}
Console.WriteLine(maxVertex.Label);
Console.WriteLine("{0} vertices and {1} connections", n.VertexCount, n.EdgeCount);
Network.SaveToGraphML(args[2], n);
//NetworkVisualizer.Start(n, new FruchtermanReingoldLayout(10));
}
public static void Main(string[] args)
{
hierarchy = new Network();
root = hierarchy.CreateVertex();
root.Tag = NodeType.Root;
c[root] = Color.Orange;
// Assign node types and estimates
for (int i = 0; i<individuals; i++)
{
Vertex aggregate = hierarchy.CreateVertex();
hierarchy.CreateEdge(root, aggregate, EdgeType.DirectedAB);
c[aggregate] = Color.Black;
Aggregates.Add(aggregate);
aggregate.Tag = NodeType.Aggregate;
Vertex individual = hierarchy.CreateVertex();
individual.Tag = NodeType.Individual;
Variance[individual] = r.NextDouble();
c[individual] = Color.FromArgb(255 - (int) (255d * Variance[individual]), (int) (255d * Variance[individual]), 0);
hierarchy.CreateEdge(aggregate, individual, EdgeType.DirectedAB);
Individuals.Add(individual);
}
Application.Init();
slider = new ConsensusHierarchy.TemperatureWindow();
slider.Show();
System.Threading.ThreadPool.QueueUserWorkItem( delegate(object o) {
FruchtermanReingoldLayout layout = new FruchtermanReingoldLayout(15);
NETGen.Visualization.NetworkVisualizer.Start(hierarchy, layout, c, 800, 600);
layout.DoLayoutAsync();
Logger.ShowInfos = false;
while(true)
{
Change();
c.RecomputeColors(new Func<Vertex,Color>(v => {
if (((NodeType)v.Tag) == NodeType.Aggregate)
{
if(v.OutDegree==0)
return Color.White;
else
return Color.Black;
}
else
return c[v];
}));
c.RecomputeColors(new Func<Edge,Color>(e => {
if (((NodeType)e.Target.Tag) == NodeType.Aggregate && e.Target.OutDegree==0)
return Color.White;
else
return c.DefaultEdgeColor;
}));
NetworkVisualizer.Layout.DoLayout();
}
});
Application.Run();
}
/// <summary>
/// Loads a network from a textfile in which each edge is given by a line of whitespace- or comma-seperated strings representing two nodes
/// </summary>
/// <param name="path">
/// The path of the textfile
/// </param>
/// <returns>
/// The network
/// </returns>
public static Network LoadFromEdgeFile(string path)
{
// First read all lines
string[] lines = System.IO.File.ReadAllLines(path);
Network net = new Network();
// Then process them in parallel
System.Threading.Tasks.Parallel.ForEach(lines, s =>
{
string[] vertices = s.Split(' ', '\t');
if(vertices.Length>=2)
{
Vertex v1 = net.SearchVertex(vertices[0]);
Vertex v2 = net.SearchVertex(vertices[1]);
// this needs to be atomic
lock(net)
{
if(v1 == null)
v1 = net.CreateVertex(vertices[0]);
if (v2 == null)
v2 = net.CreateVertex(vertices[1]);
}
Edge e = net.CreateEdge(v1, v2, EdgeType.Undirected);
if (vertices.Length==3) {
try {
e.Weight = float.Parse(vertices[2]);
}
catch
{
Logger.AddMessage(LogEntryType.Warning, "Could not parse edge weight.");
}
}
}
});
return net;
}
public static Network LoadFromCXF(string filename)
{
string[] cxf = System.IO.File.ReadAllLines(filename);
Network n = new Network();
foreach(string s in cxf)
{
string type = s.Substring(0, s.IndexOf(":"));
if(type=="node")
{
string label = ExtractNodeLabel(s);
n.CreateVertex(label);
// if(colorizer!= null && extractColor(s)!=Color.Empty)
// colorizer[v] = extractColor(s);
}
else if (type=="edge")
{
string sourceLabel = ExtractSourceLabel (s);
string targetLabel = ExtractTargetLabel (s);
n.CreateEdge(n.SearchVertex(sourceLabel), n.SearchVertex(targetLabel));
}
}
return n;
}
/// <summary>
/// Loads a network from a textfile in which each edge is given by a line of whitespace- or comma-seperated strings representing two nodes
/// </summary>
/// <param name="path">
/// The path of the textfile
/// </param>
/// <returns>
/// The network
/// </returns>
public static Network LoadFromEdgeFile(string path)
{
// First read all lines
string[] lines = System.IO.File.ReadAllLines(path);
Network net = new Network();
// Then process them in parallel
System.Threading.Tasks.Parallel.ForEach(lines, s =>
{
string[] vertices = s.Split(' ', '\t', ',');
if(vertices.Length==2)
{
Vertex v1 = net.SearchVertex(vertices[0]);
Vertex v2 = net.SearchVertex(vertices[1]);
// this needs to be atomic
lock(net)
{
if(v1 == null)
v1 = net.CreateVertex(vertices[0]);
if (v2 == null)
v2 = net.CreateVertex(vertices[1]);
}
net.CreateEdge(v1, v2, EdgeType.Undirected);
}
});
return net;
}
