First commit on github -- NetBunch 1.0

1 files changed, 316 insertions, 0 deletions

diff --git a/src/betweenness/betweenness.c b/src/betweenness/betweenness.c
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+++ b/src/betweenness/betweenness.c
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+/**
+ *  This program is free software: you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ *
+ *  This program computes the betweenness of all the nodes of a graph,
+ *  using Brandes' algorithm, and counting all the shortest paths
+ *  originating from a set of nodes (potentially the whole set of
+ *  vertices).
+ *
+ *  References: 
+ *     U. Brandes. "A Faster Algorithm for Betweenness 
+ *     Centrality". J. Math. Sociol. 25 (2001), 163-177.  
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <time.h>
+
+#include "utils.h"
+
+
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                      -*-  betweenness  -*-                     **\n"
+         "**                                                                **\n"
+         "**  Compute the betweenness of all the nodes and edges of a       **\n"
+         "**  network due to the shortest paths originating from a set      **\n"
+         "**  of initial nodes.  The set can be either a sequence of        **\n"
+         "**  nodes (if the second argument is 'SEQ') or a random sample    **\n"
+         "**  from the set of all the nodes (if it is 'RND').               **\n"
+         "**                                                                **\n"
+         "**  The input file is an edge-list (use '-' to read from STDIN).  **\n"
+         "**                                                                **\n"
+         "**  With 'SEQ':                                                   **\n"
+         "**  If <node_start> is not specified, computes the betweenness    **\n"
+         "**  using shortest paths from *all* the nodes (WARNING: This can  **\n"
+         "**  be slow for large graphs!). If <node_end> is not specified,   **\n"
+         "**  use shortest paths from all the nodes between <node_start>    **\n"
+         "**  and the node with the largest label.                          **\n"
+         "**                                                                **\n"
+         "**  With 'RND':                                                   **\n"
+         "**  Compute the betweenness based on the shortest paths from      **\n"
+         "**  <num> nodes sampled uniformly at random.                      **\n"
+         "**                                                                **\n"
+         "**  When called with just <graph_in>, use all the nodes.          **\n"
+         "**                                                                **\n"
+         "**  The betweenness of all the nodes is printed on standard       **\n"
+         "**  output (STDOUT), while the edge betweenness is printed on     **\n"
+         "**  standard error (STDERR)                                       **\n"
+         "**                                                                **\n"
+         "********************************************************************\n"
+         "\n\n"
+         " This is Free Software - You can use and distribute it under \n"
+         " the terms of the GNU General Public License, version 3 or later\n\n"
+         " (c) Vincenzo Nicosia 2009-2017 (v.nicosia@qmul.ac.uk)\n\n");
+  printf("Usage: %s <graph_in> [SEQ <node_start> [<node_end>]]\n" , argv[0]);
+  printf("Usage: %s <graph_in> [RND <num>]\n" , argv[0]);
+
+}
+
+/*
+ * Add a node the a list of predecessors
+ */
+
+void add_predecessor(unsigned int **pred, unsigned int k){
+  
+  (*pred)[0] += 1;
+  *pred = realloc(*pred, ((*pred)[0] + 1)  * sizeof(unsigned int));
+  (*pred)[ (*pred)[0] ] = k;
+}
+
+
+
+/*
+ *
+ * Compute node and edge betweenness, based on shortest paths
+ * originating on the "num" nodes specified in "nlist".  "edge_bet"
+ * should be an appropriately allocated (and initialised to zero!!!!)
+ * vector of length equal to J_slap, and will contain the values of
+ * edge betweenness.
+ *
+ */
+double* compute_bet_dependency(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, 
+                               unsigned int *nlist, unsigned int num, double *edge_bet){
+  
+  int i, j, k, w, idx, cur_node, m;
+  unsigned int  *marked, **preds, *dist, *nj;
+  double  *delta, *cB, val;
+  unsigned int d;
+  unsigned int n, nd, ndp;
+  unsigned int edge_pos;
+  
+  dist = malloc(N * sizeof(unsigned int));
+  marked = malloc(N * sizeof(unsigned int));
+  preds = malloc(N * sizeof(unsigned int *));
+  
+  nj = malloc(N * sizeof(unsigned int));
+  delta = malloc(N * sizeof(double));
+  cB = malloc(N * sizeof(double));
+  
+  for (i=0; i<N; i++){
+    cB[i] = 0;
+    preds[i] = NULL;
+  }
+
+  for (m=0; m<num; m++){
+    /* We start from the m-th node in nlist*/
+    j = nlist[m];
+
+    for(i=0; i<N; i ++){
+      dist[i] = N;
+      if (! preds[i]){
+        preds[i] = malloc(sizeof(unsigned int));
+      }
+      preds[i][0] = 0; /* The list of predecessors is now empty! */
+      
+      nj[i] = 0;
+      delta[i]= 0;
+    }
+    dist[j] = 0;
+    nj[j] = 1;
+    marked[0] = j;
+    d = 0;
+    n = 0;
+    nd = 1;
+    ndp = 0;
+    while (d<N && nd > 0){
+      for(i = n; i< n+nd; i ++){
+        cur_node = marked[i];
+        for (k=r_slap[cur_node]; k<r_slap[cur_node +1] ; k++){
+          w = J_slap[k];
+          if ( dist[w] == d+1){
+            add_predecessor((unsigned int **)(preds + w), cur_node);
+            nj[w] += nj[cur_node];
+          }
+          if ( dist[w] == N){
+            dist[w] = d+1;
+            marked[n + nd + ndp] = w;
+            add_predecessor(preds + w, cur_node);
+            ndp +=1;
+            nj[w] += nj[cur_node];
+          }
+        }
+      }
+      n = n + nd;
+      nd = ndp;
+      ndp = 0;
+      d += 1; 
+    }
+    for (k= n-1; k>=1; k--){
+      w = marked[k];
+      for (idx=1; idx <= preds[w][0]; idx ++ ){
+        i = preds[w][idx];
+        val = 1.0 * nj[i] / nj[w] * (1 + delta[w]);
+        delta[i] += val;
+        /* Now we should update the betweenness of the edge (i,w) in
+           the appropriate position of the vector  edge_bet*/
+        find_neigh_in_Jslap(J_slap, r_slap, N, i, w, &edge_pos);
+        edge_bet[edge_pos] += val;
+        find_neigh_in_Jslap(J_slap, r_slap, N, w, i, &edge_pos);
+        edge_bet[edge_pos] += val;
+      }
+      cB[w] += delta[w];
+    }
+  }
+  free(dist);
+  free(marked);
+  for (i=0; i<N; i++){
+    free(preds[i]);
+  }
+  free(preds);
+  free(nj);
+  free(delta);
+  return cB;
+}
+
+
+
+/*
+ * print of STDOUT the betweenness of each node
+ */
+void dump_cB(double *cB, unsigned int N){
+
+  unsigned int i;
+  for (i=0; i<N; i++){
+    printf("%g\n", cB[i]);
+  }
+}
+
+/*
+ * print on STDERR the betweenness of each edge
+ */
+
+void dump_edge_bet(unsigned int *J_slap, unsigned int *r_slap, unsigned int N,
+                   double *v,  FILE *fout){
+
+  unsigned int i, j;
+
+  for(i=0; i<N; i++){
+    for (j=r_slap[i]; j<r_slap[i+1]; j++)
+      fprintf(fout, "%d %d %g\n", i, J_slap[j], v[j]);
+  }
+}
+
+
+
+int main(int argc, char *argv[]){
+  
+  unsigned int *J_slap=NULL, *r_slap=NULL;
+  unsigned int K, N, i;
+  unsigned int n_start, n_end;
+  unsigned int *nlist=NULL;
+  unsigned int num;
+  double *edge_bet = NULL;
+  double *cB;
+  FILE *filein;
+  
+
+  if(argc < 2){
+    usage(argv);
+    exit(1);
+  }
+
+  srand(time(NULL));
+
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[1], "r", 2);
+  }
+
+  read_slap(filein, &K, &N, &J_slap, &r_slap);
+
+  nlist = malloc(N * sizeof(unsigned int));
+
+  for(i=0; i<N; i++){
+    nlist[i] = i;
+  }
+
+  n_start = 0;
+  n_end = N-1;
+  num = N;
+
+
+  if (argc > 3){
+    if(!my_strcasecmp(argv[2], "SEQ")){
+      n_start = atoi(argv[3]);
+      if (n_start > N-1)
+        n_start = 0;
+      if (argc > 4){
+        n_end = atoi(argv[4]);
+      }
+      else{
+        n_end = N-1;
+      }
+      num = n_end - n_start + 1;
+    }
+    else if (!my_strcasecmp(argv[2], "RND")){
+      num = atoi(argv[3]);
+      n_start = 0;
+      n_end = num-1;
+      if (num > N || num < 1)
+        num = N;
+      shuffle_vector(nlist, N);
+    }
+  }
+  
+  sort_neighbours(J_slap, r_slap, N);
+  edge_bet = malloc(K * sizeof(double));
+  memset(edge_bet, 0, K * sizeof(double));
+  cB = compute_bet_dependency(N, J_slap, r_slap, nlist+n_start, num, edge_bet);
+
+  dump_cB(cB, N);
+  dump_edge_bet(J_slap, r_slap, N, edge_bet, stderr);
+
+  free(cB);
+  free(J_slap);
+  free(r_slap);
+  free(edge_bet);
+  free(nlist);
+  
+}