First commit on github -- NetBunch 1.0

5 files changed, 1012 insertions, 0 deletions

diff --git a/src/dijkstra/Makefile.am b/src/dijkstra/Makefile.am
new file mode 100644
index 0000000..c43cf4f
--- /dev/null
+++ b/src/dijkstra/Makefile.am
@@ -0,0 +1,7 @@
+include ../common.mk 
+bin_PROGRAMS = dijkstra
+dijkstra_SOURCES = dijkstra.c node_w_funs.c node_w_funs.h \
+../utils/utils.c ../utils/gen_pqueue.c \
+../include/utils.h ../include/gen_pqueue.h
+dijkstra_LDADD = -lm
+
diff --git a/src/dijkstra/Makefile.in b/src/dijkstra/Makefile.in
new file mode 100644
index 0000000..96a1988
--- /dev/null
+++ b/src/dijkstra/Makefile.in
@@ -0,0 +1,586 @@
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+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/dijkstra/dijkstra.c b/src/dijkstra/dijkstra.c
new file mode 100644
index 0000000..4e8a63f
--- /dev/null
+++ b/src/dijkstra/dijkstra.c
@@ -0,0 +1,242 @@
+/**
+ *  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 implements the Dijkstra's algorithm to find the
+ *  shortest paths from a given node (source) to all the other nodes
+ *  of a weighted graph given as input.
+ *
+ *  References:
+ * 
+ *  [1] E. W. Dijkstra. "A Note on Two Problems in Connexion with
+ *      Graphs". Num. Math.  1 (1959), 269-271.
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <float.h>
+
+#include "utils.h"
+#include "gen_pqueue.h"
+
+#include "node_w_funs.h"
+
+#define INFINITY DBL_MAX
+
+
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                        -*-  dijkstra  -*-                      **\n"
+         "**                                                                **\n"
+         "**  Compute the distance from the given 'node' to all the other   **\n"
+         "**  nodes of a weighted 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.  If a node is     **\n"
+         "**  not reachable from <node>, the corresponding distance is set  **\n"         
+         "**  to 'inf'.                                                     **\n"         
+         "**                                                                **\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]);
+}
+
+
+
+void init_prio_queue(gen_pqueue_t **q, unsigned int N){
+  
+  gen_pqueue_func_t *funs;
+  
+  funs = malloc(sizeof(gen_pqueue_func_t));
+  (*funs).compare = compare_node_w;
+  (*funs).alloc_vector = alloc_vector_node_w;
+  (*funs).dealloc_vector = dealloc_vector_node_w;
+  (*funs).dealloc_elem = dealloc_elem_node_w;
+  (*funs).print_elem = print_elem_node_w;
+  (*funs).get_id = get_id_node_w;
+  (*funs).set_key = set_key_node_w;
+  (*funs).get_key = get_key_node_w;
+  (*funs).compare_to_key = compare_to_key_node_w;
+  
+  *q = gen_pqueue_init(N, MIN_QUEUE, funs);
+  free(funs);
+}
+
+void flatten_pqueue_to_array(gen_pqueue_t *q, double *v, unsigned int N){
+  
+  int i;
+  double *val;
+  
+  for(i=0; i<N; i++){
+    val = gen_pqueue_get_key(q, gen_pqueue_get_handle(q, i));
+    v[i] = *val;
+  }
+}
+
+
+void dijkstra(unsigned int N, unsigned int K, unsigned int *r_slap, unsigned int *J_slap, 
+              double *W_slap, int s, double *dist, int *prev){
+  
+  int i, cur_node, n;
+  double dist_cur_node, dist_neigh_node, w;
+  
+  gen_pqueue_t *qdist;
+  node_w_t *elem;
+  
+  
+  init_prio_queue(&qdist, N);
+  
+  for (i=0; i<N; i++){
+    elem = malloc(sizeof(node_w_t));
+    elem->i = i;
+    if (i != s)
+      elem->w = INFINITY;
+    else
+      elem->w = 0.0;
+    gen_pqueue_insert(qdist, elem);
+    prev[i] = -1;
+    dist[i] = INFINITY;
+  }
+  
+  
+  while (!gen_pqueue_delete(qdist, (void**)&elem)){ /* get the node with minimum distance */
+    cur_node = qdist->funs.get_id(elem);
+    dist_cur_node = *((double*) qdist->funs.get_key(elem));
+    if (dist_cur_node == INFINITY){ /* No more nodes are reachable from the origin */
+      free(elem);
+      gen_pqueue_destroy(qdist);
+      return;
+    }
+    dist[cur_node] = dist_cur_node;
+    for(i=r_slap[cur_node]; i<r_slap[cur_node + 1]; i++){
+      n = J_slap[i];
+      w = W_slap[i];
+      
+      dist_neigh_node = dist_cur_node + w;
+      if (dist[n] >= dist_neigh_node){
+        /* now we call gen_pqueue_change_key, which updates the key of node n */
+        gen_pqueue_change_key(qdist, gen_pqueue_get_handle(qdist, n), &dist_neigh_node);
+        prev[n] = cur_node;
+      }
+    }
+    free(elem);
+  }
+  gen_pqueue_destroy(qdist);
+}
+
+
+void dump_dists(double *v, unsigned int N){
+  
+  int i;
+
+  for(i=0; i<N-1; i++){
+    if (v[i] == INFINITY){
+      printf("inf ");
+    }
+    else{
+      printf("%g ", v[i]);
+    }
+  }
+  if (v[N-1] == INFINITY){
+    printf("inf\n");
+  }
+  else{
+    printf("%g\n", v[N-1]);
+  }
+}
+
+int main(int argc, char *argv[]){
+  
+  
+  double *dists;
+  int *prev;
+  unsigned int N, K, s;
+  unsigned int *r_slap = NULL, *J_slap=NULL;
+  double *W_slap = 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_w(filein, &K, &N, &J_slap, &r_slap, &W_slap);
+
+  fclose(filein);
+  
+  s = atoi(argv[2]);
+  if (s >= N){
+    fprintf(stderr, "Error!!! Source node index should be in the range [0:%d]\n", 
+            N-1);
+    exit(3);
+  }
+  
+  dists = malloc(N * sizeof(double));
+  prev = malloc(N * sizeof(int));
+
+  dijkstra(N, K, r_slap, J_slap, W_slap, s, dists, prev);
+  dump_dists(dists, N);
+  free(J_slap);
+  free(r_slap);
+  free(W_slap);
+  free(dists);
+  free(prev);
+}
diff --git a/src/dijkstra/node_w_funs.c b/src/dijkstra/node_w_funs.c
new file mode 100644
index 0000000..112140f
--- /dev/null
+++ b/src/dijkstra/node_w_funs.c
@@ -0,0 +1,111 @@
+/**
+ *  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
+ *
+ ***********************************************************************
+ *
+ *  Definition of the functions to be used with the Priority Queue
+ *
+ */
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "gen_pqueue.h"
+#include "node_w_funs.h"
+
+
+int compare_node_w(const void *e1, const void *e2){
+
+  node_w_t *n1, *n2;
+  
+  n1 = (node_w_t*) e1;
+  n2 = (node_w_t*) e2;
+
+  return (n1->w == n2->w ? 0 : (n1->w < n2->w ?  -1  : 1));
+}
+
+
+void* alloc_vector_node_w(unsigned int N){
+
+  return malloc(N * sizeof(node_w_t));
+}
+
+void dealloc_vector_node_w(void *v){
+  free(v);
+}
+
+
+void dealloc_elem_node_w(void *e){
+
+  free(e);
+}
+
+void print_elem_node_w(void *e){
+
+  node_w_t *elem;
+  
+  elem = (node_w_t*)e;
+  
+  printf("[%d, %2.8g]", elem->i, elem->w);
+}
+
+int get_id_node_w(void *e){
+  
+  node_w_t *elem;
+  
+  elem = (node_w_t*)e;
+  return elem->i;
+}
+
+void set_key_node_w(void *e, void *k){
+
+  node_w_t *elem;
+  
+
+  elem = (node_w_t*)e;
+  elem-> w = *((double*)(k));
+}
+
+int compare_to_key_node_w(void *e, void *k){
+
+  node_w_t *elem;
+  double d;
+
+  elem = (node_w_t*)e;
+  d = *((double*)k);
+  
+  return (elem->w == d ? 0 : (elem->w < d ? -1 : 1));
+}
+
+void* get_key_node_w(void *e){
+  
+  node_w_t *n;
+
+  n = (node_w_t*)e;
+  return &(n->w);
+}
diff --git a/src/dijkstra/node_w_funs.h b/src/dijkstra/node_w_funs.h
new file mode 100644
index 0000000..3b670a1
--- /dev/null
+++ b/src/dijkstra/node_w_funs.h
@@ -0,0 +1,66 @@
+/**
+ *  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
+ *
+ ***********************************************************************
+ *
+ *  Declaration of the functions to be used with the Priority Queue
+ *
+ */
+#ifndef __NODE_W_FUNS_H__
+#define __NODE_W_FUNS_H__
+
+
+
+typedef struct{
+  int i;
+  double w;
+} node_w_t;
+
+
+int compare_node_w(const void *e1, const void *e2);
+
+void* alloc_vector_node_w(unsigned int N);
+
+void dealloc_vector_node_w(void *v);
+
+void dealloc_elem_node_w(void *e);
+
+void print_elem_node_w(void *e);
+
+int get_id_node_w(void *e);
+
+void set_key_node_w(void *e, void *k);
+
+void* get_key_node_w(void *e);
+
+int compare_to_key_node_w(void *e, void *k);
+
+
+
+#endif //__NODE_W_FUNS_H__