diff options
Diffstat (limited to 'src/modularity/modularity.c')
| -rw-r--r-- | src/modularity/modularity.c | 220 |
1 files changed, 220 insertions, 0 deletions
diff --git a/src/modularity/modularity.c b/src/modularity/modularity.c new file mode 100644 index 0000000..2b01ff9 --- /dev/null +++ b/src/modularity/modularity.c @@ -0,0 +1,220 @@ +/** + * 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); +} |