First commit on github -- NetBunch 1.0

4 files changed, 1077 insertions, 0 deletions

diff --git a/src/shortest/Makefile.am b/src/shortest/Makefile.am
new file mode 100644
index 0000000..71cabc2
--- /dev/null
+++ b/src/shortest/Makefile.am
@@ -0,0 +1,6 @@
+include ../common.mk 
+bin_PROGRAMS = shortest shortest_avg_max_hist
+shortest_SOURCES = shortest.c ../utils/utils.c ../include/utils.h
+shortest_LDADD = -lm
+shortest_avg_max_hist_SOURCES = shortest_avg_max_hist.c ../utils/utils.c ../include/utils.h
+shortest_avg_max_hist_LDADD = -lm
diff --git a/src/shortest/Makefile.in b/src/shortest/Makefile.in
new file mode 100644
index 0000000..8a0723a
--- /dev/null
+++ b/src/shortest/Makefile.in
@@ -0,0 +1,589 @@
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+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	      install; \
+	else \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+	fi
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+	-rm -f ../utils/$(DEPDIR)/$(am__dirstamp)
+	-rm -f ../utils/$(am__dirstamp)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-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/shortest/shortest.c b/src/shortest/shortest.c
new file mode 100644
index 0000000..9ea9a1a
--- /dev/null
+++ b/src/shortest/shortest.c
@@ -0,0 +1,259 @@
+/**
+ *  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 computes the distance from a given node to all the
+ *  other nodes of an undirected graph, using the Breadth-First Search
+ *  algorithm. 
+ *
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "utils.h"
+
+
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                        -*-  shortest  -*-                      **\n"
+         "**                                                                **\n"
+         "**  Compute the distance from the given 'node' to all the other   **\n"
+         "**  nodes of an undirected graph. The first parameter 'graph_in'  **\n"
+         "**  is the name of the file containing the edge list of the       **\n"
+         "**  graph. The second parameter 'node' is the label of the node   **\n"
+         "**  for which we want to compute the distances to all the other   **\n"
+         "**  nodes.                                                        **\n"
+         "**                                                                **\n"
+         "**  If 'graph_in' is equal to '-' (dash), read the edge list      **\n"
+         "**  from standard input (STDIN)                                   **\n"
+         "**                                                                **\n"
+         "**  The program prints on output a row of values:                 **\n"
+         "**                                                                **\n"
+         "**        d0 d1 d2 d3 d4......                                    **\n"
+         "**                                                                **\n"
+         "**  where d0 is the distance between 'node' and '0', 'd1' is the  **\n"
+         "**  distance between 'node' and '1', and so on.                   **\n"
+         "**                                                                **\n"         
+         "**  If the third parameter is equal to 'SHOW', the program will   **\n"         
+         "**  dump all the shortest paths from 'node' to all the other      **\n"
+         "**  nodes on the standard error (STDERR).                         **\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> <node> [SHOW]\n\n" , argv[0]);
+}
+
+
+/*
+ * Add 'k' to a list of predecessors
+ */
+
+void add_predecessor(unsigned int **pred, unsigned int k){
+  
+  (*pred)[0] += 1;
+  *pred = realloc(*pred, ((*pred)[0] + 1)  * sizeof(unsigned int));
+  (*pred)[ (*pred)[0] ] = k;
+}
+
+
+
+/*
+ *  
+ * This is the implementation of the Breadth-First Search algorithm
+ * (BFS) to compute the shortest paths, and the distances, between a
+ * given node 'i' and all the other nodes of a graph. 
+ * 
+ */
+unsigned int** compute_shortest_paths(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, 
+                            unsigned int i, unsigned int **dist){
+  
+  unsigned int j, k, cur_node;
+  unsigned int  *marked, **preds;
+  unsigned int d;
+  unsigned int n, nd, ndp;
+  
+  *dist = malloc(N * sizeof(unsigned int));
+  marked = malloc(N * sizeof(unsigned int));
+  preds = malloc(N * sizeof(unsigned int *));
+  
+  for(j=0; j<N; j ++){
+    (*dist)[j] = N;
+    preds[j] = malloc(sizeof(unsigned int));
+    preds[j][0] = 0; /* The list of predecessors is empty! */
+  }
+  (*dist)[i] = 0;
+  marked[0] = i;
+  d = 0;
+  n = 0;
+  nd = 1;
+  ndp = 0;
+  while (d<N && nd > 0){
+    for(k = n; k< n+nd; k ++){
+      cur_node = marked[k];
+      for (j=r_slap[cur_node]; j<r_slap[cur_node +1] ; j++){
+        if ( (*dist)[ J_slap[j] ] == d+1){
+          add_predecessor((unsigned int **)(preds + J_slap[j]), cur_node);
+        }
+        if ( (*dist)[ J_slap[j] ] == N){
+          (*dist)[ J_slap[j] ] = d+1;
+          marked[n + nd + ndp] = J_slap[j];
+          add_predecessor(preds + J_slap[j], cur_node);
+          ndp +=1;
+        }
+      }
+    
+    }
+    n = n + nd;
+    nd = ndp;
+    ndp = 0;
+    d += 1; 
+  }
+  free(marked);
+  return preds;
+}
+
+/*
+ * Dump on output the distances between 'node' and all the other nodes
+ * of the graph
+ *
+ */
+
+void dump_dists(unsigned int *dists, unsigned int N){
+
+  unsigned int i;
+  for (i=0; i<N; i++){
+    printf("%d ", dists[i]);
+  }
+  printf("\n");
+}
+
+
+/*
+ * recursively show the shortest paths from 'node' to all the other
+ * nodes ot the graph
+ *
+ */
+void recursive_show_paths(unsigned int **preds, unsigned int N, unsigned int k, 
+                          char *buff, int pos, FILE *fileout){
+  
+  int i;
+  char lbuff[10];
+
+  
+  if (preds[k][0] == 0){
+    sprintf(buff + pos, "%5d\n", k);
+    fprintf(fileout, "%s", buff );
+    return;
+  }
+ 
+  sprintf(lbuff, "%5d  ", k);
+  strncpy(buff + pos, lbuff, 7);
+  for(i=1; i<= preds[k][0]; i ++){
+    recursive_show_paths(preds, N, preds[k][i], buff, pos + 7, fileout);
+  }
+  return;
+}
+
+/*
+ *
+ * This function calls recursive_show_paths() for each of the nodes of
+ * the graph, to dump the shortest paths between 'node' and all the
+ * other nodes of the graph.
+ *
+ */
+
+void show_paths(unsigned int **preds, unsigned int N, FILE *fileout){
+  
+  int j;
+  char buff[256];
+
+  for (j = 0; j<N; j++){
+    if (preds[j][0] > 0)
+      recursive_show_paths(preds, N, j, buff, 0, fileout);
+  }
+  
+}
+
+int main(int argc, char *argv[]){
+  
+  unsigned int *J_slap=NULL, *r_slap=NULL;
+  unsigned int K, N, i;
+  unsigned int **preds, *dists=NULL;
+  FILE *filein;
+  
+  if (argc < 3){
+    usage(argv);
+    exit(1);
+  }
+
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[1], "r", 2);
+  }
+  
+  read_slap(filein, &K, &N, &J_slap, &r_slap);
+  i = atoi(argv[2]);
+  if (i>N){
+    printf("Node id '%d' does not exist!!!! Exiting....\n", i);
+    exit(3);
+  }
+
+  fclose(filein);
+  
+  preds = compute_shortest_paths(N, J_slap, r_slap, i, &dists);
+  dump_dists(dists, N);
+  /* check if we should dump the shortest paths on stderr */
+  if (argc > 3 && !strcmp(argv[3], "SHOW")){
+    show_paths(preds, N, stderr);
+  }
+
+  /* Cleanup */
+
+  for (i=0; i<N; i++){
+    free(preds[i]);
+  }
+  free(preds);
+  free(dists);
+  free(J_slap);
+  free(r_slap);
+}
diff --git a/src/shortest/shortest_avg_max_hist.c b/src/shortest/shortest_avg_max_hist.c
new file mode 100644
index 0000000..287c8a6
--- /dev/null
+++ b/src/shortest/shortest_avg_max_hist.c
@@ -0,0 +1,223 @@
+/**
+ *  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 computes the distance from a given node to all the
+ *  other nodes of an undirected graph, using the Breadth-First Search
+ *  algorithm. 
+ *
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "utils.h"
+
+
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                -*-  shortest_avg_max_hist  -*-                 **\n"
+         "**                                                                **\n"
+         "**  Compute the distance from the given 'node' to all the other   **\n"
+         "**  nodes of an undirected graph. The first parameter 'graph_in'  **\n"
+         "**  is the name of the file containing the edge list of the       **\n"
+         "**  graph. The second parameter 'node' is the label of the node   **\n"
+         "**  for which we want to compute the distances to all the other   **\n"
+         "**  nodes.                                                        **\n"
+         "**                                                                **\n"
+         "**  If 'graph_in' is equal to '-' (dash), read the edge list      **\n"
+         "**  from standard input (STDIN)                                   **\n"
+         "**                                                                **\n"
+         "**  The program prints on output a row containing:                **\n"
+         "**                                                                **\n"
+         "**   - The average shortest path length between 'node' and        **\n"
+         "**     all the other nodes                                        **\n"
+         "**   - The maximum distance to any other node (eccentricity)      **\n" 
+         "**   - The number of nodes at distance 1, 2, 3, .... from 'node'  **\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 2010-2017 (v.nicosia@qmul.ac.uk)\n"
+         "********************************************************************\n\n"
+         );
+  printf("Usage: %s <graph_in> <node>\n\n" , argv[0]);
+}
+
+
+/*
+ * Add 'k' to a list of predecessors
+ */
+
+void add_predecessor(unsigned int **pred, unsigned int k){
+  
+  (*pred)[0] += 1;
+  *pred = realloc(*pred, ((*pred)[0] + 1)  * sizeof(unsigned int));
+  (*pred)[ (*pred)[0] ] = k;
+}
+
+
+
+/*
+ *  
+ * This is the implementation of the Breadth-First Search algorithm
+ * (BFS) to compute the shortest paths, and the distances, between a
+ * given node 'i' and all the other nodes of a graph. 
+ * 
+ */
+unsigned int** compute_shortest_paths(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, 
+                            unsigned int i, unsigned int **dist){
+  
+  unsigned int j, k, cur_node;
+  unsigned int  *marked, **preds;
+  unsigned int d;
+  unsigned int n, nd, ndp;
+  
+  *dist = malloc(N * sizeof(unsigned int));
+  marked = malloc(N * sizeof(unsigned int));
+  preds = malloc(N * sizeof(unsigned int *));
+  
+  for(j=0; j<N; j ++){
+    (*dist)[j] = N;
+    preds[j] = malloc(sizeof(unsigned int));
+    preds[j][0] = 0; /* The list of predecessors is empty! */
+  }
+  (*dist)[i] = 0;
+  marked[0] = i;
+  d = 0;
+  n = 0;
+  nd = 1;
+  ndp = 0;
+  while (d<N && nd > 0){
+    for(k = n; k< n+nd; k ++){
+      cur_node = marked[k];
+      for (j=r_slap[cur_node]; j<r_slap[cur_node +1] ; j++){
+        if ( (*dist)[ J_slap[j] ] == d+1){
+          add_predecessor((unsigned int **)(preds + J_slap[j]), cur_node);
+        }
+        if ( (*dist)[ J_slap[j] ] == N){
+          (*dist)[ J_slap[j] ] = d+1;
+          marked[n + nd + ndp] = J_slap[j];
+          add_predecessor(preds + J_slap[j], cur_node);
+          ndp +=1;
+        }
+      }
+    
+    }
+    n = n + nd;
+    nd = ndp;
+    ndp = 0;
+    d += 1; 
+  }
+  free(marked);
+  return preds;
+}
+
+
+void dump_avg_max_hist(unsigned int *dists, unsigned int N){
+
+  unsigned int i;
+  double res = 0;
+  double max = 0;
+  double *hist;
+
+  for (i=0; i<N; i++){
+    res += dists[i];
+    if (dists[i] > max)
+      max = dists[i];
+  }
+  hist = malloc((max + 1) * sizeof(double));
+  for (i=0; i<=max; i++){
+    hist[i] = 0;
+  }
+  for (i=0; i<N; i++){
+    if(dists[i]){
+      hist[dists[i]] ++;
+    }
+  }
+  
+  res = res/(N-1);
+  
+  printf("%g %g", res, max);
+  for (i=1; i<=max; i++){
+    printf(" %g", hist[i]);
+  }
+  printf("\n");
+  free(hist);
+}
+
+
+
+
+int main(int argc, char *argv[]){
+  
+  unsigned int *J_slap=NULL, *r_slap=NULL;
+  unsigned int K, N, i;
+  unsigned int **preds, *dists=NULL;
+  FILE *filein;
+  
+  if (argc < 3){
+    usage(argv);
+    exit(1);
+  }
+
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[1], "r", 2);
+  }
+  
+  read_slap(filein, &K, &N, &J_slap, &r_slap);
+  fclose(filein);
+  i = atoi(argv[2]);
+  if (i>N){
+    printf("Node id '%d' does not exist!!!! Exiting....\n", i);
+    exit(3);
+  }
+  preds = compute_shortest_paths(N, J_slap, r_slap, i, &dists);
+  dump_avg_max_hist(dists, N);
+
+  /* Cleanup */
+  
+  for (i=0; i<N; i++){
+    free(preds[i]);
+  }
+  free(preds);
+  free(dists);
+  free(J_slap);
+  free(r_slap);
+}