First commit on github -- NetBunch 1.0

3 files changed, 998 insertions, 0 deletions

diff --git a/src/label_prop/Makefile.am b/src/label_prop/Makefile.am
new file mode 100644
index 0000000..1ab1240
--- /dev/null
+++ b/src/label_prop/Makefile.am
@@ -0,0 +1,5 @@
+include ../common.mk 
+bin_PROGRAMS = label_prop
+label_prop_SOURCES = label_prop.c ../utils/utils.c ../include/utils.h
+label_prop_LDADD = -lm
+
diff --git a/src/label_prop/Makefile.in b/src/label_prop/Makefile.in
new file mode 100644
index 0000000..57a3c99
--- /dev/null
+++ b/src/label_prop/Makefile.in
@@ -0,0 +1,578 @@
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+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+	clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+	distclean distclean-compile distclean-generic distclean-tags \
+	distdir dvi dvi-am html html-am info info-am install \
+	install-am install-binPROGRAMS install-data install-data-am \
+	install-dvi install-dvi-am install-exec install-exec-am \
+	install-html install-html-am install-info install-info-am \
+	install-man install-pdf install-pdf-am install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs maintainer-clean maintainer-clean-generic \
+	mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+	ps ps-am tags tags-am uninstall uninstall-am \
+	uninstall-binPROGRAMS
+
+.PRECIOUS: Makefile
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/label_prop/label_prop.c b/src/label_prop/label_prop.c
new file mode 100644
index 0000000..3488834
--- /dev/null
+++ b/src/label_prop/label_prop.c
@@ -0,0 +1,415 @@
+/**
+ *  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 finds the communities in a graph using the
+ *  label-propagation algorithm proposed by Raghavan, Albert, and
+ *  Kumara.
+ *
+ *  References:
+ * 
+ * [1] U. N. Raghavan, R. Albert, and S. Kumara. "Near linear time
+ *     algorithm to detect community structures in large-scale
+ *     networks". Phys. Rev. E 76 (2007), 036106.
+ * 
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+#include <math.h>
+
+
+#include "iltree.h"
+#include "utils.h"
+
+
+typedef struct{
+  int label;
+  int freq;
+} label_freq_t;
+
+#define MODE_SYNC  0x0
+#define MODE_ASYNC 0x1
+
+
+
+/* Usage */
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                   -*-    label_prop    -*-                     **\n"
+         "**                                                                **\n"
+         "**   Find the communities in 'graph_in' using the label           **\n"
+         "**   propagation algorithm.                                       **\n"
+         "**                                                                **\n"
+         "**   The first parameter is used to choose between synchronous    **\n"
+         "**   (SYNC) and asynchronous (ASYNC) update.                      **\n"
+         "**                                                                **\n"
+         "**   The input file 'graph_in' is an edge-list.                   **\n"
+         "**   If 'graph_in' is equal to '-' (dash), read the file from     **\n" 
+         "**   the standard input (STDIN).                                  **\n"
+         "**                                                                **\n"
+         "**   If 'max_epochs' is specified, the program stops after        **\n"
+         "**   'max_epochs' epochs (useful in conjunction with SYNC, to     **\n"
+         "**   exit from loops).                                            **\n"
+         "**                                                                **\n"
+         "**   The program prints on STDOUT the partition obtained when     **\n"
+         "**   no more label flips are possible, in the format:             **\n"
+         "**                                                                **\n"
+         "**        node_1 comm_1                                           **\n"
+         "**        node_2 comm_2                                           **\n"
+         "**        node_3 comm_3                                           **\n"
+         "**       .....                                                    **\n"
+         "**                                                                **\n"
+         "**   where 'comm_1' is the community to which 'node_1' belongs.   **\n"
+         "**                                                                **\n"
+         "**   The program prints on STDERR one line for each epoch,        **\n"
+         "**   in the format:                                               **\n"
+         "**                                                                **\n"
+         "**       epoch_1 Q_1 flips_1                                      **\n"
+         "**       epoch_2 Q_2 flips_2                                      **\n"
+         "**       .....                                                    **\n"
+         "**                                                                **\n"
+         "**   where 'epoch_i' is the epoch number, 'Q_i' is the modularity **\n"
+         "**   of the partition found at that epoch, and 'flips_i' is the   **\n"
+         "**   number of label flips occurred in 'epoch_i'.                 **\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 [SYNC|ASYNC] <graph_in> [<max_epochs>]\n\n" , argv[0]);
+}
+
+
+
+
+/* Compare the frequency of two labels and return a value which allows
+   to sort them in reverse order (i.e., -v, if v=f1-f2) */
+
+int compare_label_freq_reverse(const void *e1, const void *e2){
+  
+  label_freq_t v1, v2;
+
+  v1 = *((label_freq_t*)e1);
+  v2 = *((label_freq_t*)e2);
+  
+  return - (v1.freq - v2.freq);
+
+}
+
+/* get the most common label in neighs (that is the list of the k
+   neighbours of a node) */
+unsigned int get_most_common_label(unsigned int *neighs, unsigned int k, 
+                                   unsigned int *labels, unsigned int ref_label, 
+                                   int *is_max){
+  
+  static label_freq_t *neigh_labels = NULL;
+  static int size = 0;
+  int num, i, j, max_freq;
+  
+  if (size < k){
+    size = k;
+    neigh_labels = realloc(neigh_labels, size * sizeof(label_freq_t));
+  }
+  
+  neigh_labels[0].label = labels[neighs[0]];
+  neigh_labels[0].freq = 1;
+  num = 1;
+  
+  for (i=1; i<k; i ++){
+    for(j=0; j<num; j++){
+      if (labels[neighs[i]] == neigh_labels[j].label)
+        break;
+    }
+    if (j == num){ /* new label */
+      neigh_labels[j].label = labels[neighs[i]];
+      neigh_labels[j].freq = 1;
+      num += 1;
+    }
+    else{/* the label already exists  -> increase the counter */
+      neigh_labels[j].freq += 1;
+    }
+  }
+
+  /* Now we sort the array neigh_labels */
+  qsort(neigh_labels, num, sizeof(label_freq_t), compare_label_freq_reverse);
+  
+  /* we determine how many neighbours have the maximum freq*/
+  max_freq = neigh_labels[0].freq;
+  i = 1;
+  while(i < num && neigh_labels[i].freq == max_freq){
+    i ++;
+  }
+
+  /* check whether ref_label is one of the most common labels */
+  *is_max = 0;
+  for (j=0; j<i; j++){
+    if (neigh_labels[j].label == ref_label)
+      *is_max = 1;
+  }
+  /* now that we know that there are "i" max_freqs, let's select one
+     of them at random */
+  j = rand() % i;
+  
+  return neigh_labels[j].label;
+}
+
+/* reassign the labels so that communities are numbered from 1 to NC */
+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;
+}
+
+
+void dump_partition(unsigned int *labels, unsigned int *label_count, unsigned int N){
+  
+  int i;
+  
+  for(i=0; i<N; i ++){
+    fprintf(stdout, "%d %d\n", i, labels[i]);//, label_count[labels[i]]);
+  }
+}
+
+
+/* compute the modularity of the current partition */
+
+double modularity(unsigned int *J_slap, unsigned int *r_slap, unsigned int N,
+                  unsigned int K, unsigned int *comm, unsigned int NC){
+
+  double Q=0;
+  int i, j;
+  unsigned int c_i, c_j;
+  double *pmm, *am;
+
+  pmm = malloc(NC * sizeof(double));
+  am = malloc(NC * sizeof(double));
+
+  for (i=0; i<NC; i++){
+    pmm[i] = am[i] = 0;
+  }
+
+  for(i=0; i<N; i ++){
+    c_i = comm[i];
+    am[c_i] += degree(r_slap, i);
+    for(j=r_slap[i]; j<r_slap[i+1]; j++){
+      c_j = comm[J_slap[j]]; 
+      if ( c_j == c_i ){
+        pmm[c_i] += 0.5;
+      }
+    }
+  }
+  Q = 0.0;
+  for(i=0; i < NC; i++){
+    Q += (pmm[i]* 2.0 / K - pow((am[i] * 1.0 / K), 2));
+  }
+  free(am);
+  free(pmm);
+  return Q;
+}
+
+
+
+unsigned int* label_propagation(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, 
+                                unsigned int K, unsigned int *num_epochs,
+                                int max_epochs, char mode){
+  
+  unsigned int *labels, *next_labels, *tmp_labels, *ids, tmp, new_label;
+  int i, epochs, j, k, cont, is_max;
+  long long int num_flips;
+  double Q;
+
+
+  
+  labels = malloc(N * sizeof(unsigned int));
+  ids = malloc(N * sizeof(unsigned int));
+  
+  if(mode == MODE_ASYNC){
+    next_labels = labels;
+  }
+  else if (mode == MODE_SYNC){
+    next_labels = malloc(N * sizeof(unsigned int));
+  }
+
+  /* We initialize the list of ids and labels */
+  for (i=0; i<N; i ++){
+    ids[i] = labels[i] = i;
+  }
+  
+  cont = 1;
+  epochs = 0;
+  while(cont){
+    if (max_epochs > 0 && epochs > max_epochs)
+      break;
+    cont = 0;
+    if (epochs > 0){
+      Q= modularity(J_slap, r_slap, N, K, labels, N);
+      fprintf(stderr, "%d %g %g\n", epochs, Q, (double)num_flips);
+    }
+    num_flips = 0;
+
+    epochs += 1;
+    for (i=N-1; i>=0; i--){
+      j = rand() % (i+1);
+      tmp = ids[j]; /* This is the id to be considered */
+
+      ids[j] = ids[i];
+      ids[i] = tmp;
+      k = r_slap[tmp + 1] - r_slap[tmp];
+      new_label = get_most_common_label(J_slap+r_slap[tmp], k,labels, labels[tmp], &is_max);
+      
+      /* Stop criterion: if the new label is not equal to the
+         old one, continue to another epoch */
+      
+      if (mode == MODE_ASYNC  && labels[tmp] != new_label){
+        labels[tmp] = new_label;
+        cont = 1;
+        num_flips += 1 ;
+      }
+      if (mode == MODE_SYNC){
+        next_labels[tmp] = new_label;
+        if (labels[tmp] != next_labels[tmp]){
+          cont = 1;
+          num_flips += 1;
+        }
+      }
+    }
+    if (mode == MODE_SYNC){
+      /* Now we can swap labels and next_labels */
+      tmp_labels = labels;
+      labels = next_labels;
+      next_labels = tmp_labels;
+    }
+  }
+  free(ids);
+  *num_epochs = epochs - 1;
+
+  if (mode == MODE_SYNC){
+    free(next_labels);
+  }
+  
+  return labels;
+}
+
+
+
+
+
+
+int main(int argc, char *argv[]){
+  
+  unsigned int N, K, nc;
+  unsigned int *J_slap, *r_slap, *labels, *label_count, num_epochs, max_epochs;
+  FILE *filein;
+  double Q;
+  char mode;
+
+  
+  if (argc < 3){
+    usage(argv);
+    exit(1);
+  }
+  
+  srand(time(NULL));
+  
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[2], "r", 2);
+  }
+
+  
+  read_slap(filein, &K, &N, &J_slap, &r_slap);
+
+  fclose(filein);
+  
+  if (!my_strcasecmp(argv[1], "sync")){
+    mode = MODE_SYNC;
+  }
+  else{
+    mode = MODE_ASYNC;
+  }
+  
+  if (argc > 3)
+    max_epochs = atoi(argv[3]);
+  else
+    max_epochs = 0;
+  
+  labels = label_propagation(J_slap, r_slap, N, K, &num_epochs, max_epochs, mode);
+  label_count = malloc(N * sizeof(unsigned int));
+  
+  nc = normalise_labels(labels, N, label_count);
+  
+  Q= modularity(J_slap, r_slap, N, K, labels, nc);
+  
+  printf("### nc: %d Q_max: %f Epochs: %d\n", nc, Q, num_epochs);
+  dump_partition(labels, label_count,  N);
+  free(J_slap);
+  free(r_slap);
+  free(label_count);
+  free(labels);
+}
+
+
+