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authorKatolaZ <katolaz@freaknet.org>2017-09-27 15:06:31 +0100
committerKatolaZ <katolaz@freaknet.org>2017-09-27 15:06:31 +0100
commit3aee2fd43e3059a699af2b63c6f2395e5a55e515 (patch)
tree58c95505a0906ed9cfa694f9dbd319403fd8f01d /src/modularity/modularity.c
First commit on github -- NetBunch 1.0
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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);
+}