First commit on github -- NetBunch 1.0

1 files changed, 220 insertions, 0 deletions

diff --git a/src/modularity/modularity.c b/src/modularity/modularity.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
+ *
+ ***********************************************************************
+ *
+ *  Take a graph and a partition, and compute the modularity function
+ *  associated to that partition.
+ *
+ *  References:
+ *  
+ *  [1] M. E. J. Newman and M. Girvan. "Finding and evaluating
+ *      community structure in networks". Phys. Rev. E 69, (2004),
+ *      026113.
+ *
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+
+#include "utils.h"
+
+void usage(char *argv[]){
+
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                    -*- modularity -*-                          **\n"
+         "**                                                                **\n"
+         "**  Compute the modularity function associated to a partition     **\n"
+         "**  of the nodes of the graph provided as input.                  **\n"
+         "**                                                                **\n"
+         "**  If 'graph_in' is equal to '-' (dash), read the edge list      **\n"
+         "**  from standard input (STDIN). The parameter 'partition' MUST   **\n"
+         "**  be a file in the format:                                      **\n"
+         "**                                                                **\n"
+         "**    node_0 community_0                                          **\n"
+         "**    node_1 community_1                                          **\n"
+         "**    node_2 community_2                                          **\n"
+         "**    .....                                                       **\n"
+         "**                                                                **\n"
+         "**  where 'node_0', 'node_1', etc. are node labels, and           **\n"
+         "**  'community_0', 'community_1', etc. is the label of the        **\n"
+         "**  community to which a node belongs. Notice that a node can     **\n"
+         "**  belong to exactly one community. This format is compatible    **\n"
+         "**  with the output of the programs which compute community       **\n"
+         "**  partitions, such as `gn`, `cnm`, `label_prop`, etc.           **\n"
+         "**                                                                **\n"
+         "**  The program prints on STDOUT the modularity of the partition, **\n"
+         "**  and prints on STDERR a single line in the format:             **\n"
+         "**                                                                **\n"
+         "**    ## nc: NUM_COMMUNITIES                                      **\n"
+         "**                                                                **\n"
+         "**  where 'NUM_COMMUNITIES' is the number of communities in the   **\n"
+         "**  partition given as input.                                     **\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"
+         " Please visit http://www.complex-networks.net for more information\n\n"
+         " (c) Vincenzo Nicosia 2009-2017 (v.nicosia@qmul.ac.uk)\n"
+         "********************************************************************\n\n"
+         );
+  printf("Usage: %s <graph_in> <partition>\n", argv[0]);
+}
+
+
+/* This is the function that computes the value of the modularity function */
+
+double compute_modularity(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, 
+                          unsigned int *part, unsigned int nc){
+  static double *e, *a;
+  
+  unsigned int i, j, n, K, deg_i;
+  unsigned int ci, cj;
+  double Q;
+
+  if(!e)
+    e = malloc((N+1) * sizeof(double));
+  if(!a)
+    a = malloc((N+1) * sizeof(double));
+
+  memset(e, 0, (N+1) * sizeof(double));
+  memset(a, 0, (N+1) * sizeof(double));
+
+  K = r_slap[N];
+  
+  for (i=0; i<N; i++){
+    ci = part[i];
+    deg_i = (r_slap[i+1] - r_slap[i]); 
+    if (deg_i == 0)
+      continue;
+    a[ci] += deg_i;
+    for(j=r_slap[i]; j< r_slap[i+1]; j++){
+      cj = part[J_slap[j]];
+      if (ci == cj){
+        e[ci] += 1;
+      }
+    }
+  }
+  
+  Q = 0.0;
+  fprintf(stderr, "### nc: %d\n", nc);
+  for (n=0; n<=nc; n++){
+    Q += 1.0 * e[n]/(1.0 * K ) - pow(1.0 * a[n]/K, 2);
+  }
+  free(a);
+  free(e);
+  return Q;
+}
+
+
+/* 
+ * This function remaps the original partition labels into a
+ *  consecutive set of integers, starting at 0 (zero) 
+ */
+int normalise_labels(unsigned int *labels, unsigned int N, 
+                     unsigned int *label_count){
+  
+  unsigned int *label_map;
+  int i, j, num = 0;
+  
+  
+  label_map = malloc(N * sizeof(unsigned int));
+  
+  label_map[0] = labels[0];
+  labels[0] = 0;
+  label_count[0] = 1;
+  num = 1;
+  
+  for(i=1; i<N; i ++){
+    for(j=0; j<num; j++){
+      if (labels[i] == label_map[j])
+        break;
+    }
+    if (j == num){
+      label_map[j] = labels[i];
+      label_count[j] = 0;
+      num +=1;
+    }
+    labels[i] = j;
+    label_count[j] += 1;
+  }
+
+  free(label_map);
+  return num;
+}
+
+
+int main(int argc, char *argv[]){
+
+  unsigned int N, K, nc;
+  unsigned int *J_slap=NULL, *r_slap=NULL, *part = NULL;
+  unsigned int *label_count;
+  FILE *f_net, *f_part;
+  double Q;
+
+
+  if (argc < 3){
+    usage(argv);
+    exit(1);
+  }
+
+  if(!strcmp(argv[1], "-")){
+    f_net = stdin;
+  }
+  else{
+    f_net = openfile_or_exit(argv[1], "r", 2);
+  }
+
+  f_part = openfile_or_exit(argv[2], "r", 3);
+  
+  read_slap(f_net, &K, &N, &J_slap, &r_slap);
+
+  part = malloc(N * sizeof(unsigned int));
+  memset(part, 0, N * sizeof(unsigned int));
+
+  label_count = malloc(N * sizeof(unsigned int));
+
+  nc = read_partition(f_part, N, part);
+
+  fclose(f_net);
+  fclose(f_part);
+  
+  nc = normalise_labels(part, N, label_count);
+  
+  Q = compute_modularity(J_slap, r_slap, N, part, nc);
+
+  printf("%g\n", Q);
+  free(J_slap);
+  free(r_slap);
+  free(part);
+  free(label_count);
+}