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diff --git a/src/utils/utils.c b/src/utils/utils.c
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+++ b/src/utils/utils.c
@@ -0,0 +1,785 @@
+/**
+ * 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 file contains general utilities to handle input/output of
+ * graphs, convert between different sparse matrix representations,
+ * and other ancillary functions. It is linked against most of the
+ * programs in NetBunch.
+ *
+ */
+
+
+
+#include <stdlib.h>
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "utils.h"
+
+
+
+/* Read a degree distribution -- OBSOLETE */
+int read_deg_distr(FILE *filein, unsigned int **degs, unsigned int **Nk, double **p){
+
+ int n_degs = 0;
+ int size = 10;
+ char buff[256];
+ int k_i, num_i;
+ double p_i;
+ char *ptr;
+
+
+ *degs = realloc(*degs, size*sizeof(unsigned int));
+ *Nk = realloc(*Nk, size*sizeof(unsigned int));
+ *p = realloc(*p, size*sizeof(double));
+
+
+ while(fgets(buff, 256, filein)){
+ ptr = strtok(buff, " ");
+ VALID_PTR_OR_EXIT(ptr, 7);
+ if (ptr[0] == '#')
+ continue;
+ k_i = atoi(ptr);
+ ptr = strtok(NULL, " " );
+ VALID_PTR_OR_EXIT(ptr, 7);
+ num_i = atoi(ptr);
+ ptr = strtok(NULL, " \n");
+ VALID_PTR_OR_EXIT(ptr, 7);
+ p_i = atof(ptr);
+ if (n_degs == size){
+ size += 10;
+ *degs = realloc(*degs, size*sizeof(unsigned int));
+ *Nk = realloc(*Nk, size*sizeof(unsigned int));
+ *p = realloc(*p, size*sizeof(double));
+ }
+ (*degs)[n_degs] = k_i;
+ (*Nk)[n_degs] = num_i;
+ (*p)[n_degs] = p_i;
+ n_degs += 1;
+ }
+ if (n_degs > 0){
+ *degs = realloc(*degs, n_degs*sizeof(unsigned int));
+ *Nk = realloc(*Nk, n_degs*sizeof(unsigned int));
+ *p = realloc(*p, n_degs*sizeof(double));
+ }
+ return n_degs;
+}
+
+
+int read_deg_seq(FILE *filein, unsigned int **nodes){
+
+ int size, N, k;
+ char buff[256];
+ char *ptr;
+
+ N = 0;
+ size = 10;
+
+ *nodes = (unsigned int*)malloc(size * sizeof(unsigned int));
+
+ while(fgets(buff, 256, filein)){
+ ptr = strtok(buff, " ");
+ VALID_PTR_OR_EXIT(ptr, 7);
+ if (ptr[0] == '#')
+ continue;
+ k = atoi(ptr);
+
+ if (N == size){
+ size += 10;
+ *nodes = realloc(*nodes, size*sizeof(unsigned int));
+ }
+ (*nodes)[N] = k;
+ N += 1;
+ }
+ if (N > 0)
+ *nodes = realloc(*nodes, N * sizeof(unsigned int));
+ return N;
+}
+
+int read_stubs(FILE *filein, unsigned int **S){
+
+ int size, K;
+ char buff[256];
+ char *ptr;
+
+ K=0;
+ size = 20;
+ *S = malloc(size * sizeof(unsigned int));
+
+ while(fgets(buff, 256, filein)){
+ if (K == size){
+ size += 20;
+ *S = realloc(*S, size*sizeof(unsigned int));
+ }
+ ptr = strtok(buff, " "); /* read the first node */
+ VALID_PTR_OR_EXIT(ptr, 7);
+ (*S)[K++] = atoi(ptr);
+ ptr = strtok(NULL, " "); /* read the second node */
+ VALID_PTR_OR_EXIT(ptr, 7);
+ (*S)[K++] = atoi(ptr);
+ }
+ if (K > 0)
+ *S = realloc(*S, K * sizeof(unsigned int));
+ return K;
+}
+
+/*
+ * Read a file in ij format
+ */
+int read_ij(FILE *filein, unsigned int **I, unsigned int **J){
+
+ unsigned int size, K;
+ char buff[256];
+ char *ptr;
+
+ size = 20;
+ K = 0;
+
+ *I = malloc(size * sizeof(unsigned int));
+ *J = malloc(size * sizeof(unsigned int));
+ while(fgets(buff, 256, filein)){
+ if (buff[0] == '#')
+ continue;
+ if (K == size){
+ size += 20;
+ *I = realloc(*I, size*sizeof(unsigned int));
+ *J = realloc(*J, size*sizeof(unsigned int));
+ }
+ ptr = strtok(buff, " "); /* read the first node */
+ VALID_PTR_OR_EXIT(ptr, 7);
+ (*I)[K] = atoi(ptr);
+ ptr = strtok(NULL, " "); /* read the second node */
+ VALID_PTR_OR_EXIT(ptr, 7);
+ (*J)[K] = atoi(ptr);
+ K += 1;
+ }
+ if (K > 0){
+ *I = realloc(*I, K * sizeof(unsigned int));
+ *J = realloc(*J, K * sizeof(unsigned int));
+ }
+ return K;
+}
+
+
+/*
+ * Read a file in ij format -- weighted graphs -- if the input file is
+ * unweighted (i.e., no weights are provided), all the edges are
+ * assumed to have weight equal to 1.0
+ */
+int read_ij_w(FILE *filein, unsigned int **I, unsigned int **J,
+ double **W){
+
+ unsigned int size, K;
+ char buff[256];
+ char *ptr;
+
+ size = 20;
+ K = 0;
+
+ *I = malloc(size * sizeof(unsigned int));
+ *J = malloc(size * sizeof(unsigned int));
+ *W = malloc(size * sizeof(double));
+ while(fgets(buff, 256, filein)){
+ if (buff[0] == '#')
+ continue;
+ if (K == size){
+ size += 20;
+ *I = realloc(*I, size*sizeof(unsigned int));
+ *J = realloc(*J, size*sizeof(unsigned int));
+ *W = realloc(*W, size*sizeof(double));
+ }
+ ptr = strtok(buff, " "); /* read the first node */
+ VALID_PTR_OR_EXIT(ptr, 7);
+ (*I)[K] = atoi(ptr);
+ ptr = strtok(NULL, " "); /* read the second node */
+ VALID_PTR_OR_EXIT(ptr, 7);
+ (*J)[K] = atoi(ptr);
+ ptr = strtok(NULL, " "); /* read the weight */
+ if (!ptr)
+ (*W)[K] = 1.0;
+ else
+ (*W)[K] = atof(ptr);
+ K += 1;
+ }
+ if (K > 0){
+ *I = realloc(*I, K * sizeof(unsigned int));
+ *J = realloc(*J, K * sizeof(unsigned int));
+ *W = realloc(*W, K * sizeof(double));
+ }
+ return K;
+}
+
+
+
+void read_slap(FILE *filein, unsigned int *K, unsigned int *N,
+ unsigned int **J_slap, unsigned int **r_slap){
+
+ unsigned int *I=NULL, *J=NULL;
+ unsigned int i, k;
+
+ k = read_ij(filein, &I, &J);
+ *K = 2 * k;
+ I = realloc(I, 2*k * sizeof(unsigned int));
+ J = realloc(J, 2*k * sizeof(unsigned int));
+ for (i=k; i<2*k; i ++){
+ I[i] = J[i-k];
+ J[i] = I[i-k];
+ }
+
+ *N = convert_ij2slap(I, J, 2*k, r_slap, J_slap);
+ free(I);
+ free(J);
+ return;
+}
+
+void read_slap_w(FILE *filein, unsigned int *K, unsigned int *N,
+ unsigned int **J_slap, unsigned int **r_slap, double **W_slap){
+
+ unsigned int *I=NULL, *J=NULL;
+ double *W=NULL;
+ unsigned int i, k;
+
+ k = read_ij_w(filein, &I, &J, &W);
+ *K = 2 * k;
+ if (*K > 0){
+ I = realloc(I, (*K) * sizeof(unsigned int));
+ J = realloc(J, (*K) * sizeof(unsigned int));
+ W = realloc(W, (*K) * sizeof(double));
+ }
+ for (i=k; i<2*k; i ++){
+ I[i] = J[i-k];
+ J[i] = I[i-k];
+ W[i] = W[i-k];
+ }
+
+ *N = convert_ij2slap_w(I, J, W, 2*k, r_slap, J_slap, W_slap);
+ free(I);
+ free(J);
+ free(W);
+ return;
+}
+
+/**
+ *
+ * Read an I-J (directed) edge list, and transform it in SLAP
+ * notation, where the members of J_slap will be the outgoing
+ * neighbours
+ *
+ */
+void read_slap_dir(FILE *filein, unsigned int *K, unsigned int *N,
+ unsigned int **J_slap, unsigned int **r_slap){
+
+ unsigned int *I=NULL, *J=NULL;
+ unsigned int k;
+
+ k = read_ij(filein, &I, &J);
+ *K = k;
+
+ *N = convert_ij2slap(I, J, k, r_slap, J_slap);
+ free(I);
+ free(J);
+ return;
+}
+
+/**
+ *
+ * Read an I-J (directed) edge list, and transform it in SLAP
+ * notation, where the members of J_slap will be the incoming
+ * neighbours
+ *
+ */
+void read_slap_dir_incoming(FILE *filein, unsigned int *K, unsigned int *N,
+ unsigned int **J_slap, unsigned int **r_slap){
+
+ unsigned int *I=NULL, *J=NULL;
+ unsigned int k;
+
+ k = read_ij(filein, &I, &J);
+ *K = k;
+
+ *N = convert_ij2slap(J, I, k, r_slap, J_slap);
+ free(I);
+ free(J);
+ return;
+}
+
+
+
+
+unsigned int find_max(unsigned int *v, unsigned int N){
+
+ unsigned int i, max;
+
+ max = v[0];
+ i = 0;
+ while(++i < N){
+ if (v[i] > max)
+ max = v[i];
+ }
+ return max;
+}
+
+
+int convert_ij2slap(unsigned int *I, unsigned int *J, unsigned int K,
+ unsigned int ** r_slap, unsigned int **J_slap){
+
+ unsigned int tmp, max;
+ unsigned int i, pos;
+ unsigned int *p;
+
+ if (K < 1){
+ return 0;
+ }
+
+ max = find_max(I, K) + 1;
+ tmp = find_max(J, K) + 1;
+ if (tmp > max){
+ max = tmp ;
+ }
+
+ *r_slap = malloc( (max+1) * sizeof(unsigned int));
+ p = malloc(max * sizeof(unsigned int));
+
+ *J_slap = malloc(K * sizeof(unsigned int));
+
+ memset(*r_slap, 0, (max+1) * sizeof(unsigned int));
+ for(i=0; i<max + 1; i++)
+ (*r_slap)[i] = 0;
+ memset(p, 0, max * sizeof(unsigned int));
+ (*r_slap)[0] = 0;
+ for(i=0; i<K; i++){
+ (*r_slap)[ I[i] + 1] += 1;
+ }
+ for(i=1; i<=max; i++){
+ (*r_slap)[i] += (*r_slap)[i-1];
+ }
+ for(i=0; i<K; i++){
+ pos = (*r_slap) [ I[i] ] + p[ I[i] ];
+ (*J_slap)[pos] = J[i];
+ p[ I[i] ] += 1;
+ }
+ free(p);
+ return max;
+}
+
+
+
+int convert_ij2slap_w(unsigned int *I, unsigned int *J, double *W, unsigned int K,
+ unsigned int ** r_slap, unsigned int **J_slap,
+ double **W_slap){
+
+ unsigned int tmp, max;
+ unsigned int i, pos;
+ unsigned int *p;
+
+ max = find_max(I, K) + 1;
+ tmp = find_max(J, K) + 1;
+ if (tmp > max){
+ max = tmp ;
+ }
+ if (K<1){
+ return 0;
+ }
+
+ *r_slap = malloc( (max+1) * sizeof(unsigned int));
+ p = malloc(max * sizeof(unsigned int));
+
+ *J_slap = malloc(K * sizeof(unsigned int));
+ *W_slap = malloc(K * sizeof(double));
+
+ memset(*r_slap, 0, (max+1) * sizeof(unsigned int));
+ for(i=0; i<max + 1; i++)
+ (*r_slap)[i] = 0;
+ memset(p, 0, max * sizeof(unsigned int));
+ (*r_slap)[0] = 0;
+ for(i=0; i<K; i++){
+ (*r_slap)[ I[i] + 1] += 1;
+ }
+ for(i=1; i<=max; i++){
+ (*r_slap)[i] += (*r_slap)[i-1];
+ }
+ for(i=0; i<K; i++){
+ pos = (*r_slap) [ I[i] ] + p[ I[i] ];
+ (*J_slap)[pos] = J[i];
+ (*W_slap)[pos] = W[i];
+ p[ I[i] ] += 1;
+ }
+ free(p);
+ return max;
+}
+
+
+int convert_ij2slap_N(unsigned int *I, unsigned int *J, unsigned int K,
+ unsigned int N, unsigned int ** r_slap,
+ unsigned int **J_slap){
+
+ unsigned int max;
+ unsigned int i, pos;
+ unsigned int *p;
+
+ max = N;
+
+ *r_slap = malloc( (max+1) * sizeof(unsigned int));
+ p = malloc(max * sizeof(unsigned int));
+
+ *J_slap = malloc(K * sizeof(unsigned int));
+
+ memset(*r_slap, 0, (max+1) * sizeof(unsigned int));
+ for(i=0; i<max + 1; i++)
+ (*r_slap)[i] = 0;
+ memset(p, 0, max * sizeof(unsigned int));
+ (*r_slap)[0] = 0;
+ for(i=0; i<K; i++){
+ (*r_slap)[ I[i] + 1] += 1;
+ }
+ for(i=1; i<=max; i++){
+ (*r_slap)[i] += (*r_slap)[i-1];
+ }
+ for(i=0; i<K; i++){
+ pos = (*r_slap) [ I[i] ] + p[ I[i] ];
+ (*J_slap)[pos] = J[i];
+ p[ I[i] ] += 1;
+ }
+ free(p);
+ return max;
+}
+
+
+
+/* RIVEDERE QUESTA FUNZIONE...... PASSARE UN FILE COME ARGOMENTO E
+ USARE fprintf */
+void dump_deg_distr(unsigned int *degs, double *p, int n){
+
+ int i;
+
+ for(i=0; i<n; i++){
+ printf("%d %2.6f\n", degs[i], p[i]);
+ }
+}
+
+
+
+/* RIVEDERE QUESTA FUNZIONE...... PASSARE UN FILE COME ARGOMENTO E
+ USARE fprintf */
+void dump_deg_seq(unsigned int *nodes, int N){
+
+ int i;
+ for(i=0; i<N; i++){
+ printf("%d: %d\n", i, nodes[i]);
+ }
+}
+
+
+FILE* openfile_or_exit(char *filename, char *mode, int exitcode){
+
+ FILE *fileout;
+ char error_str[256];
+
+ fileout = fopen(filename, mode);
+ if (!fileout){
+ sprintf(error_str, "Error opening file %s", filename);
+ perror(error_str);
+ exit(exitcode);
+ }
+ return fileout;
+}
+
+int compare_int(const void *x1, const void *x2){
+ return *((unsigned int*)x1) - *((unsigned int*)x2);
+}
+
+int compare_double(const void *elem1, const void *elem2){
+
+ double *l1, *l2;
+
+ l1 = (double*)elem1;
+ l2 = (double*)elem2;
+ return (*l1 < *l2 ? -1 : (*l1 > *l2 ? 1 : 0));
+}
+
+void print_int(void *e){
+
+ int d;
+
+ d = *((int*)e);
+ printf("%d ", d);
+}
+
+void print_double(void *e){
+
+ double d;
+
+ d = *((double*)e);
+ printf("%g ", d);
+}
+
+
+
+void write_edges(FILE *fileout, unsigned int *J_slap,
+ unsigned int *r_slap, unsigned int N){
+
+ unsigned int i, j;
+
+ for(i=0; i<N; i++){
+ for (j=r_slap[i]; j<r_slap[i+1]; j++){
+ if (J_slap[j] > i){
+ fprintf(fileout, "%d %d\n", i, J_slap[j]);
+ }
+ }
+ }
+}
+
+
+void write_edges_dir(FILE *fileout, unsigned int *J_slap,
+ unsigned int *r_slap, unsigned int N){
+
+ unsigned int i, j;
+
+ for(i=0; i<N; i++){
+ for (j=r_slap[i]; j<r_slap[i+1]; j++){
+ fprintf(fileout, "%d %d\n", i, J_slap[j]);
+ }
+ }
+}
+
+
+
+
+/* Check if j is a neighbour of i */
+int is_neigh(unsigned int *J_slap, unsigned int *r_slap, unsigned int N,
+ unsigned int i, unsigned int j){
+
+ unsigned int l;
+ unsigned int count;
+ count = 0;
+ if (i >=N || j >=N)
+ return 0;
+ for(l=r_slap[i]; l<r_slap[i+1]; l++){
+ if (J_slap[l] == j)
+ count ++;
+ }
+ return count;
+}
+
+
+/* Check if j is a neighbour of i, using bsearch.
+
+ BE CAREFUL!!!! THIS WORKS ONLY IF THE LIST OF NEIGHBOURS HAS BEEN
+ PREVIOUSLY SORTED APPROPRIATELY, E.G. BY CALLING
+ sort_neighbours()
+
+*/
+int is_neigh_bs(unsigned int *J_slap, unsigned int *r_slap, unsigned int N,
+ unsigned int i, unsigned int j){
+
+ unsigned int *ptr;
+
+ ptr = bsearch(&j, & (J_slap[r_slap[i]]), r_slap[i+1] - r_slap[i], sizeof(unsigned int),
+ compare_int);
+ return (ptr == NULL ? 0: 1);
+}
+
+int find_neigh_in_Jslap(unsigned int *J_slap, unsigned int *r_slap, unsigned int N,
+ unsigned int i, unsigned int j, unsigned int *ret){
+
+ unsigned int *ptr;
+
+ ptr = bsearch(&j, & (J_slap[r_slap[i]]), r_slap[i+1] - r_slap[i], sizeof(unsigned int),
+ compare_int);
+ if (ptr == NULL){
+ return 0;
+ }
+ else{
+ *ret = (ptr - J_slap);
+ return 1;
+ }
+}
+
+
+double get_neigh_weight(unsigned int *J_slap, unsigned int *r_slap, double *W_slap,
+ unsigned int N, unsigned int i, unsigned int j){
+
+ unsigned int l;
+ double w = 0.0;
+
+ for(l=r_slap[i]; l<r_slap[i+1]; l++){
+ if (J_slap[l] == j)
+ w += W_slap[l];
+ }
+ return w;
+}
+
+
+
+
+
+void sort_neighbours(unsigned int *J_slap, unsigned int *r_slap, unsigned int N){
+
+ unsigned int i, *base;
+
+ for(i=0; i<N; i++){
+ base = J_slap + r_slap[i];
+ qsort(base, r_slap[i+1] - r_slap[i], sizeof(unsigned int), compare_int);
+ }
+}
+
+double strength(unsigned int *r_slap, double *W_slap, int i){
+
+ double s = 0;
+ int j;
+
+ for(j = r_slap[i]; j<r_slap[i+1]; j++){
+ s += W_slap[j];
+ }
+ return s;
+
+}
+
+
+void convert_slap2ij(unsigned int *J_slap, unsigned int *r_slap, int N, unsigned int *I, unsigned int *J){
+
+ int i, j, num;
+
+ num = 0;
+ for(i=0; i<N; i++){
+ for(j=r_slap[i]; j< r_slap[i+1]; j++){
+ I[num] = i;
+ J[num] = J_slap[j];
+ num += 1;
+ }
+ }
+}
+
+void show_progress(FILE *fout, char *s, unsigned int progress, unsigned int total){
+
+ char str[21]; /* 20 spaces */
+ double frac;
+ int num_char, i;
+
+ if (total){
+ frac = 1.0*progress/total;
+ }
+ else{
+ frac = 0.0;
+ }
+
+ num_char = (int)(frac * 20) - 1;
+ i = 20;
+ while(--i >= 0){
+ if (i > num_char)
+ str[i] = ' ';
+ else
+ str[i] = '.';
+ }
+ str[20] = '\0';
+ fprintf(fout, "\r%s [%s] %3d%%\r", s, str, (int)(frac * 100));
+}
+
+
+void shuffle_vector(unsigned int *v, unsigned int N){
+
+ int i, pos;
+
+ for(i=N-1; i>=0; i--){
+ pos = rand() % N;
+ if (pos != i){
+ v[i] ^= v[pos];
+ v[pos] ^= v[i];
+ v[i] ^= v[pos];
+ }
+ }
+}
+
+
+unsigned int read_partition(FILE *fin, unsigned int N, unsigned int *part){
+
+ unsigned int i;
+ char *ptr;
+ char buff[256];
+ unsigned int max_part = 0, val;
+
+
+ while(fgets(buff, 256, fin)){
+ if (buff[0] == '#')
+ continue;
+ ptr = strtok(buff, " "); /* read the node */
+ VALID_PTR_OR_EXIT(ptr, 7);
+ i = atoi(ptr);
+ if(i >= N){
+ fprintf(stderr, "Index %d out of bounds (0, %d) in read_partition (%s: %d)\n",
+ i, N, __FILE__, __LINE__);
+ }
+ ptr = strtok(NULL, " "); /* read the partition number */
+ VALID_PTR_OR_EXIT(ptr, 7);
+ val = atoi(ptr);
+ if (val > max_part){
+ max_part = val;
+ }
+ part[i] = val;
+ }
+ return max_part;
+}
+
+int degree(unsigned int *r_slap, unsigned int i){
+
+ return r_slap[i+1] - r_slap[i];
+}
+
+int my_strcasecmp(const char *s1, const char *s2){
+
+ char *c1, *c2;
+ int l1, l2;
+ int res, i;
+
+ l1 = strlen(s1);
+ l2 = strlen(s2);
+
+ c1 = malloc((1 + l1) * sizeof(char));
+ c2 = malloc((1 + l2) * sizeof(char));
+
+ for (i=0; i<l1; i++){
+ c1[i] = tolower(s1[i]);
+ }
+ c1[i] = '\0';
+
+ for (i=0; i<l2; i++){
+ c2[i] = tolower(s2[i]);
+ }
+ c2[i] = '\0';
+
+ res = strcmp(c1, c2);
+ free(c2);
+ free(c1);
+ return res;
+}
+
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-04 02:02:19 +0000