int ComputeKCore(const PUNGraph& G) {
int cnt = 0;
for(TUNGraph::TNodeI NI = G->BegNI(); NI < G->EndNI(); NI++)
cnt = max(cnt, NI.GetOutDeg());
THashSet <TInt> D[cnt+1];
THash <TInt, TInt> deg;
for(TUNGraph::TNodeI NI = G->BegNI(); NI < G->EndNI(); NI++) {
TInt tmp = NI.GetOutDeg() - G->IsEdge(NI.GetId(), NI.GetId() );
D[tmp.Val].AddKey(NI.GetId());
deg.AddDat(NI.GetId()) = tmp;
}
int max_k = 0;
for(int num_iters = 0;num_iters < G->GetNodes(); num_iters++)
for(int i = 0; i < cnt; i++)
if(D[i].Empty() == 0) {
max_k = max(max_k, i);
TInt a = *(D[i].BegI());
D[i].DelKey(a);
deg.AddDat(a.Val) = -1; // Hope overwriting works
TUNGraph::TNodeI NI = G->GetNI(a.Val);
for(int e = 0; e < NI.GetOutDeg(); e++) {
TInt b = NI.GetOutNId(e);
if(deg.GetDat(b) >= 0) {
int Id = deg.GetKeyId(b);
D[deg[Id].Val].DelKey(b);
deg[Id] = deg[Id] - 1; //Hope the overwriting works
D[deg[Id]].AddKey(b);
}
}
break;
}
return max_k;
}
double TAGMUtil::GetConductance(const PUNGraph& Graph, const TIntSet& CmtyS, const int Edges) {
const int Edges2 = Edges >= 0 ? 2*Edges : Graph->GetEdges();
int Vol = 0, Cut = 0;
double Phi = 0.0;
for (int i = 0; i < CmtyS.Len(); i++) {
if (! Graph->IsNode(CmtyS[i])) {
continue;
}
TUNGraph::TNodeI NI = Graph->GetNI(CmtyS[i]);
for (int e = 0; e < NI.GetOutDeg(); e++) {
if (! CmtyS.IsKey(NI.GetOutNId(e))) {
Cut += 1;
}
}
Vol += NI.GetOutDeg();
}
// get conductance
if (Vol != Edges2) {
if (2 * Vol > Edges2) {
Phi = Cut / double (Edges2 - Vol);
}
else if (Vol == 0) {
Phi = 0.0;
}
else {
Phi = Cut / double(Vol);
}
} else {
if (Vol == Edges2) {
Phi = 1.0;
}
}
return Phi;
}
void GetEigenVectorCentr(const PUNGraph& Graph, TIntFltH& EigenH, const double& Eps, const int& MaxIter) {
const int NNodes = Graph->GetNodes();
EigenH.Gen(NNodes);
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
EigenH.AddDat(NI.GetId(), 1.0/NNodes);
IAssert(NI.GetId() == EigenH.GetKey(EigenH.Len()-1));
}
TFltV TmpV(NNodes);
double diff = TFlt::Mx;
for (int iter = 0; iter < MaxIter; iter++) {
int j = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++, j++) {
TmpV[j] = 0;
for (int e = 0; e < NI.GetOutDeg(); e++) {
TmpV[j] += EigenH.GetDat(NI.GetOutNId(e)); }
}
double sum = 0;
for (int i = 0; i < TmpV.Len(); i++) {
EigenH[i] = TmpV[i];
sum += EigenH[i];
}
for (int i = 0; i < EigenH.Len(); i++) {
EigenH[i] /= sum; }
if (fabs(diff-sum) < Eps) { break; }
//printf("\tdiff:%f\tsum:%f\n", fabs(diff-sum), sum);
diff = sum;
}
}
double GetAsstyCor(const PUNGraph& Graph) {
TIntFltH deg(Graph->GetNodes()), deg_sq(Graph->GetNodes());
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
deg.AddDat(NI.GetId()) = NI.GetOutDeg();
deg_sq.AddDat(NI.GetId()) = NI.GetOutDeg() * NI.GetOutDeg();
}
double m = Graph->GetEdges(), num1 = 0.0, num2 = 0.0, den1 = 0.0;
for (TUNGraph::TEdgeI EI = Graph->BegEI(); EI < Graph->EndEI(); EI++) {
double t1 = deg.GetDat(EI.GetSrcNId()).Val, t2 = deg.GetDat(EI.GetDstNId()).Val;
num1 += t1 * t2;
num2 += t1 + t2;
den1 += deg_sq.GetDat(EI.GetSrcNId()).Val + deg_sq.GetDat(EI.GetDstNId()).Val;
}
num1 /= m;
den1 /= (2.0 * m);
num2 = (num2 / (2.0 * m)) * (num2 / (2.0 * m));
return (num1 - num2) / (den1 - num2);
}
void Init(const PUNGraph& Graph) {
const double M = 0.5/Graph->GetEdges(); // 1/2m
Q = 0.0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
CmtyIdUF.Add(NI.GetId());
const int OutDeg = NI.GetOutDeg();
if (OutDeg == 0) { continue; }
TCmtyDat& Dat = CmtyQH.AddDat(NI.GetId(), TCmtyDat(M * OutDeg, OutDeg));
for (int e = 0; e < NI.GetOutDeg(); e++) {
const int DstNId = NI.GetOutNId(e);
const double DstMod = 2 * M * (1.0 - OutDeg * Graph->GetNI(DstNId).GetOutDeg() * M);
Dat.AddQ(DstNId, DstMod);
}
Q += -1.0*TMath::Sqr(OutDeg*M);
if (NI.GetId() < Dat.GetMxQNId()) {
MxQHeap.Add(TFltIntIntTr(Dat.GetMxQ(), NI.GetId(), Dat.GetMxQNId())); }
}
MxQHeap.MakeHeap();
}
// RenumberNodes ... Renumber node ids in the subgraph to 0...N-1
PUNGraph GetSubGraph(const PUNGraph& Graph, const TIntV& NIdV, const bool& RenumberNodes) {
//if (! RenumberNodes) { return TSnap::GetSubGraph(Graph, NIdV); }
PUNGraph NewGraphPt = TUNGraph::New();
TUNGraph& NewGraph = *NewGraphPt;
NewGraph.Reserve(NIdV.Len(), -1);
TIntSet NIdSet(NIdV.Len());
for (int n = 0; n < NIdV.Len(); n++) {
if (Graph->IsNode(NIdV[n])) {
NIdSet.AddKey(NIdV[n]);
if (! RenumberNodes) {
NewGraph.AddNode(NIdV[n]);
}
else {
NewGraph.AddNode(NIdSet.GetKeyId(NIdV[n]));
}
}
}
if (! RenumberNodes) {
for (int n = 0; n < NIdSet.Len(); n++) {
const int SrcNId = NIdSet[n];
const TUNGraph::TNodeI NI = Graph->GetNI(SrcNId);
for (int edge = 0; edge < NI.GetOutDeg(); edge++) {
const int OutNId = NI.GetOutNId(edge);
if (NIdSet.IsKey(OutNId)) {
NewGraph.AddEdge(SrcNId, OutNId);
}
}
}
} else {
for (int n = 0; n < NIdSet.Len(); n++) {
const int SrcNId = NIdSet[n];
const TUNGraph::TNodeI NI = Graph->GetNI(SrcNId);
for (int edge = 0; edge < NI.GetOutDeg(); edge++) {
const int OutNId = NI.GetOutNId(edge);
if (NIdSet.IsKey(OutNId)) {
NewGraph.AddEdge(NIdSet.GetKeyId(SrcNId), NIdSet.GetKeyId(OutNId));
}
}
}
}
return NewGraphPt;
}
// Loads a (directed, undirected or multi) graph from a text file InFNm with 1 node and all its edges in a single line.
void IOConnListStr() {
const int NNodes = 500;
const int NEdges = 2000;
const char *FName = "demo.graph.dat";
PUNGraph GOut, GIn;
GOut = GenRndGnm<PUNGraph>(NNodes, NEdges);
// Output nodes as random strings
TIntStrH OutNIdStrH;
TStrHash<TInt> OutStrNIdH;
// Generate unique random strings for graph
for (TUNGraph::TNodeI NI = GOut->BegNI(); NI < GOut->EndNI(); NI++) {
TStr RandStr = "";
do {
TInt RandLen = TInt::Rnd.GetUniDevInt(5, 10);
for (int i = 0; i < RandLen; i++) {
// TStr RandChar(TInt::Rnd.GetUniDevInt(33, 126));
TStr RandChar(TInt::Rnd.GetUniDevInt(97, 122));
RandStr += RandChar;
}
}
while (OutStrNIdH.IsKey(RandStr) || RandStr[0] == '#');
OutNIdStrH.AddDat(NI.GetId(), RandStr);
OutStrNIdH.AddDat(RandStr, NI.GetId());
}
// Create graph file
FILE *F = fopen(FName, "w");
for (TUNGraph::TNodeI NI = GOut->BegNI(); NI < GOut->EndNI(); NI++) {
fprintf(F, "%s", OutNIdStrH[NI.GetId()].CStr());
for (int e = 0; e < NI.GetOutDeg(); e++) {
fprintf(F, " %s", OutNIdStrH[NI.GetOutNId(e)].CStr());
}
fprintf(F, "\n");
}
fclose(F);
TStrHash<TInt> InStrToNIdH;
GIn = LoadConnListStr<PUNGraph>(FName, InStrToNIdH);
PrintGStats("ConnListStr - Out", GOut);
PrintGStats("ConnListStr - In", GIn);
}
// Connected components of a graph define clusters
// OutDegH and OrigEdges stores node degrees and number of edges in the original graph
double _GirvanNewmanGetModularity(const PUNGraph& G, const TIntH& OutDegH, const int& OrigEdges, TCnComV& CnComV) {
TSnap::GetWccs(G, CnComV); // get communities
double Mod = 0;
for (int c = 0; c < CnComV.Len(); c++) {
const TIntV& NIdV = CnComV[c]();
double EIn=0, EEIn=0;
for (int i = 0; i < NIdV.Len(); i++) {
TUNGraph::TNodeI NI = G->GetNI(NIdV[i]);
EIn += NI.GetOutDeg();
EEIn += OutDegH.GetDat(NIdV[i]);
}
Mod += (EIn-EEIn*EEIn/(2.0*OrigEdges));
}
if (Mod == 0) { return 0; }
else { return Mod/(2.0*OrigEdges); }
}
void GetEigenVectorCentr(const PUNGraph& Graph, TIntFltH& NIdEigenH, const double& Eps, const int& MaxIter) {
const int NNodes = Graph->GetNodes();
NIdEigenH.Gen(NNodes);
// initialize vector values
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
NIdEigenH.AddDat(NI.GetId(), 1.0 / NNodes);
IAssert(NI.GetId() == NIdEigenH.GetKey(NIdEigenH.Len() - 1));
}
TFltV TmpV(NNodes);
for (int iter = 0; iter < MaxIter; iter++) {
int j = 0;
// add neighbor values
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++, j++) {
TmpV[j] = 0;
for (int e = 0; e < NI.GetOutDeg(); e++) {
TmpV[j] += NIdEigenH.GetDat(NI.GetOutNId(e));
}
}
// normalize
double sum = 0;
for (int i = 0; i < TmpV.Len(); i++) {
sum += (TmpV[i] * TmpV[i]);
}
sum = sqrt(sum);
for (int i = 0; i < TmpV.Len(); i++) {
TmpV[i] /= sum;
}
// compute difference
double diff = 0.0;
j = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++, j++) {
diff += fabs(NIdEigenH.GetDat(NI.GetId()) - TmpV[j]);
}
// set new values
j = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++, j++) {
NIdEigenH.AddDat(NI.GetId(), TmpV[j]);
}
if (diff < Eps) {
break;
}
}
}
// network cascade: add spurious edges
// for more details see "Correcting for Missing Data in Information Cascades" by E. Sadikov, M. Medina, J. Leskovec, H. Garcia-Molina. WSDM, 2011
PNGraph AddSpuriousEdges(const PUNGraph& Graph, const PNGraph& Casc, TIntH NIdTmH) {
TIntPrV EdgeV;
for (TNGraph::TNodeI NI = Casc->BegNI(); NI < Casc->EndNI(); NI++) {
TUNGraph::TNodeI GNI = Graph->GetNI(NI.GetId());
const int Tm = NIdTmH.GetDat(NI.GetId());
for (int i=0,j=0; i < GNI.GetOutDeg(); i++) {
const int Dst = GNI.GetOutNId(i);
if (NIdTmH.IsKey(Dst) && Tm<NIdTmH.GetDat(Dst) && ! NI.IsNbhNId(Dst)) {
EdgeV.Add(TIntPr(GNI.GetId(), Dst)); }
}
}
PNGraph NetCasc = TNGraph::New();
*NetCasc = *Casc;
for (int e = 0; e < EdgeV.Len(); e++) {
NetCasc->AddEdge(EdgeV[e].Val1, EdgeV[e].Val2); }
return NetCasc;
}
/// Rewire the network. Keeps node degrees as is but randomly rewires the edges.
/// Use this function to generate a random graph with the same degree sequence
/// as the OrigGraph.
/// See: On the uniform generation of random graphs with prescribed degree
/// sequences by R. Milo, N. Kashtan, S. Itzkovitz, M. E. J. Newman, U. Alon
/// URL: http://arxiv.org/abs/cond-mat/0312028
PUNGraph GenRewire(const PUNGraph& OrigGraph, const int& NSwitch, TRnd& Rnd) {
const int Nodes = OrigGraph->GetNodes();
const int Edges = OrigGraph->GetEdges();
PUNGraph GraphPt = TUNGraph::New();
TUNGraph& Graph = *GraphPt;
Graph.Reserve(Nodes, -1);
TExeTm ExeTm;
// generate a graph that satisfies the constraints
printf("Randomizing edges (%d, %d)...\n", Nodes, Edges);
TIntPrSet EdgeSet(Edges);
for (TUNGraph::TNodeI NI = OrigGraph->BegNI(); NI < OrigGraph->EndNI(); NI++) {
const int NId = NI.GetId();
for (int e = 0; e < NI.GetOutDeg(); e++) {
if (NId <= NI.GetOutNId(e)) { continue; }
EdgeSet.AddKey(TIntPr(NId, NI.GetOutNId(e)));
}
Graph.AddNode(NI.GetId());
}
// edge switching
uint skip=0;
for (uint swps = 0; swps < 2*uint(Edges)*uint(NSwitch); swps++) {
const int keyId1 = EdgeSet.GetRndKeyId(Rnd);
const int keyId2 = EdgeSet.GetRndKeyId(Rnd);
if (keyId1 == keyId2) { skip++; continue; }
const TIntPr& E1 = EdgeSet[keyId1];
const TIntPr& E2 = EdgeSet[keyId2];
TIntPr NewE1(E1.Val1, E2.Val1), NewE2(E1.Val2, E2.Val2);
if (NewE1.Val1 > NewE1.Val2) { Swap(NewE1.Val1, NewE1.Val2); }
if (NewE2.Val1 > NewE2.Val2) { Swap(NewE2.Val1, NewE2.Val2); }
if (NewE1!=NewE2 && NewE1.Val1!=NewE1.Val2 && NewE2.Val1!=NewE2.Val2 && ! EdgeSet.IsKey(NewE1) && ! EdgeSet.IsKey(NewE2)) {
EdgeSet.DelKeyId(keyId1); EdgeSet.DelKeyId(keyId2);
EdgeSet.AddKey(TIntPr(NewE1));
EdgeSet.AddKey(TIntPr(NewE2));
} else { skip++; }
if (swps % Edges == 0) {
printf("\r %uk/%uk: %uk skip [%s]", swps/1000u, 2*uint(Edges)*uint(NSwitch)/1000u, skip/1000u, ExeTm.GetStr());
if (ExeTm.GetSecs() > 2*3600) { printf(" *** Time limit!\n"); break; } // time limit 2 hours
}
}
printf("\r total %uk switchings attempted, %uk skiped [%s]\n", 2*uint(Edges)*uint(NSwitch)/1000u, skip/1000u, ExeTm.GetStr());
for (int e = 0; e < EdgeSet.Len(); e++) {
Graph.AddEdge(EdgeSet[e].Val1, EdgeSet[e].Val2); }
return GraphPt;
}
// simulate SI model cascade using infection probability Beta until the cascade stops or reaches size MxCascSz
PNGraph RunSICascade2(PUNGraph G, const double& Beta, const int& MxCascSz, TIntH& NIdInfTmH) {
PNGraph Casc = TNGraph::New();
const int StartNId = G->GetRndNId();
Casc->AddNode(StartNId);
NIdInfTmH.AddDat(StartNId, NIdInfTmH.Len());
TIntQ Q; Q.Push(StartNId);
while (! Q.Empty()) {
const TUNGraph::TNodeI NI = G->GetNI(Q.Top()); Q.Pop();
for (int i = 0; i < NI.GetOutDeg(); i++) {
if (TInt::Rnd.GetUniDev() < Beta && ! NIdInfTmH.IsKey(NI.GetOutNId(i))) {
Casc->AddNode(NI.GetOutNId(i));
NIdInfTmH.AddDat(NI.GetOutNId(i), NIdInfTmH.Len());
Casc->AddEdge(NI.GetId(), NI.GetOutNId(i));
if (Casc->GetNodes() == MxCascSz) { return Casc; }
Q.Push(NI.GetOutNId(i));
}
}
}
return Casc;
}
// simulate SI model cascade using infection probability Beta until the cascade reaches size CascSz
PNGraph RunSICascade(PUNGraph G, const double& Beta, const int& CascSz, TIntH& NIdInfTmH) {
PNGraph Casc = TNGraph::New();
const int StartId = G->GetRndNId();
Casc->AddNode(StartId);
NIdInfTmH.AddDat(StartId, NIdInfTmH.Len());
for (int X = 0; X < 10*CascSz; X++) {
TIntV CascNIdV; Casc->GetNIdV(CascNIdV);
for (int n = 0; n < CascNIdV.Len(); n++) {
const TUNGraph::TNodeI NI = G->GetNI(CascNIdV[n]);
for (int i = 0; i < NI.GetOutDeg(); i++) {
if (Casc->IsNode(NI.GetOutNId(i))) { continue; }
if (TInt::Rnd.GetUniDev() < Beta) {
Casc->AddNode(NI.GetOutNId(i));
NIdInfTmH.AddDat(NI.GetOutNId(i), NIdInfTmH.Len());
Casc->AddEdge(NI.GetId(), NI.GetOutNId(i));
if (Casc->GetNodes() == CascSz) { return Casc; }
}
}
}
}
return Casc;
}
// Maximum modularity clustering by Girvan-Newman algorithm (slow)
// Girvan M. and Newman M. E. J., Community structure in social and biological networks, Proc. Natl. Acad. Sci. USA 99, 7821–7826 (2002)
double CommunityGirvanNewman(PUNGraph& Graph, TCnComV& CmtyV) {
TIntH OutDegH;
const int NEdges = Graph->GetEdges();
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
OutDegH.AddDat(NI.GetId(), NI.GetOutDeg());
}
double BestQ = -1; // modularity
TCnComV CurCmtyV;
CmtyV.Clr();
TIntV Cmty1, Cmty2;
while (true) {
CmtyGirvanNewmanStep(Graph, Cmty1, Cmty2);
const double Q = _GirvanNewmanGetModularity(Graph, OutDegH, NEdges, CurCmtyV);
//printf("current modularity: %f\n", Q);
if (Q > BestQ) {
BestQ = Q;
CmtyV.Swap(CurCmtyV);
}
if (Cmty1.Len()==0 || Cmty2.Len() == 0) { break; }
}
return BestQ;
}
void GetMotifCount(const PUNGraph& G, const int MotifSize, TVec <int64> & MotifV, const int num) {
if (MotifSize == 3) {
MotifV = TVec <int64> (2);
MotifV.PutAll(0);
TSnap::GetTriads(G,MotifV[mtThreeClosed],MotifV[mtThreeOpen],num);
}
else {
MotifV = TVec <int64> (6);
MotifV.PutAll(0);
TIntPrV V(G->GetEdges(), 0);
for (TUNGraph::TEdgeI EI = G->BegEI(); EI < G->EndEI(); EI++) {
V.Add(TIntPr(EI.GetSrcNId(), EI.GetDstNId()));
}
TRnd blargh;
V.Shuffle(blargh);
for (int z = 0; z < num; z++) {
int SrcNId = V[z].Val1.Val, DstNId = V[z].Val2.Val;
TUNGraph::TNodeI SrcNI = G->GetNI(SrcNId), DstNI = G->GetNI(DstNId);
TIntV SrcV(SrcNI.GetOutDeg(),0), DstV(DstNI.GetOutDeg(),0), BothV(min(SrcNI.GetOutDeg(), DstNI.GetOutDeg()),0);
SrcV.Clr(0,-1);
DstV.Clr(0,-1);
BothV.Clr(0,-1);
//Grouping the vertices into sets
for (int e = 0; e < SrcNI.GetOutDeg(); e++) {
if (SrcNI.GetOutNId(e) == DstNId) continue;
if (G->IsEdge(DstNId, SrcNI.GetOutNId(e)) ) { BothV.Add(SrcNI.GetOutNId(e)); }
else { SrcV.Add(SrcNI.GetOutNId(e)); }
}
for (int e = 0; e < DstNI.GetOutDeg(); e++) {
if (DstNI.GetOutNId(e) == SrcNId) continue;
if (G->IsEdge(SrcNId, DstNI.GetOutNId(e)) == 0) { DstV.Add(DstNI.GetOutNId(e)); }
}
//Compute Motif 0 and 1
for (int i = 0; i < SrcV.Len(); i++) {
for (int j = 0; j < DstV.Len(); j++) {
if (G->IsEdge(SrcV[i], DstV[j]) ) { MotifV[mfFourSquare]++; }
else MotifV[mfFourLine]++;
}
}
//Compute Motif 2 and 3
for (int i = 0; i < SrcV.Len(); i++) {
for (int j = i + 1; j < SrcV.Len(); j++) {
if (G->IsEdge(SrcV[i], SrcV[j]) ) { MotifV[mfFourTriangleEdge]++; }
else MotifV[mfFourStar]++;
}
}
for (int i = 0; i < DstV.Len(); i++) {
for (int j = i + 1; j < DstV.Len(); j++) {
if (G->IsEdge(DstV[i], DstV[j]) ) { MotifV[mfFourTriangleEdge]++; }
else MotifV[mfFourStar]++;
}
}
//Compute Motif 4 and 5
for (int i = 0; i < BothV.Len(); i++) {
for (int j = i + 1; j < BothV.Len(); j++) {
if (G->IsEdge(BothV[i], BothV[j]) ) { MotifV[mfFourComplete]++; }
else MotifV[mfFourSquareDiag]++;
}
}
}
MotifV[mfFourSquare] /= 4ll;
MotifV[mfFourStar] /= 3ll;
MotifV[mfFourComplete] /= 6ll;
}
}
void GetBetweennessCentr(const PUNGraph& Graph, const TIntV& BtwNIdV, TIntFltH& NodeBtwH, const bool& DoNodeCent, TIntPrFltH& EdgeBtwH, const bool& DoEdgeCent) {
if (DoNodeCent) { NodeBtwH.Clr(); }
if (DoEdgeCent) { EdgeBtwH.Clr(); }
const int nodes = Graph->GetNodes();
TIntS S(nodes);
TIntQ Q(nodes);
TIntIntVH P(nodes); // one vector for every node
TIntFltH delta(nodes);
TIntH sigma(nodes), d(nodes);
// init
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
if (DoNodeCent) {
NodeBtwH.AddDat(NI.GetId(), 0);
}
if (DoEdgeCent) {
for (int e = 0; e < NI.GetOutDeg(); e++) {
if (NI.GetId() < NI.GetOutNId(e)) {
EdgeBtwH.AddDat(TIntPr(NI.GetId(), NI.GetOutNId(e)), 0);
}
}
}
sigma.AddDat(NI.GetId(), 0);
d.AddDat(NI.GetId(), -1);
P.AddDat(NI.GetId(), TIntV());
delta.AddDat(NI.GetId(), 0);
}
// calc betweeness
for (int k = 0; k < BtwNIdV.Len(); k++) {
const TUNGraph::TNodeI NI = Graph->GetNI(BtwNIdV[k]);
// reset
for (int i = 0; i < sigma.Len(); i++) {
sigma[i] = 0; d[i] = -1; delta[i] = 0; P[i].Clr(false);
}
S.Clr(false);
Q.Clr(false);
sigma.AddDat(NI.GetId(), 1);
d.AddDat(NI.GetId(), 0);
Q.Push(NI.GetId());
while (!Q.Empty()) {
const int v = Q.Top(); Q.Pop();
const TUNGraph::TNodeI NI2 = Graph->GetNI(v);
S.Push(v);
const int VDat = d.GetDat(v);
for (int e = 0; e < NI2.GetOutDeg(); e++) {
const int w = NI2.GetOutNId(e);
if (d.GetDat(w) < 0) { // find w for the first time
Q.Push(w);
d.AddDat(w, VDat + 1);
}
//shortest path to w via v ?
if (d.GetDat(w) == VDat + 1) {
sigma.AddDat(w) += sigma.GetDat(v);
P.GetDat(w).Add(v);
}
}
}
while (!S.Empty()) {
const int w = S.Top();
const double SigmaW = sigma.GetDat(w);
const double DeltaW = delta.GetDat(w);
const TIntV NIdV = P.GetDat(w);
S.Pop();
for (int i = 0; i < NIdV.Len(); i++) {
const int nid = NIdV[i];
const double c = (sigma.GetDat(nid)*1.0 / SigmaW) * (1 + DeltaW);
delta.AddDat(nid) += c;
if (DoEdgeCent) {
EdgeBtwH.AddDat(TIntPr(TMath::Mn(nid, w), TMath::Mx(nid, w))) += c;
}
}
if (DoNodeCent && w != NI.GetId()) {
NodeBtwH.AddDat(w) += delta.GetDat(w) / 2.0;
}
}
}
}
/// save graph into a gexf file which Gephi can read
void TAGMUtil::SaveGephi(const TStr& OutFNm, const PUNGraph& G, const TVec<TIntV>& CmtyVVAtr, const double MaxSz, const double MinSz, const TIntStrH& NIDNameH, const THash<TInt, TIntTr>& NIDColorH ) {
THash<TInt,TIntV> NIDComVHAtr;
TAGMUtil::GetNodeMembership(NIDComVHAtr, CmtyVVAtr);
FILE* F = fopen(OutFNm.CStr(), "wt");
fprintf(F, "<?xml version='1.0' encoding='UTF-8'?>\n");
fprintf(F, "<gexf xmlns='http://www.gexf.net/1.2draft' xmlns:viz='http://www.gexf.net/1.1draft/viz' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xsi:schemaLocation='http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd' version='1.2'>\n");
fprintf(F, "\t<graph mode='static' defaultedgetype='undirected'>\n");
if (CmtyVVAtr.Len() > 0) {
fprintf(F, "\t<attributes class='node'>\n");
for (int c = 0; c < CmtyVVAtr.Len(); c++) {
fprintf(F, "\t\t<attribute id='%d' title='c%d' type='boolean'>", c, c);
fprintf(F, "\t\t<default>false</default>\n");
fprintf(F, "\t\t</attribute>\n");
}
fprintf(F, "\t</attributes>\n");
}
fprintf(F, "\t\t<nodes>\n");
for (TUNGraph::TNodeI NI = G->BegNI(); NI < G->EndNI(); NI++) {
int NID = NI.GetId();
TStr Label = NIDNameH.IsKey(NID)? NIDNameH.GetDat(NID): "";
Label.ChangeChAll('<', ' ');
Label.ChangeChAll('>', ' ');
Label.ChangeChAll('&', ' ');
Label.ChangeChAll('\'', ' ');
TIntTr Color = NIDColorH.IsKey(NID)? NIDColorH.GetDat(NID) : TIntTr(120, 120, 120);
double Size = MinSz;
double SizeStep = (MaxSz - MinSz) / (double) CmtyVVAtr.Len();
if (NIDComVHAtr.IsKey(NID)) {
Size = MinSz + SizeStep * (double) NIDComVHAtr.GetDat(NID).Len();
}
double Alpha = 1.0;
fprintf(F, "\t\t\t<node id='%d' label='%s'>\n", NID, Label.CStr());
fprintf(F, "\t\t\t\t<viz:color r='%d' g='%d' b='%d' a='%.1f'/>\n", Color.Val1.Val, Color.Val2.Val, Color.Val3.Val, Alpha);
fprintf(F, "\t\t\t\t<viz:size value='%.3f'/>\n", Size);
//specify attributes
if (NIDComVHAtr.IsKey(NID)) {
fprintf(F, "\t\t\t\t<attvalues>\n");
for (int c = 0; c < NIDComVHAtr.GetDat(NID).Len(); c++) {
int CID = NIDComVHAtr.GetDat(NID)[c];
fprintf(F, "\t\t\t\t\t<attvalue for='%d' value='true'/>\n", CID);
}
fprintf(F, "\t\t\t\t</attvalues>\n");
}
fprintf(F, "\t\t\t</node>\n");
}
fprintf(F, "\t\t</nodes>\n");
//plot edges
int EID = 0;
fprintf(F, "\t\t<edges>\n");
for (TUNGraph::TNodeI NI = G->BegNI(); NI < G->EndNI(); NI++) {
for (int e = 0; e < NI.GetOutDeg(); e++) {
if (NI.GetId() > NI.GetOutNId(e)) {
continue;
}
fprintf(F, "\t\t\t<edge id='%d' source='%d' target='%d'/>\n", EID++, NI.GetId(), NI.GetOutNId(e));
}
}
fprintf(F, "\t\t</edges>\n");
fprintf(F, "\t</graph>\n");
fprintf(F, "</gexf>\n");
fclose(F);
}
// Test node, edge creation
void ManipulateNodesEdges() {
int NNodes = 10000;
int NEdges = 100000;
const char *FName = "test.graph";
PUNGraph Graph;
PUNGraph Graph1;
PUNGraph Graph2;
int i;
int n;
int NCount;
int ECount1;
int ECount2;
int x,y;
bool t;
Graph = TUNGraph::New();
t = Graph->Empty();
// create the nodes
for (i = 0; i < NNodes; i++) {
Graph->AddNode(i);
}
t = Graph->Empty();
n = Graph->GetNodes();
// create random edges
NCount = NEdges;
while (NCount > 0) {
x = (long) (drand48() * NNodes);
y = (long) (drand48() * NNodes);
// Graph->GetEdges() is not correct for the loops (x == y),
// skip the loops in this test
if (x != y && !Graph->IsEdge(x,y)) {
n = Graph->AddEdge(x, y);
NCount--;
}
}
PrintGStats("ManipulateNodesEdges:Graph",Graph);
// get all the nodes
NCount = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
NCount++;
}
// get all the edges for all the nodes
ECount1 = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
for (int e = 0; e < NI.GetOutDeg(); e++) {
ECount1++;
}
}
ECount1 /= 2;
// get all the edges directly
ECount2 = 0;
for (TUNGraph::TEdgeI EI = Graph->BegEI(); EI < Graph->EndEI(); EI++) {
ECount2++;
}
printf("graph ManipulateNodesEdges:Graph, nodes %d, edges1 %d, edges2 %d\n",
NCount, ECount1, ECount2);
// assignment
Graph1 = TUNGraph::New();
*Graph1 = *Graph;
PrintGStats("ManipulateNodesEdges:Graph1",Graph1);
// save the graph
{
TFOut FOut(FName);
Graph->Save(FOut);
FOut.Flush();
}
// load the graph
{
TFIn FIn(FName);
Graph2 = TUNGraph::Load(FIn);
}
PrintGStats("ManipulateNodesEdges:Graph2",Graph2);
// remove all the nodes and edges
for (i = 0; i < NNodes; i++) {
n = Graph->GetRndNId();
Graph->DelNode(n);
}
PrintGStats("ManipulateNodesEdges:Graph",Graph);
Graph1->Clr();
PrintGStats("ManipulateNodesEdges:Graph1",Graph1);
}
// Test node, edge creation
TEST(TUNGraph, ManipulateNodesEdges) {
int NNodes = 10000;
int NEdges = 100000;
const char *FName = "test.graph";
PUNGraph Graph;
PUNGraph Graph1;
PUNGraph Graph2;
int i;
int n;
int NCount;
int x,y;
int Deg, InDeg, OutDeg;
Graph = TUNGraph::New();
EXPECT_EQ(1,Graph->Empty());
// create the nodes
for (i = 0; i < NNodes; i++) {
Graph->AddNode(i);
}
EXPECT_EQ(0,Graph->Empty());
EXPECT_EQ(NNodes,Graph->GetNodes());
// create random edges
NCount = NEdges;
while (NCount > 0) {
x = (long) (drand48() * NNodes);
y = (long) (drand48() * NNodes);
// Graph->GetEdges() is not correct for the loops (x == y),
// skip the loops in this test
if (x != y && !Graph->IsEdge(x,y)) {
n = Graph->AddEdge(x, y);
NCount--;
}
}
EXPECT_EQ(NEdges,Graph->GetEdges());
EXPECT_EQ(0,Graph->Empty());
EXPECT_EQ(1,Graph->IsOk());
for (i = 0; i < NNodes; i++) {
EXPECT_EQ(1,Graph->IsNode(i));
}
EXPECT_EQ(0,Graph->IsNode(NNodes));
EXPECT_EQ(0,Graph->IsNode(NNodes+1));
EXPECT_EQ(0,Graph->IsNode(2*NNodes));
// nodes iterator
NCount = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
NCount++;
}
EXPECT_EQ(NNodes,NCount);
// edges per node iterator
NCount = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
for (int e = 0; e < NI.GetOutDeg(); e++) {
NCount++;
}
}
EXPECT_EQ(NEdges*2,NCount);
// edges iterator
NCount = 0;
for (TUNGraph::TEdgeI EI = Graph->BegEI(); EI < Graph->EndEI(); EI++) {
NCount++;
}
EXPECT_EQ(NEdges,NCount);
// node degree
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
Deg = NI.GetDeg();
InDeg = NI.GetInDeg();
OutDeg = NI.GetOutDeg();
EXPECT_EQ(Deg,InDeg);
EXPECT_EQ(Deg,OutDeg);
}
// assignment
Graph1 = TUNGraph::New();
*Graph1 = *Graph;
EXPECT_EQ(NNodes,Graph1->GetNodes());
EXPECT_EQ(NEdges,Graph1->GetEdges());
EXPECT_EQ(0,Graph1->Empty());
EXPECT_EQ(1,Graph1->IsOk());
// saving and loading
{
TFOut FOut(FName);
Graph->Save(FOut);
FOut.Flush();
}
{
TFIn FIn(FName);
Graph2 = TUNGraph::Load(FIn);
}
EXPECT_EQ(NNodes,Graph2->GetNodes());
EXPECT_EQ(NEdges,Graph2->GetEdges());
EXPECT_EQ(0,Graph2->Empty());
EXPECT_EQ(1,Graph2->IsOk());
// remove all the nodes and edges
for (i = 0; i < NNodes; i++) {
n = Graph->GetRndNId();
Graph->DelNode(n);
}
EXPECT_EQ(0,Graph->GetNodes());
EXPECT_EQ(0,Graph->GetEdges());
EXPECT_EQ(1,Graph->IsOk());
EXPECT_EQ(1,Graph->Empty());
Graph1->Clr();
EXPECT_EQ(0,Graph1->GetNodes());
EXPECT_EQ(0,Graph1->GetEdges());
EXPECT_EQ(1,Graph1->IsOk());
EXPECT_EQ(1,Graph1->Empty());
}
