int main() {
igraph_t g;
long int i;
igraph_integer_t size;
/* DIRECTED */
igraph_star(&g, 10, IGRAPH_STAR_OUT, 0);
for (i=0; i<100; i++) {
igraph_es_t es;
igraph_eit_t it;
igraph_es_pairs_small(&es, IGRAPH_DIRECTED,
0,1,0,2,0,5,0,2,0,3,0,4,0,7,0,9, -1);
igraph_eit_create(&g, es, &it);
igraph_es_size(&g, &es, &size);
IGRAPH_EIT_RESET(it);
while (!IGRAPH_EIT_END(it)) {
IGRAPH_EIT_GET(it);
IGRAPH_EIT_NEXT(it);
size--;
}
if (size != 0) return 1;
igraph_eit_destroy(&it);
igraph_es_destroy(&es);
}
igraph_destroy(&g);
/* UNDIRECTED */
igraph_star(&g, 10, IGRAPH_STAR_UNDIRECTED, 0);
for (i=0; i<100; i++) {
igraph_es_t es;
igraph_eit_t it;
igraph_es_pairs_small(&es, IGRAPH_DIRECTED,
0,1,2,0,5,0,0,2,3,0,0,4,7,0,0,9, -1);
igraph_eit_create(&g, es, &it);
IGRAPH_EIT_RESET(it);
while (!IGRAPH_EIT_END(it)) {
IGRAPH_EIT_GET(it);
IGRAPH_EIT_NEXT(it);
}
igraph_eit_destroy(&it);
igraph_es_destroy(&es);
}
igraph_destroy(&g);
return 0;
}
/**
* \ingroup structural
* \function igraph_similarity_jaccard_es
* \brief Jaccard similarity coefficient for a given edge selector.
*
* </para><para>
* The Jaccard similarity coefficient of two vertices is the number of common
* neighbors divided by the number of vertices that are neighbors of at
* least one of the two vertices being considered. This function calculates
* the pairwise Jaccard similarities for the endpoints of edges in a given edge
* selector.
*
* \param graph The graph object to analyze
* \param res Pointer to a vector, the result of the calculation will
* be stored here. The number of elements is the same as the number
* of edges in \p es.
* \param es An edge selector that specifies the edges to be included in the
* result.
* \param mode The type of neighbors to be used for the calculation in
* directed graphs. Possible values:
* \clist
* \cli IGRAPH_OUT
* the outgoing edges will be considered for each node.
* \cli IGRAPH_IN
* the incoming edges will be considered for each node.
* \cli IGRAPH_ALL
* the directed graph is considered as an undirected one for the
* computation.
* \endclist
* \param loops Whether to include the vertices themselves in the neighbor
* sets.
* \return Error code:
* \clist
* \cli IGRAPH_ENOMEM
* not enough memory for temporary data.
* \cli IGRAPH_EINVVID
* invalid vertex id passed.
* \cli IGRAPH_EINVMODE
* invalid mode argument.
* \endclist
*
* Time complexity: O(nd), n is the number of edges in the edge selector, d is
* the (maximum) degree of the vertices in the graph.
*
* \sa \ref igraph_similarity_jaccard() and \ref igraph_similarity_jaccard_pairs()
* to calculate the Jaccard similarity between all pairs of a vertex set or
* some selected vertex pairs, or \ref igraph_similarity_dice(),
* \ref igraph_similarity_dice_pairs() and \ref igraph_similarity_dice_es() for a
* measure very similar to the Jaccard coefficient
*
* \example examples/simple/igraph_similarity.c
*/
int igraph_similarity_jaccard_es(const igraph_t *graph, igraph_vector_t *res,
const igraph_es_t es, igraph_neimode_t mode, igraph_bool_t loops) {
igraph_vector_t v;
igraph_eit_t eit;
IGRAPH_VECTOR_INIT_FINALLY(&v, 0);
IGRAPH_CHECK(igraph_eit_create(graph, es, &eit));
IGRAPH_FINALLY(igraph_eit_destroy, &eit);
while (!IGRAPH_EIT_END(eit)) {
long int eid = IGRAPH_EIT_GET(eit);
igraph_vector_push_back(&v, IGRAPH_FROM(graph, eid));
igraph_vector_push_back(&v, IGRAPH_TO(graph, eid));
IGRAPH_EIT_NEXT(eit);
}
igraph_eit_destroy(&eit);
IGRAPH_FINALLY_CLEAN(1);
IGRAPH_CHECK(igraph_similarity_jaccard_pairs(graph, res, &v, mode, loops));
igraph_vector_destroy(&v);
IGRAPH_FINALLY_CLEAN(1);
return IGRAPH_SUCCESS;
}
int igraph_get_edgelist(const igraph_t *graph, igraph_vector_t *res, igraph_bool_t bycol) {
igraph_eit_t edgeit;
long int no_of_edges=igraph_ecount(graph);
long int vptr=0;
igraph_integer_t from, to;
IGRAPH_CHECK(igraph_vector_resize(res, no_of_edges*2));
IGRAPH_CHECK(igraph_eit_create(graph, igraph_ess_all(IGRAPH_EDGEORDER_ID),
&edgeit));
IGRAPH_FINALLY(igraph_eit_destroy, &edgeit);
if (bycol) {
while (!IGRAPH_EIT_END(edgeit)) {
igraph_edge(graph, IGRAPH_EIT_GET(edgeit), &from, &to);
VECTOR(*res)[vptr]=from;
VECTOR(*res)[vptr+no_of_edges]=to;
vptr++;
IGRAPH_EIT_NEXT(edgeit);
}
} else {
while (!IGRAPH_EIT_END(edgeit)) {
igraph_edge(graph, IGRAPH_EIT_GET(edgeit), &from, &to);
VECTOR(*res)[vptr++]=from;
VECTOR(*res)[vptr++]=to;
IGRAPH_EIT_NEXT(edgeit);
}
}
igraph_eit_destroy(&edgeit);
IGRAPH_FINALLY_CLEAN(1);
return 0;
}
/* Shrinks communities into single vertices, keeping all the edges.
* This method is internal because it destroys the graph in-place and
* creates a new one -- this is fine for the multilevel community
* detection where a copy of the original graph is used anyway.
* The membership vector will also be rewritten by the underlying
* igraph_membership_reindex call */
int igraph_i_multilevel_shrink(igraph_t *graph, igraph_vector_t *membership) {
igraph_vector_t edges;
long int no_of_nodes = igraph_vcount(graph);
long int no_of_edges = igraph_ecount(graph);
igraph_bool_t directed = igraph_is_directed(graph);
long int i;
igraph_eit_t eit;
if (no_of_nodes == 0)
return 0;
if (igraph_vector_size(membership) < no_of_nodes) {
IGRAPH_ERROR("cannot shrink graph, membership vector too short",
IGRAPH_EINVAL);
}
IGRAPH_VECTOR_INIT_FINALLY(&edges, no_of_edges * 2);
IGRAPH_CHECK(igraph_reindex_membership(membership, 0));
/* Create the new edgelist */
igraph_eit_create(graph, igraph_ess_all(IGRAPH_EDGEORDER_ID), &eit);
IGRAPH_FINALLY(igraph_eit_destroy, &eit);
i = 0;
while (!IGRAPH_EIT_END(eit)) {
igraph_integer_t from, to;
IGRAPH_CHECK(igraph_edge(graph, IGRAPH_EIT_GET(eit), &from, &to));
VECTOR(edges)[i++] = VECTOR(*membership)[(long int) from];
VECTOR(edges)[i++] = VECTOR(*membership)[(long int) to];
IGRAPH_EIT_NEXT(eit);
}
igraph_eit_destroy(&eit);
IGRAPH_FINALLY_CLEAN(1);
/* Create the new graph */
igraph_destroy(graph);
no_of_nodes = (long int) igraph_vector_max(membership)+1;
IGRAPH_CHECK(igraph_create(graph, &edges, (igraph_integer_t) no_of_nodes,
directed));
igraph_vector_destroy(&edges);
IGRAPH_FINALLY_CLEAN(1);
return 0;
}
int igraph_edges(const igraph_t *graph, igraph_es_t eids,
igraph_vector_t *edges) {
igraph_eit_t eit;
long int n, ptr=0;
IGRAPH_CHECK(igraph_eit_create(graph, eids, &eit));
IGRAPH_FINALLY(igraph_eit_destroy, &eit);
n=IGRAPH_EIT_SIZE(eit);
IGRAPH_CHECK(igraph_vector_resize(edges, n*2));
for (; !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit)) {
long int e=IGRAPH_EIT_GET(eit);
VECTOR(*edges)[ptr++]=IGRAPH_FROM(graph, e);
VECTOR(*edges)[ptr++]=IGRAPH_TO(graph, e);
}
igraph_eit_destroy(&eit);
IGRAPH_FINALLY_CLEAN(1);
return 0;
}
igraph_vector_t * ggen_analyze_longest_antichain(igraph_t *g)
{
/* The following steps are implemented :
* - Convert our DAG to a specific bipartite graph B
* - solve maximum matching on B
* - conver maximum matching to min vectex cover
* - convert min vertex cover to antichain on G
*/
int err;
unsigned long i,vg,found,added;
igraph_t b,gstar;
igraph_vector_t edges,*res = NULL;
igraph_vector_t c,s,t,todo,n,next,l,r;
igraph_eit_t eit;
igraph_es_t es;
igraph_integer_t from,to;
igraph_vit_t vit;
igraph_vs_t vs;
igraph_real_t value;
if(g == NULL)
return NULL;
/* before creating the bipartite graph, we need all relations
* between any two vertices : the transitive closure of g */
err = igraph_copy(&gstar,g);
if(err) return NULL;
err = ggen_transform_transitive_closure(&gstar);
if(err) goto error;
/* Bipartite convertion : let G = (S,C),
* we build B = (U,V,E) with
* - U = V = S (each vertex is present twice)
* - (u,v) \in E iff :
* - u \in U
* - v \in V
* - u < v in C (warning, this means that we take
* transitive closure into account, not just the
* original edges)
* We will also need two additional nodes further in the code.
*/
vg = igraph_vcount(g);
err = igraph_empty(&b,vg*2,1);
if(err) goto error;
/* id and id+vg will be a vertex in U and its copy in V,
* iterate over gstar edges to create edges in b
*/
err = igraph_vector_init(&edges,igraph_ecount(&gstar));
if(err) goto d_b;
igraph_vector_clear(&edges);
err = igraph_eit_create(&gstar,igraph_ess_all(IGRAPH_EDGEORDER_ID),&eit);
if(err) goto d_edges;
for(IGRAPH_EIT_RESET(eit); !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit))
{
err = igraph_edge(&gstar,IGRAPH_EIT_GET(eit),&from,&to);
if(err)
{
igraph_eit_destroy(&eit);
goto d_edges;
}
to += vg;
igraph_vector_push_back(&edges,(igraph_real_t)from);
igraph_vector_push_back(&edges,(igraph_real_t)to);
}
igraph_eit_destroy(&eit);
err = igraph_add_edges(&b,&edges,NULL);
if(err) goto d_edges;
/* maximum matching on b */
igraph_vector_clear(&edges);
err = bipartite_maximum_matching(&b,&edges);
if(err) goto d_edges;
/* Let M be the max matching, and N be E - M
* Define T as all unmatched vectices from U as well as all vertices
* reachable from those by going left-to-right along N and right-to-left along
* M.
* Define L = U - T, R = V \inter T
* C:= L + R
* C is a minimum vertex cover
*/
err = igraph_vector_init_seq(&n,0,igraph_ecount(&b)-1);
if(err) goto d_edges;
err = vector_diff(&n,&edges);
if(err) goto d_n;
err = igraph_vector_init(&c,vg);
if(err) goto d_n;
igraph_vector_clear(&c);
/* matched vertices : S */
err = igraph_vector_init(&s,vg);
if(err) goto d_c;
igraph_vector_clear(&s);
for(i = 0; i < igraph_vector_size(&edges); i++)
{
err = igraph_edge(&b,VECTOR(edges)[i],&from,&to);
if(err) goto d_s;
igraph_vector_push_back(&s,from);
}
/* we may have inserted the same vertex multiple times */
err = vector_uniq(&s);
if(err) goto d_s;
/* unmatched */
err = igraph_vector_init_seq(&t,0,vg-1);
if(err) goto d_s;
err = vector_diff(&t,&s);
if(err) goto d_t;
/* alternating paths
*/
err = igraph_vector_copy(&todo,&t);
if(err) goto d_t;
err = igraph_vector_init(&next,vg);
if(err) goto d_todo;
igraph_vector_clear(&next);
do {
vector_uniq(&todo);
added = 0;
for(i = 0; i < igraph_vector_size(&todo); i++)
{
if(VECTOR(todo)[i] < vg)
{
/* scan edges */
err = igraph_es_adj(&es,VECTOR(todo)[i],IGRAPH_OUT);
if(err) goto d_next;
err = igraph_eit_create(&b,es,&eit);
if(err)
{
igraph_es_destroy(&es);
goto d_next;
}
for(IGRAPH_EIT_RESET(eit); !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit))
{
if(igraph_vector_binsearch(&n,IGRAPH_EIT_GET(eit),NULL))
{
err = igraph_edge(&b,IGRAPH_EIT_GET(eit),&from,&to);
if(err)
{
igraph_eit_destroy(&eit);
igraph_es_destroy(&es);
goto d_next;
}
if(!igraph_vector_binsearch(&t,to,NULL))
{
igraph_vector_push_back(&next,to);
added = 1;
}
}
}
}
else
{
/* scan edges */
err = igraph_es_adj(&es,VECTOR(todo)[i],IGRAPH_IN);
if(err) goto d_next;
err = igraph_eit_create(&b,es,&eit);
if(err)
{
igraph_es_destroy(&es);
goto d_next;
}
for(IGRAPH_EIT_RESET(eit); !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit))
{
if(igraph_vector_binsearch(&edges,IGRAPH_EIT_GET(eit),NULL))
{
err = igraph_edge(&b,IGRAPH_EIT_GET(eit),&from,&to);
if(err)
{
igraph_eit_destroy(&eit);
igraph_es_destroy(&es);
goto d_next;
}
if(!igraph_vector_binsearch(&t,to,NULL))
{
igraph_vector_push_back(&next,from);
added = 1;
}
}
}
}
igraph_es_destroy(&es);
igraph_eit_destroy(&eit);
}
igraph_vector_append(&t,&todo);
igraph_vector_clear(&todo);
igraph_vector_append(&todo,&next);
igraph_vector_clear(&next);
} while(added);
err = igraph_vector_init_seq(&l,0,vg-1);
if(err) goto d_t;
err = vector_diff(&l,&t);
if(err) goto d_l;
err = igraph_vector_update(&c,&l);
if(err) goto d_l;
err = igraph_vector_init(&r,vg);
if(err) goto d_l;
igraph_vector_clear(&r);
/* compute V \inter T */
for(i = 0; i < igraph_vector_size(&t); i++)
{
if(VECTOR(t)[i] >= vg)
igraph_vector_push_back(&r,VECTOR(t)[i]);
}
igraph_vector_add_constant(&r,(igraph_real_t)-vg);
err = vector_union(&c,&r);
if(err) goto d_r;
/* our antichain is U - C */
res = malloc(sizeof(igraph_vector_t));
if(res == NULL) goto d_r;
err = igraph_vector_init_seq(res,0,vg-1);
if(err) goto f_res;
err = vector_diff(res,&c);
if(err) goto d_res;
goto ret;
d_res:
igraph_vector_destroy(res);
f_res:
free(res);
res = NULL;
ret:
d_r:
igraph_vector_destroy(&r);
d_l:
igraph_vector_destroy(&l);
d_next:
igraph_vector_destroy(&next);
d_todo:
igraph_vector_destroy(&todo);
d_t:
igraph_vector_destroy(&t);
d_s:
igraph_vector_destroy(&s);
d_c:
igraph_vector_destroy(&c);
d_n:
igraph_vector_destroy(&n);
d_edges:
igraph_vector_destroy(&edges);
d_b:
igraph_destroy(&b);
error:
igraph_destroy(&gstar);
return res;
}
int ggen_write_graph(igraph_t *g, FILE *output)
{
Agraph_t *cg;
Agnode_t *f,*t;
Agedge_t *edge;
igraph_vector_ptr_t vertices;
igraph_eit_t eit;
int err;
unsigned long i,j;
unsigned long vcount = igraph_vcount(g);
igraph_integer_t from,to;
char name[GGEN_DEFAULT_NAME_SIZE];
char *str = NULL;
igraph_strvector_t gnames,vnames,enames;
igraph_vector_t gtypes,vtypes,etypes;
Agsym_t *attr;
/* see warning below */
igraph_error_handler_t *error_handler;
err = igraph_vector_ptr_init(&vertices,vcount);
if(err) return 1;
/* WARNING: this should be changed if igraph-0.6 gets
* stable.
* We need to ignore some igraph_cattribute errors
* because we try to retrieve special attributes (ggen specifics).
* igraph version 0.6 include a cattribute_has_attr that should be
* used instead of ignoring errors.
*/
error_handler = igraph_set_error_handler(igraph_error_handler_ignore);
/* open graph
* its name is saved in __ggen_graph_name if it exists
*/
str =(char *) GAS(g,GGEN_GRAPH_NAME_ATTR);
if(!str)
cg = agopen(GGEN_DEFAULT_GRAPH_NAME,Agdirected,NULL);
else
cg = agopen(str,Agdirected,NULL);
if(!cg)
{
err = 1;
goto d_v;
}
/* save a pointer to each vertex */
for(i = 0; i < vcount; i++)
{
/* find a vertex name */
str = vid2vname_unsafe(name,g,i);
if(!str)
f = agnode(cg,name,1);
else
f = agnode(cg,str,1);
VECTOR(vertices)[i] = (void *)f;
}
/* We have finished with dangerous attributes accesses */
igraph_set_error_handler(error_handler);
/* now loop through edges in the igraph */
err = igraph_eit_create(g,igraph_ess_all(IGRAPH_EDGEORDER_ID),&eit);
if(err) goto c_ag;
for(IGRAPH_EIT_RESET(eit); !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit))
{
err = igraph_edge(g,IGRAPH_EIT_GET(eit),&from,&to);
if(err) goto d_eit;
f = (Agnode_t *) VECTOR(vertices)[(unsigned long)from];
t = (Agnode_t *) VECTOR(vertices)[(unsigned long)to];
agedge(cg,f,t,NULL,1);
}
/* find all properties */
igraph_strvector_init(&gnames,1);
igraph_strvector_init(&vnames,vcount);
igraph_strvector_init(&enames,igraph_ecount(g));
igraph_vector_init(>ypes,1);
igraph_vector_init(&vtypes,vcount);
igraph_vector_init(&etypes,igraph_ecount(g));
err = igraph_cattribute_list(g,&gnames,>ypes,&vnames,&vtypes,&enames,&etypes);
if(err) goto d_eit;
/* add graph properties */
for(i = 0; i < igraph_strvector_size(&gnames); i++)
{
if(strcmp(GGEN_GRAPH_NAME_ATTR,STR(gnames,i)))
{
if(VECTOR(gtypes)[i]==IGRAPH_ATTRIBUTE_NUMERIC) {
snprintf(name,GGEN_DEFAULT_NAME_SIZE,"%f",
(double)GAN(g,STR(gnames,i)));
agattr(cg,AGRAPH,(char *)STR(gnames,i),name);
}
else
agattr(cg,AGRAPH,(char *)STR(gnames,i),
(char *)GAS(g,STR(gnames,i)));
}
}
/* add vertex properties */
for(i = 0; i < igraph_strvector_size(&vnames); i++)
{
if(strcmp(GGEN_VERTEX_NAME_ATTR,STR(vnames,i)))
{
/* creates the attribute but we still need to set it for each vertex */
attr = agattr(cg,AGNODE,(char *)STR(vnames,i),GGEN_CGRAPH_DEFAULT_VALUE);
for(j = 0; j < vcount; j++)
{
f = (Agnode_t *) VECTOR(vertices)[j];
if(VECTOR(vtypes)[i]==IGRAPH_ATTRIBUTE_NUMERIC) {
snprintf(name,GGEN_DEFAULT_NAME_SIZE,"%f",
(double)VAN(g,STR(vnames,i),j));
agxset(f,attr,name);
}
else
agxset(f,attr,(char *)VAS(g,STR(vnames,i),j));
}
}
}
/* add edges properties */
for(i = 0; i < igraph_strvector_size(&enames); i++)
{
/* creates the attribute but we still need to set it for each edge */
attr = agattr(cg,AGEDGE,(char *)STR(enames,i),GGEN_CGRAPH_DEFAULT_VALUE);
for(j = 0; j < igraph_ecount(g); j++)
{
igraph_edge(g,j,&from,&to);
f = (Agnode_t *) VECTOR(vertices)[(unsigned long)from];
t = (Agnode_t *) VECTOR(vertices)[(unsigned long)to];
edge = agedge(cg,f,t,NULL,0);
if(VECTOR(etypes)[i]==IGRAPH_ATTRIBUTE_NUMERIC) {
snprintf(name,GGEN_DEFAULT_NAME_SIZE,"%f",
(double)EAN(g,STR(enames,i),j));
agxset(edge,attr,name);
}
else
agxset(edge,attr,(char *)EAS(g,STR(enames,i),j));
}
}
/* write the graph */
err = agwrite(cg,(void *)output);
d_eit:
igraph_eit_destroy(&eit);
c_ag:
agclose(cg);
d_v:
igraph_vector_ptr_destroy(&vertices);
return err;
}
static GError* _tgengraph_parseGraphEdges(TGenGraph* g) {
TGEN_ASSERT(g);
tgen_debug("checking graph edges...");
/* we will iterate through the edges */
igraph_eit_t edgeIterator;
gint result = igraph_eit_create(g->graph, igraph_ess_all(IGRAPH_EDGEORDER_ID), &edgeIterator);
if(result != IGRAPH_SUCCESS) {
return g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_PARSE,
"igraph_eit_create return non-success code %i", result);
}
/* count the edges as we iterate */
igraph_integer_t edgeCount = 0;
GError* error = NULL;
while (!IGRAPH_EIT_END(edgeIterator)) {
igraph_integer_t edgeIndex = IGRAPH_EIT_GET(edgeIterator);
igraph_integer_t fromVertexIndex, toVertexIndex;
gint result = igraph_edge(g->graph, edgeIndex, &fromVertexIndex, &toVertexIndex);
if(result != IGRAPH_SUCCESS) {
error = g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_PARSE,
"igraph_edge return non-success code %i", result);
break;
}
const gchar* fromIDStr = (g->knownAttributes&TGEN_VA_ID) ?
VAS(g->graph, "id", fromVertexIndex) : NULL;
if(!fromIDStr) {
error = g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_MISSING_ATTRIBUTE,
"found vertex %li with missing 'id' attribute", (glong)fromVertexIndex);
break;
}
const gchar* toIDStr = (g->knownAttributes&TGEN_VA_ID) ?
VAS(g->graph, "id", toVertexIndex) : NULL;
if(!toIDStr) {
error = g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_MISSING_ATTRIBUTE,
"found vertex %li with missing 'id' attribute", (glong)toVertexIndex);
break;
}
tgen_debug("found edge %li from vertex %li (%s) to vertex %li (%s)",
(glong)edgeIndex, (glong)fromVertexIndex, fromIDStr, (glong)toVertexIndex, toIDStr);
const gchar* weightStr = (g->knownAttributes&TGEN_EA_WEIGHT) ?
EAS(g->graph, "weight", edgeIndex) : NULL;
if(weightStr != NULL) {
if(g_ascii_strncasecmp(weightStr, "\0", (gsize) 1)) {
gdouble weight = g_ascii_strtod(weightStr, NULL);
_tgengraph_storeWeight(g, weight, edgeIndex);
}
}
edgeCount++;
IGRAPH_EIT_NEXT(edgeIterator);
}
igraph_eit_destroy(&edgeIterator);
if(!error) {
g->edgeCount = igraph_ecount(g->graph);
if(g->edgeCount != edgeCount) {
tgen_warning("igraph_vcount %f does not match iterator count %f", g->edgeCount, edgeCount);
}
tgen_info("%u graph edges ok", (guint) g->edgeCount);
}
return error;
}
static GError* _tgengraph_parseChooseVertex(TGenGraph* g, const gchar* idStr,
igraph_integer_t vertexIndex) {
TGEN_ASSERT(g);
tgen_debug("found vertex %li (%s)", (glong)vertexIndex, idStr);
GError* error = NULL;
/* Assure the edges from this choose action have either all weights or no weights. Store in data */
igraph_es_t edgeSelector;
igraph_eit_t edgeIterator;
gint result = igraph_es_incident(&edgeSelector, vertexIndex, IGRAPH_OUT);
if(result != IGRAPH_SUCCESS) {
return g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_PARSE,
"igraph_es_incident return non-success code %i", result);
}
result = igraph_eit_create(g->graph, edgeSelector, &edgeIterator);
if(result != IGRAPH_SUCCESS) {
return g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_PARSE,
"igraph_eit_create return non-success code %i", result);
}
/* Get initial case for first edge */
igraph_integer_t edgeIndex = IGRAPH_EIT_GET(edgeIterator);
gdouble* weight = _tgengraph_getWeight(g, edgeIndex);
gboolean lastWeight;
gdouble totalWeight = 0.0;
if(weight != NULL) {
lastWeight = TRUE;
totalWeight += *weight;
}
else {
lastWeight = FALSE;
}
IGRAPH_EIT_NEXT(edgeIterator);
while (!IGRAPH_EIT_END(edgeIterator)) {
edgeIndex = IGRAPH_EIT_GET(edgeIterator);
gdouble* weight = _tgengraph_getWeight(g, edgeIndex);
gboolean thisWeight;
if(weight != NULL) {
thisWeight = TRUE;
totalWeight += *weight;
}
else {
thisWeight = FALSE;
}
/* Assure weights is still constant */
if (thisWeight != lastWeight){
igraph_es_destroy(&edgeSelector);
igraph_eit_destroy(&edgeIterator);
return g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_INVALID_CONTENT,
"choose action must have all weights or no weights");
}
lastWeight = thisWeight;
IGRAPH_EIT_NEXT(edgeIterator);
}
TGenAction* a = tgenaction_newChooseAction(&error, lastWeight, totalWeight);
/* clean up */
igraph_es_destroy(&edgeSelector);
igraph_eit_destroy(&edgeIterator);
if(a) {
_tgengraph_storeAction(g, a, vertexIndex);
}
return error;
}
/**
* \ingroup interface
* \function igraph_delete_edges
* \brief Removes edges from a graph.
*
* </para><para>
* The edges to remove are given as an edge selector.
*
* </para><para>
* This function cannot remove vertices, they will be kept, even if
* they lose all their edges.
*
* </para><para>
* This function invalidates all iterators.
* \param graph The graph to work on.
* \param edges The edges to remove.
* \return Error code.
*
* Time complexity: O(|V|+|E|) where
* |V|
* and |E| are the number of vertices
* and edges in the \em original graph, respectively.
*/
int igraph_delete_edges(igraph_t *graph, igraph_es_t edges) {
long int no_of_edges=igraph_ecount(graph);
long int no_of_nodes=igraph_vcount(graph);
long int edges_to_remove=0;
long int remaining_edges;
igraph_eit_t eit;
igraph_vector_t newfrom, newto, newoi;
int *mark;
long int i, j;
mark=igraph_Calloc(no_of_edges, int);
if (mark==0) {
IGRAPH_ERROR("Cannot delete edges", IGRAPH_ENOMEM);
}
IGRAPH_FINALLY(igraph_free, mark);
IGRAPH_CHECK(igraph_eit_create(graph, edges, &eit));
IGRAPH_FINALLY(igraph_eit_destroy, &eit);
for (IGRAPH_EIT_RESET(eit); !IGRAPH_EIT_END(eit); IGRAPH_EIT_NEXT(eit)) {
long int e=IGRAPH_EIT_GET(eit);
if (mark[e]==0) {
edges_to_remove++;
mark[e]++;
}
}
remaining_edges=no_of_edges-edges_to_remove;
/* We don't need the iterator any more */
igraph_eit_destroy(&eit);
IGRAPH_FINALLY_CLEAN(1);
IGRAPH_VECTOR_INIT_FINALLY(&newfrom, remaining_edges);
IGRAPH_VECTOR_INIT_FINALLY(&newto, remaining_edges);
/* Actually remove the edges, move from pos i to pos j in newfrom/newto */
for (i=0,j=0; j<remaining_edges; i++) {
if (mark[i]==0) {
VECTOR(newfrom)[j] = VECTOR(graph->from)[i];
VECTOR(newto)[j] = VECTOR(graph->to)[i];
j++;
}
}
/* Create index, this might require additional memory */
IGRAPH_VECTOR_INIT_FINALLY(&newoi, remaining_edges);
IGRAPH_CHECK(igraph_vector_order(&newfrom, &newto, &newoi, no_of_nodes));
IGRAPH_CHECK(igraph_vector_order(&newto, &newfrom, &graph->ii, no_of_nodes));
/* Attributes, we use the original from vector to create an index,
needed for the attribute handler. This index is the same as the
one used for copying the edges of course The attribute handler is
safe, never returns error. */
if (graph->attr) {
long int i, j=1;
for (i=0; i<igraph_vector_size(&graph->from); i++) {
if (mark[i] == 0) {
VECTOR(graph->from)[i]=j++;
} else {
VECTOR(graph->from)[i]=0;
}
}
igraph_i_attribute_delete_edges(graph, &graph->from);
}
/* Ok, we've all memory needed, free the old structure */
igraph_vector_destroy(&graph->from);
igraph_vector_destroy(&graph->to);
igraph_vector_destroy(&graph->oi);
graph->from=newfrom;
graph->to=newto;
graph->oi=newoi;
IGRAPH_FINALLY_CLEAN(3);
igraph_Free(mark);
IGRAPH_FINALLY_CLEAN(1);
/* Create start vectors, no memory is needed for this */
igraph_i_create_start(&graph->os, &graph->from, &graph->oi, no_of_nodes);
igraph_i_create_start(&graph->is, &graph->to, &graph->ii, no_of_nodes);
/* Nothing to deallocate... */
return 0;
}
int TEgraphMF::readTopology(const char *file_name) {
int ret = 0;
Bitvector* lid;
Bitvector* ilid;
ifstream infile;
string str;
size_t found, first, second;
FILE *instream;
infile.open(file_name, ifstream::in);
/*first the Global graph attributes - c igraph does not do it!!*/
while (infile.good()) {
getline(infile, str);
found = str.find("<data key=\"FID_LEN\">");
if (found != string::npos) {
first = str.find(">");
second = str.find("<", first);
sscanf(str.substr(first + 1, second - first - 1).c_str(), "%d", &fid_len);
}
found = str.find("<data key=\"TM\">");
if (found != string::npos) {
first = str.find(">");
second = str.find("<", first);
nodeID = str.substr(first + 1, second - first - 1);
}
found = str.find("<data key=\"RV\">");
if (found != string::npos) {
first = str.find(">");
second = str.find("<", first);
RVnodeID = str.substr(first + 1, second - first - 1);
}
found = str.find("<data key=\"TM_MODE\">");
if (found != string::npos) {
first = str.find(">");
second = str.find("<", first);
mode = str.substr(first + 1, second - first - 1);
}
}
infile.close();
instream = fopen(file_name, "r");
if (instream == NULL) {
return -1;
}
//EF_ALLOW_MALLOC_0=1;
ret = igraph_read_graph_graphml(&graph, instream, 0);
//EF_ALLOW_MALLOC_0=0;
fclose(instream);
if (ret < 0) {
return ret;
}
//cout << "TM: " << igraph_vcount(&graph) << " nodes" << endl;
//cout << "TM: " << igraph_ecount(&graph) << " edges" << endl;
for (int i = 0; i < igraph_vcount(&graph); i++) {
string nID = string(igraph_cattribute_VAS(&graph, "NODEID", i));
string iLID = string(igraph_cattribute_VAS(&graph, "iLID", i));
reverse_node_index.insert(pair<string, int>(nID, i));
ilid = new Bitvector(iLID);
nodeID_iLID.insert(pair<string, Bitvector* >(nID, ilid));
vertex_iLID.insert(pair<int, Bitvector* >(i, ilid));
cout<<"node "<<i<<" has NODEID"<<nID<<endl;
cout<<"node "<<i<<" has ILID"<<ilid->to_string()<<endl;
}
for (int i = 0; i < igraph_ecount(&graph); i++) {
string LID = string(igraph_cattribute_EAS(&graph, "LID", i));
reverse_edge_index.insert(pair<string, int>(LID, i));
lid = new Bitvector(LID);
edge_LID.insert(pair<int, Bitvector* >(i, lid));
igraph_integer_t head;
igraph_integer_t tail;
igraph_edge(&graph, i,&head,&tail);
cout << "edge " << i
<<" "<<head<<"->"<<tail<<" has LID "
<< lid->to_string() << endl;
}
std::vector<int> edgepairs;
std::vector<double> capacities;
igraph_eit_t ieit;
igraph_eit_create(&graph,igraph_ess_all(IGRAPH_EDGEORDER_ID),&ieit);
while(!IGRAPH_EIT_END(ieit)) {
igraph_integer_t edgeid = IGRAPH_EIT_GET(ieit);
igraph_integer_t head;
igraph_integer_t tail;
// WARNING all edge capacities are give the same value
// this needs to come from deployment script
capacities.push_back(defaultBW);
igraph_edge(&graph, edgeid,&head,&tail);
cout<<"edge"<<head<<"->"<<tail<<endl;
edgepairs.push_back(head);
edgepairs.push_back(tail);
IGRAPH_EIT_NEXT(ieit);
}
igraph_eit_destroy(&ieit);
// create an initial dmand matrix assuming equal traffic
// between all node pairs - unlikely to be correct but
// as booststrap we do not know any better
// THIS WILL NEED TO BE DYNAMICALLY UPDATED LATER
for (int i = 0; i < igraph_vcount(&graph); i++) {
for (int j = 0; j < igraph_vcount(&graph); j++) {
if( i == j) continue;
mf_demand demand;
demand.source = i;
demand.sink = j;
// WARNING HARDCODED VALUE, ok for initial boostrap
// as it is all relative. It should be obtained from
// the deployment script as an initial demand.
demand.demand = 1.0;
demandMapMeasured.insert(pair<intpair,mf_demand>(intpair(i,j),
demand));
}
}
graphMF = Graph_mf((int)igraph_vcount(&graph),edgepairs,capacities);
// now demands are set to half the maximum flow when
// using shortest paths assuming equal flow between
// all pairs - enough for boostrapping
// initial demand matrix done!
//update_paths();
preCalculateFids();
return ret;
}
/**
* \function igraph_community_fastgreedy
* \brief Finding community structure by greedy optimization of modularity
*
* This function implements the fast greedy modularity optimization
* algorithm for finding community structure, see
* A Clauset, MEJ Newman, C Moore: Finding community structure in very
* large networks, http://www.arxiv.org/abs/cond-mat/0408187 for the
* details.
*
* </para><para>
* Some improvements proposed in K Wakita, T Tsurumi: Finding community
* structure in mega-scale social networks,
* http://www.arxiv.org/abs/cs.CY/0702048v1 have also been implemented.
*
* \param graph The input graph. It must be a simple graph, i.e. a graph
* without multiple and without loop edges. This is checked and an
* error message is given for non-simple graphs.
* \param weights Potentially a numeric vector containing edge
* weights. Supply a null pointer here for unweighted graphs. The
* weights are expected to be non-negative.
* \param merges Pointer to an initialized matrix or NULL, the result of the
* computation is stored here. The matrix has two columns and each
* merge corresponds to one merge, the ids of the two merged
* components are stored. The component ids are numbered from zero and
* the first \c n components are the individual vertices, \c n is
* the number of vertices in the graph. Component \c n is created
* in the first merge, component \c n+1 in the second merge, etc.
* The matrix will be resized as needed. If this argument is NULL
* then it is ignored completely.
* \param modularity Pointer to an initialized matrix or NULL pointer,
* in the former case the modularity scores along the stages of the
* computation are recorded here. The vector will be resized as
* needed.
* \return Error code.
*
* \sa \ref igraph_community_walktrap(), \ref
* igraph_community_edge_betweenness() for other community detection
* algorithms, \ref igraph_community_to_membership() to convert the
* dendrogram to a membership vector.
*
* Time complexity: O(|E||V|log|V|) in the worst case,
* O(|E|+|V|log^2|V|) typically, |V| is the number of vertices, |E| is
* the number of edges.
*/
int igraph_community_fastgreedy(const igraph_t *graph,
const igraph_vector_t *weights,
igraph_matrix_t *merges, igraph_vector_t *modularity) {
long int no_of_edges, no_of_nodes, no_of_joins, total_joins;
long int i, j, k, n, m, from, to, dummy;
igraph_integer_t ffrom, fto;
igraph_eit_t edgeit;
igraph_i_fastgreedy_commpair *pairs, *p1, *p2;
igraph_i_fastgreedy_community_list communities;
igraph_vector_t a;
igraph_real_t q, maxq, *dq, weight_sum;
igraph_bool_t simple;
/*long int join_order[] = { 16,5, 5,6, 6,0, 4,0, 10,0, 26,29, 29,33, 23,33, 27,33, 25,24, 24,31, 12,3, 21,1, 30,8, 8,32, 9,2, 17,1, 11,0, 7,3, 3,2, 13,2, 1,2, 28,31, 31,33, 22,32, 18,32, 20,32, 32,33, 15,33, 14,33, 0,19, 19,2, -1,-1 };*/
/*long int join_order[] = { 43,42, 42,41, 44,41, 41,36, 35,36, 37,36, 36,29, 38,29, 34,29, 39,29, 33,29, 40,29, 32,29, 14,29, 30,29, 31,29, 6,18, 18,4, 23,4, 21,4, 19,4, 27,4, 20,4, 22,4, 26,4, 25,4, 24,4, 17,4, 0,13, 13,2, 1,2, 11,2, 8,2, 5,2, 3,2, 10,2, 9,2, 7,2, 2,28, 28,15, 12,15, 29,16, 4,15, -1,-1 };*/
no_of_nodes = igraph_vcount(graph);
no_of_edges = igraph_ecount(graph);
if (igraph_is_directed(graph)) {
IGRAPH_ERROR("fast greedy community detection works for undirected graphs only", IGRAPH_UNIMPLEMENTED);
}
total_joins=no_of_nodes-1;
if (weights != 0) {
if (igraph_vector_size(weights) < igraph_ecount(graph))
IGRAPH_ERROR("fast greedy community detection: weight vector too short", IGRAPH_EINVAL);
if (igraph_vector_any_smaller(weights, 0))
IGRAPH_ERROR("weights must be positive", IGRAPH_EINVAL);
weight_sum = igraph_vector_sum(weights);
} else weight_sum = no_of_edges;
IGRAPH_CHECK(igraph_is_simple(graph, &simple));
if (!simple) {
IGRAPH_ERROR("fast-greedy community finding works only on simple graphs", IGRAPH_EINVAL);
}
if (merges != 0) {
IGRAPH_CHECK(igraph_matrix_resize(merges, total_joins, 2));
igraph_matrix_null(merges);
}
if (modularity != 0) {
IGRAPH_CHECK(igraph_vector_resize(modularity, total_joins+1));
}
/* Create degree vector */
IGRAPH_VECTOR_INIT_FINALLY(&a, no_of_nodes);
if (weights) {
debug("Calculating weighted degrees\n");
for (i=0; i < no_of_edges; i++) {
VECTOR(a)[(long int)IGRAPH_FROM(graph, i)] += VECTOR(*weights)[i];
VECTOR(a)[(long int)IGRAPH_TO(graph, i)] += VECTOR(*weights)[i];
}
} else {
debug("Calculating degrees\n");
IGRAPH_CHECK(igraph_degree(graph, &a, igraph_vss_all(), IGRAPH_ALL, 0));
}
/* Create list of communities */
debug("Creating community list\n");
communities.n = no_of_nodes;
communities.no_of_communities = no_of_nodes;
communities.e = (igraph_i_fastgreedy_community*)calloc(no_of_nodes, sizeof(igraph_i_fastgreedy_community));
if (communities.e == 0) {
IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);
}
IGRAPH_FINALLY(free, communities.e);
communities.heap = (igraph_i_fastgreedy_community**)calloc(no_of_nodes, sizeof(igraph_i_fastgreedy_community*));
if (communities.heap == 0) {
IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);
}
IGRAPH_FINALLY(free, communities.heap);
communities.heapindex = (igraph_integer_t*)calloc(no_of_nodes, sizeof(igraph_integer_t));
if (communities.heapindex == 0) {
IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);
}
IGRAPH_FINALLY_CLEAN(2);
IGRAPH_FINALLY(igraph_i_fastgreedy_community_list_destroy, &communities);
for (i=0; i<no_of_nodes; i++) {
igraph_vector_ptr_init(&communities.e[i].neis, 0);
communities.e[i].id = i;
communities.e[i].size = 1;
}
/* Create list of community pairs from edges */
debug("Allocating dq vector\n");
dq = (igraph_real_t*)calloc(no_of_edges, sizeof(igraph_real_t));
if (dq == 0) {
IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);
}
IGRAPH_FINALLY(free, dq);
debug("Creating community pair list\n");
IGRAPH_CHECK(igraph_eit_create(graph, igraph_ess_all(0), &edgeit));
IGRAPH_FINALLY(igraph_eit_destroy, &edgeit);
pairs = (igraph_i_fastgreedy_commpair*)calloc(2*no_of_edges, sizeof(igraph_i_fastgreedy_commpair));
if (pairs == 0) {
IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);
}
IGRAPH_FINALLY(free, pairs);
i=j=0;
while (!IGRAPH_EIT_END(edgeit)) {
long int eidx = IGRAPH_EIT_GET(edgeit);
igraph_edge(graph, eidx, &ffrom, &fto);
/* Create the pairs themselves */
from = (long int)ffrom; to = (long int)fto;
if (from == to) {
IGRAPH_ERROR("loop edge detected, simplify the graph before starting community detection", IGRAPH_EINVAL);
}
if (from>to) {
dummy=from; from=to; to=dummy;
}
if (weights) {
dq[j]=2*(VECTOR(*weights)[eidx]/(weight_sum*2.0) - VECTOR(a)[from]*VECTOR(a)[to]/(4.0*weight_sum*weight_sum));
} else {
dq[j]=2*(1.0/(no_of_edges*2.0) - VECTOR(a)[from]*VECTOR(a)[to]/(4.0*no_of_edges*no_of_edges));
}
pairs[i].first = from;
pairs[i].second = to;
pairs[i].dq = &dq[j];
pairs[i].opposite = &pairs[i+1];
pairs[i+1].first = to;
pairs[i+1].second = from;
pairs[i+1].dq = pairs[i].dq;
pairs[i+1].opposite = &pairs[i];
/* Link the pair to the communities */
igraph_vector_ptr_push_back(&communities.e[from].neis, &pairs[i]);
igraph_vector_ptr_push_back(&communities.e[to].neis, &pairs[i+1]);
/* Update maximums */
if (communities.e[from].maxdq==0 || *communities.e[from].maxdq->dq < *pairs[i].dq)
communities.e[from].maxdq = &pairs[i];
if (communities.e[to].maxdq==0 || *communities.e[to].maxdq->dq < *pairs[i+1].dq)
communities.e[to].maxdq = &pairs[i+1];
/* Iterate */
i+=2; j++;
IGRAPH_EIT_NEXT(edgeit);
}
igraph_eit_destroy(&edgeit);
IGRAPH_FINALLY_CLEAN(1);
/* Sorting community neighbor lists by community IDs */
debug("Sorting community neighbor lists\n");
for (i=0, j=0; i<no_of_nodes; i++) {
igraph_vector_ptr_sort(&communities.e[i].neis, igraph_i_fastgreedy_commpair_cmp);
/* Isolated vertices won't be stored in the heap (to avoid maxdq == 0) */
if (VECTOR(a)[i] > 0) {
communities.heap[j] = &communities.e[i];
communities.heapindex[i] = j;
j++;
} else {
communities.heapindex[i] = -1;
}
}
communities.no_of_communities = j;
/* Calculate proper vector a (see paper) and initial modularity */
q=0;
igraph_vector_scale(&a, 1.0/(2.0 * (weights ? weight_sum : no_of_edges)));
for (i=0; i<no_of_nodes; i++)
q -= VECTOR(a)[i]*VECTOR(a)[i];
maxq=q;
/* Initializing community heap */
debug("Initializing community heap\n");
igraph_i_fastgreedy_community_list_build_heap(&communities);
debug("Initial modularity: %.4f\n", q);
/* Let's rock ;) */
no_of_joins=0;
while (no_of_joins<total_joins) {
IGRAPH_ALLOW_INTERRUPTION();
IGRAPH_PROGRESS("fast greedy community detection", no_of_joins*100.0/total_joins, 0);
/* Store the modularity */
if (modularity) VECTOR(*modularity)[no_of_joins] = q;
/* Some debug info if needed */
/* igraph_i_fastgreedy_community_list_check_heap(&communities); */
#ifdef DEBUG
debug("===========================================\n");
for (i=0; i<communities.n; i++) {
if (communities.e[i].maxdq == 0) {
debug("Community #%ld: PASSIVE\n", i);
continue;
}
debug("Community #%ld\n ", i);
for (j=0; j<igraph_vector_ptr_size(&communities.e[i].neis); j++) {
p1=(igraph_i_fastgreedy_commpair*)VECTOR(communities.e[i].neis)[j];
debug(" (%ld,%ld,%.4f)", p1->first, p1->second, *p1->dq);
}
p1=communities.e[i].maxdq;
debug("\n Maxdq: (%ld,%ld,%.4f)\n", p1->first, p1->second, *p1->dq);
}
debug("Global maxdq is: (%ld,%ld,%.4f)\n", communities.heap[0]->maxdq->first,
communities.heap[0]->maxdq->second, *communities.heap[0]->maxdq->dq);
for (i=0; i<communities.no_of_communities; i++)
debug("(%ld,%ld,%.4f) ", communities.heap[i]->maxdq->first, communities.heap[i]->maxdq->second, *communities.heap[0]->maxdq->dq);
debug("\n");
#endif
if (communities.heap[0] == 0) break; /* no more communities */
if (communities.heap[0]->maxdq == 0) break; /* there are only isolated comms */
to=communities.heap[0]->maxdq->second;
from=communities.heap[0]->maxdq->first;
debug("Q[%ld] = %.7f\tdQ = %.7f\t |H| = %ld\n",
no_of_joins, q, *communities.heap[0]->maxdq->dq, no_of_nodes-no_of_joins-1);
/* DEBUG */
/* from=join_order[no_of_joins*2]; to=join_order[no_of_joins*2+1];
if (to == -1) break;
for (i=0; i<igraph_vector_ptr_size(&communities.e[to].neis); i++) {
p1=(igraph_i_fastgreedy_commpair*)VECTOR(communities.e[to].neis)[i];
if (p1->second == from) communities.maxdq = p1;
} */
n = igraph_vector_ptr_size(&communities.e[to].neis);
m = igraph_vector_ptr_size(&communities.e[from].neis);
/*if (n>m) {
dummy=n; n=m; m=dummy;
dummy=to; to=from; from=dummy;
}*/
debug(" joining: %ld <- %ld\n", to, from);
q += *communities.heap[0]->maxdq->dq;
/* Merge the second community into the first */
i = j = 0;
while (i<n && j<m) {
p1 = (igraph_i_fastgreedy_commpair*)VECTOR(communities.e[to].neis)[i];
p2 = (igraph_i_fastgreedy_commpair*)VECTOR(communities.e[from].neis)[j];
debug("Pairs: %ld-%ld and %ld-%ld\n", p1->first, p1->second,
p2->first, p2->second);
if (p1->second < p2->second) {
/* Considering p1 from now on */
debug(" Considering: %ld-%ld\n", p1->first, p1->second);
if (p1->second == from) {
debug(" WILL REMOVE: %ld-%ld\n", to, from);
} else {
/* chain, case 1 */
debug(" CHAIN(1): %ld-%ld %ld, now=%.7f, adding=%.7f, newdq(%ld,%ld)=%.7f\n",
to, p1->second, from, *p1->dq, -2*VECTOR(a)[from]*VECTOR(a)[p1->second], p1->first, p1->second, *p1->dq-2*VECTOR(a)[from]*VECTOR(a)[p1->second]);
igraph_i_fastgreedy_community_update_dq(&communities, p1, *p1->dq - 2*VECTOR(a)[from]*VECTOR(a)[p1->second]);
}
i++;
} else if (p1->second == p2->second) {
/* p1->first, p1->second and p2->first form a triangle */
debug(" Considering: %ld-%ld and %ld-%ld\n", p1->first, p1->second,
p2->first, p2->second);
/* Update dq value */
debug(" TRIANGLE: %ld-%ld-%ld, now=%.7f, adding=%.7f, newdq(%ld,%ld)=%.7f\n",
to, p1->second, from, *p1->dq, *p2->dq, p1->first, p1->second, *p1->dq+*p2->dq);
igraph_i_fastgreedy_community_update_dq(&communities, p1, *p1->dq + *p2->dq);
igraph_i_fastgreedy_community_remove_nei(&communities, p1->second, from);
i++;
j++;
} else {
debug(" Considering: %ld-%ld\n", p2->first, p2->second);
if (p2->second == to) {
debug(" WILL REMOVE: %ld-%ld\n", p2->second, p2->first);
} else {
/* chain, case 2 */
debug(" CHAIN(2): %ld %ld-%ld, newdq(%ld,%ld)=%.7f\n",
to, p2->second, from, to, p2->second, *p2->dq-2*VECTOR(a)[to]*VECTOR(a)[p2->second]);
p2->opposite->second=to;
/* need to re-sort community nei list `p2->second` */
/* TODO: quicksort is O(n*logn), although we could do a deletion and
* insertion which can be done in O(logn) if deletion is O(1) */
debug(" Re-sorting community %ld\n", p2->second);
igraph_vector_ptr_sort(&communities.e[p2->second].neis, igraph_i_fastgreedy_commpair_cmp);
/* link from.neis[j] to the current place in to.neis if
* from.neis[j] != to */
p2->first=to;
IGRAPH_CHECK(igraph_vector_ptr_insert(&communities.e[to].neis,i,p2));
n++; i++;
if (*p2->dq > *communities.e[to].maxdq->dq) {
communities.e[to].maxdq = p2;
k=igraph_i_fastgreedy_community_list_find_in_heap(&communities, to);
igraph_i_fastgreedy_community_list_sift_up(&communities, k);
}
igraph_i_fastgreedy_community_update_dq(&communities, p2, *p2->dq - 2*VECTOR(a)[to]*VECTOR(a)[p2->second]);
}
j++;
}
}
while (i<n) {
p1 = (igraph_i_fastgreedy_commpair*)VECTOR(communities.e[to].neis)[i];
if (p1->second == from) {
debug(" WILL REMOVE: %ld-%ld\n", p1->first, from);
} else {
/* chain, case 1 */
debug(" CHAIN(1): %ld-%ld %ld, now=%.7f, adding=%.7f, newdq(%ld,%ld)=%.7f\n",
to, p1->second, from, *p1->dq, -2*VECTOR(a)[from]*VECTOR(a)[p1->second], p1->first, p1->second, *p1->dq-2*VECTOR(a)[from]*VECTOR(a)[p1->second]);
igraph_i_fastgreedy_community_update_dq(&communities, p1, *p1->dq - 2*VECTOR(a)[from]*VECTOR(a)[p1->second]);
}
i++;
}
while (j<m) {
p2 = (igraph_i_fastgreedy_commpair*)VECTOR(communities.e[from].neis)[j];
if (to == p2->second) { j++; continue; }
/* chain, case 2 */
debug(" CHAIN(2): %ld %ld-%ld, newdq(%ld,%ld)=%.7f\n",
to, p2->second, from, p1->first, p2->second, *p2->dq-2*VECTOR(a)[to]*VECTOR(a)[p2->second]);
p2->opposite->second=to;
/* need to re-sort community nei list `p2->second` */
/* TODO: quicksort is O(n*logn), although we could do a deletion and
* insertion which can be done in O(logn) if deletion is O(1) */
debug(" Re-sorting community %ld\n", p2->second);
igraph_vector_ptr_sort(&communities.e[p2->second].neis, igraph_i_fastgreedy_commpair_cmp);
/* link from.neis[j] to the current place in to.neis if
* from.neis[j] != to */
p2->first=to;
IGRAPH_CHECK(igraph_vector_ptr_push_back(&communities.e[to].neis,p2));
if (*p2->dq > *communities.e[to].maxdq->dq) {
communities.e[to].maxdq = p2;
k=igraph_i_fastgreedy_community_list_find_in_heap(&communities, to);
igraph_i_fastgreedy_community_list_sift_up(&communities, k);
}
igraph_i_fastgreedy_community_update_dq(&communities, p2, *p2->dq-2*VECTOR(a)[to]*VECTOR(a)[p2->second]);
j++;
}
/* Now, remove community `from` from the neighbors of community `to` */
if (communities.no_of_communities > 2) {
debug(" REMOVING: %ld-%ld\n", to, from);
igraph_i_fastgreedy_community_remove_nei(&communities, to, from);
i=igraph_i_fastgreedy_community_list_find_in_heap(&communities, from);
igraph_i_fastgreedy_community_list_remove(&communities, i);
}
communities.e[from].maxdq=0;
/* Update community sizes */
communities.e[to].size += communities.e[from].size;
communities.e[from].size = 0;
/* record what has been merged */
/* igraph_vector_ptr_clear is not enough here as it won't free
* the memory consumed by communities.e[from].neis. Thanks
* to Tom Gregorovic for pointing that out. */
igraph_vector_ptr_destroy(&communities.e[from].neis);
if (merges) {
MATRIX(*merges, no_of_joins, 0) = communities.e[to].id;
MATRIX(*merges, no_of_joins, 1) = communities.e[from].id;
communities.e[to].id = no_of_nodes+no_of_joins;
}
/* Update vector a */
VECTOR(a)[to] += VECTOR(a)[from];
VECTOR(a)[from] = 0.0;
no_of_joins++;
}
/* TODO: continue merging when some isolated communities remained. Always
* joining the communities with the least number of nodes results in the
* smallest decrease in modularity every step. Now we're simply deleting
* the excess rows from the merge matrix */
if (no_of_joins < total_joins) {
long int *ivec;
ivec=igraph_Calloc(igraph_matrix_nrow(merges), long int);
if (ivec == 0)
IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);
IGRAPH_FINALLY(free, ivec);
for (i=0; i<no_of_joins; i++) ivec[i] = i+1;
igraph_matrix_permdelete_rows(merges, ivec, total_joins-no_of_joins);
free(ivec);
IGRAPH_FINALLY_CLEAN(1);
}
EdgeIterator::~EdgeIterator() { igraph_eit_destroy(ptr()); }
int igraph_get_adjacency(const igraph_t *graph, igraph_matrix_t *res,
igraph_get_adjacency_t type) {
igraph_eit_t edgeit;
long int no_of_nodes=igraph_vcount(graph);
igraph_bool_t directed=igraph_is_directed(graph);
int retval=0;
long int from, to;
igraph_integer_t ffrom, fto;
IGRAPH_CHECK(igraph_matrix_resize(res, no_of_nodes, no_of_nodes));
igraph_matrix_null(res);
IGRAPH_CHECK(igraph_eit_create(graph, igraph_ess_all(0), &edgeit));
IGRAPH_FINALLY(igraph_eit_destroy, &edgeit);
if (directed) {
while (!IGRAPH_EIT_END(edgeit)) {
igraph_edge(graph, IGRAPH_EIT_GET(edgeit), &ffrom, &fto);
from=ffrom;
to=fto;
MATRIX(*res, from, to) += 1;
IGRAPH_EIT_NEXT(edgeit);
}
} else if (type==IGRAPH_GET_ADJACENCY_UPPER) {
while (!IGRAPH_EIT_END(edgeit)) {
igraph_edge(graph, IGRAPH_EIT_GET(edgeit), &ffrom, &fto);
from=ffrom;
to=fto;
if (to < from) {
MATRIX(*res, to, from) += 1;
} else {
MATRIX(*res, from, to) += 1;
}
IGRAPH_EIT_NEXT(edgeit);
}
} else if (type==IGRAPH_GET_ADJACENCY_LOWER) {
while (!IGRAPH_EIT_END(edgeit)) {
igraph_edge(graph, IGRAPH_EIT_GET(edgeit), &ffrom, &fto);
from=ffrom;
to=fto;
if (to < from) {
MATRIX(*res, from, to) += 1;
} else {
MATRIX(*res, to, from) += 1;
}
IGRAPH_EIT_NEXT(edgeit);
}
} else if (type==IGRAPH_GET_ADJACENCY_BOTH) {
while (!IGRAPH_EIT_END(edgeit)) {
igraph_edge(graph, IGRAPH_EIT_GET(edgeit), &ffrom, &fto);
from=ffrom;
to=fto;
MATRIX(*res, from, to) += 1;
if (from != to) {
MATRIX(*res, to, from) += 1;
}
IGRAPH_EIT_NEXT(edgeit);
}
} else {
IGRAPH_ERROR("Invalid type argument", IGRAPH_EINVAL);
}
igraph_eit_destroy(&edgeit);
IGRAPH_FINALLY_CLEAN(1);
return retval;
}
int igraph_to_undirected(igraph_t *graph,
igraph_to_undirected_t mode) {
long int no_of_nodes=igraph_vcount(graph);
long int no_of_edges=igraph_ecount(graph);
igraph_vector_t edges;
igraph_t newgraph;
if (mode != IGRAPH_TO_UNDIRECTED_EACH &&
mode != IGRAPH_TO_UNDIRECTED_COLLAPSE) {
IGRAPH_ERROR("Cannot undirect graph, invalid mode", IGRAPH_EINVAL);
}
if (!igraph_is_directed(graph)) {
return 0;
}
IGRAPH_VECTOR_INIT_FINALLY(&edges, 0);
if (mode==IGRAPH_TO_UNDIRECTED_EACH) {
igraph_es_t es;
igraph_eit_t eit;
IGRAPH_CHECK(igraph_vector_reserve(&edges, no_of_edges*2));
IGRAPH_CHECK(igraph_es_all(&es, IGRAPH_EDGEORDER_ID));
IGRAPH_FINALLY(igraph_es_destroy, &es);
IGRAPH_CHECK(igraph_eit_create(graph, es, &eit));
IGRAPH_FINALLY(igraph_eit_destroy, &eit);
while (!IGRAPH_EIT_END(eit)) {
long int edge=IGRAPH_EIT_GET(eit);
igraph_integer_t from, to;
igraph_edge(graph, edge, &from, &to);
IGRAPH_CHECK(igraph_vector_push_back(&edges, from));
IGRAPH_CHECK(igraph_vector_push_back(&edges, to));
IGRAPH_EIT_NEXT(eit);
}
igraph_eit_destroy(&eit);
igraph_es_destroy(&es);
IGRAPH_FINALLY_CLEAN(2);
IGRAPH_CHECK(igraph_create(&newgraph, &edges, no_of_nodes, IGRAPH_UNDIRECTED));
IGRAPH_FINALLY(igraph_destroy, &newgraph);
igraph_vector_destroy(&edges);
IGRAPH_I_ATTRIBUTE_DESTROY(&newgraph);
IGRAPH_I_ATTRIBUTE_COPY(&newgraph, graph, 1,1,1);
IGRAPH_FINALLY_CLEAN(2);
igraph_destroy(graph);
*graph=newgraph;
} else if (mode==IGRAPH_TO_UNDIRECTED_COLLAPSE) {
igraph_vector_t seen, nei;
long int i,j;
IGRAPH_CHECK(igraph_vector_reserve(&edges, no_of_edges*2));
IGRAPH_VECTOR_INIT_FINALLY(&seen, no_of_nodes);
IGRAPH_VECTOR_INIT_FINALLY(&nei, 0);
for (i=0; i<no_of_nodes; i++) {
IGRAPH_CHECK(igraph_neighbors(graph, &nei, i, IGRAPH_ALL));
for (j=0; j<igraph_vector_size(&nei); j++) {
long int node=VECTOR(nei)[j];
if (VECTOR(seen)[node] != i+1 && node >= i) {
IGRAPH_CHECK(igraph_vector_push_back(&edges, i));
IGRAPH_CHECK(igraph_vector_push_back(&edges, node));
VECTOR(seen)[node]=i+1;
}
}
}
igraph_vector_destroy(&nei);
igraph_vector_destroy(&seen);
IGRAPH_FINALLY_CLEAN(2);
IGRAPH_CHECK(igraph_create(&newgraph, &edges, no_of_nodes, IGRAPH_UNDIRECTED));
IGRAPH_FINALLY(igraph_destroy, &newgraph);
igraph_vector_destroy(&edges);
IGRAPH_I_ATTRIBUTE_DESTROY(&newgraph);
IGRAPH_I_ATTRIBUTE_COPY(&newgraph, graph, 1,1,0); /* no edge attributes */
IGRAPH_FINALLY_CLEAN(2);
igraph_destroy(graph);
*graph=newgraph;
}
return 0;
}
