int igraph_sample_dirichlet(igraph_integer_t n, const igraph_vector_t *alpha, igraph_matrix_t *res) { igraph_integer_t len=igraph_vector_size(alpha); igraph_integer_t i; igraph_vector_t vec; if (n < 0) { IGRAPH_ERROR("Number of samples should be non-negative", IGRAPH_EINVAL); } if (len < 2) { IGRAPH_ERROR("Dirichlet parameter vector too short, must " "have at least two entries", IGRAPH_EINVAL); } if (igraph_vector_min(alpha) <= 0) { IGRAPH_ERROR("Dirichlet concentration parameters must be positive", IGRAPH_EINVAL); } IGRAPH_CHECK(igraph_matrix_resize(res, len, n)); RNG_BEGIN(); for (i = 0; i < n; i++) { igraph_vector_view(&vec, &MATRIX(*res, 0, i), len); igraph_rng_get_dirichlet(igraph_rng_default(), alpha, &vec); } RNG_END(); return 0; }
int igraph_random_walk(const igraph_t *graph, igraph_vector_t *walk, igraph_integer_t start, igraph_neimode_t mode, igraph_integer_t steps, igraph_random_walk_stuck_t stuck) { /* TODO: - multiple walks potentially from multiple start vertices - weights */ igraph_lazy_adjlist_t adj; igraph_integer_t vc = igraph_vcount(graph); igraph_integer_t i; if (start < 0 || start >= vc) { IGRAPH_ERROR("Invalid start vertex", IGRAPH_EINVAL); } if (steps < 0) { IGRAPH_ERROR("Invalid number of steps", IGRAPH_EINVAL); } IGRAPH_CHECK(igraph_lazy_adjlist_init(graph, &adj, mode, IGRAPH_DONT_SIMPLIFY)); IGRAPH_FINALLY(igraph_lazy_adjlist_destroy, &adj); IGRAPH_CHECK(igraph_vector_resize(walk, steps)); RNG_BEGIN(); VECTOR(*walk)[0] = start; for (i = 1; i < steps; i++) { igraph_vector_t *neis; igraph_integer_t nn; neis = igraph_lazy_adjlist_get(&adj, start); nn = igraph_vector_size(neis); if (IGRAPH_UNLIKELY(nn == 0)) { igraph_vector_resize(walk, i); if (stuck == IGRAPH_RANDOM_WALK_STUCK_RETURN) { break; } else { IGRAPH_ERROR("Random walk got stuck", IGRAPH_ERWSTUCK); } } start = VECTOR(*walk)[i] = VECTOR(*neis)[ RNG_INTEGER(0, nn - 1) ]; } RNG_END(); igraph_lazy_adjlist_destroy(&adj); IGRAPH_FINALLY_CLEAN(1); return 0; }
int igraph_dot_product_game(igraph_t *graph, const igraph_matrix_t *vecs, igraph_bool_t directed) { igraph_integer_t nrow=igraph_matrix_nrow(vecs); igraph_integer_t ncol=igraph_matrix_ncol(vecs); int i, j; igraph_vector_t edges; igraph_bool_t warned_neg=0, warned_big=0; IGRAPH_VECTOR_INIT_FINALLY(&edges, 0); RNG_BEGIN(); for (i = 0; i < ncol; i++) { int from=directed ? 0 : i+1; igraph_vector_t v1; igraph_vector_view(&v1, &MATRIX(*vecs, 0, i), nrow); for (j = from; j < ncol; j++) { igraph_real_t prob; igraph_vector_t v2; if (i==j) { continue; } igraph_vector_view(&v2, &MATRIX(*vecs, 0, j), nrow); igraph_lapack_ddot(&v1, &v2, &prob); if (prob < 0 && ! warned_neg) { warned_neg=1; IGRAPH_WARNING("Negative connection probability in " "dot-product graph"); } else if (prob > 1 && ! warned_big) { warned_big=1; IGRAPH_WARNING("Greater than 1 connection probability in " "dot-product graph"); IGRAPH_CHECK(igraph_vector_push_back(&edges, i)); IGRAPH_CHECK(igraph_vector_push_back(&edges, j)); } else if (RNG_UNIF01() < prob) { IGRAPH_CHECK(igraph_vector_push_back(&edges, i)); IGRAPH_CHECK(igraph_vector_push_back(&edges, j)); } } } RNG_END(); igraph_create(graph, &edges, ncol, directed); igraph_vector_destroy(&edges); IGRAPH_FINALLY_CLEAN(1); return 0; }
int igraph_sample_sphere_surface(igraph_integer_t dim, igraph_integer_t n, igraph_real_t radius, igraph_bool_t positive, igraph_matrix_t *res) { igraph_integer_t i, j; if (dim < 2) { IGRAPH_ERROR("Sphere must be at least two dimensional to sample from " "surface", IGRAPH_EINVAL); } if (n < 0) { IGRAPH_ERROR("Number of samples must be non-negative", IGRAPH_EINVAL); } if (radius <= 0) { IGRAPH_ERROR("Sphere radius must be positive", IGRAPH_EINVAL); } IGRAPH_CHECK(igraph_matrix_resize(res, dim, n)); RNG_BEGIN(); for (i = 0; i < n; i++) { igraph_real_t *col=&MATRIX(*res, 0, i); igraph_real_t sum=0.0; for (j = 0; j < dim; j++) { col[j] = RNG_NORMAL(0, 1); sum += col[j] * col[j]; } sum = sqrt(sum); for (j = 0; j < dim; j++) { col[j] = radius * col[j] / sum; } if (positive) { for (j = 0; j < dim; j++) { col[j] = fabs(col[j]); } } } RNG_END(); return 0; }
int igraph_sample_sphere_volume(igraph_integer_t dim, igraph_integer_t n, igraph_real_t radius, igraph_bool_t positive, igraph_matrix_t *res) { igraph_integer_t i, j; /* Arguments are checked by the following call */ IGRAPH_CHECK(igraph_sample_sphere_surface(dim, n, radius, positive, res)); RNG_BEGIN(); for (i = 0; i < n; i++) { igraph_real_t *col=&MATRIX(*res, 0, i); igraph_real_t U=pow(RNG_UNIF01(), 1.0/dim); for (j = 0; j < dim; j++) { col[j] *= U; } } RNG_END(); return 0; }
int igraph_community_spinglass_single(const igraph_t *graph, const igraph_vector_t *weights, igraph_integer_t vertex, igraph_vector_t *community, igraph_real_t *cohesion, igraph_real_t *adhesion, igraph_integer_t *inner_links, igraph_integer_t *outer_links, igraph_integer_t spins, igraph_spincomm_update_t update_rule, igraph_real_t gamma) { igraph_bool_t use_weights=0; double prob; ClusterList<NNode*> *cl_cur; network *net; PottsModel *pm; char startnode[255]; /* Check arguments */ if (spins < 2 || spins > 500) { IGRAPH_ERROR("Invalid number of spins", IGRAPH_EINVAL); } if (update_rule != IGRAPH_SPINCOMM_UPDATE_SIMPLE && update_rule != IGRAPH_SPINCOMM_UPDATE_CONFIG) { IGRAPH_ERROR("Invalid update rule", IGRAPH_EINVAL); } if (weights) { if (igraph_vector_size(weights) != igraph_ecount(graph)) { IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL); } use_weights=1; } if (gamma < 0.0) { IGRAPH_ERROR("Invalid gamme value", IGRAPH_EINVAL); } if (vertex < 0 || vertex > igraph_vcount(graph)) { IGRAPH_ERROR("Invalid vertex id", IGRAPH_EINVAL); } /* Check whether we have a single component */ igraph_bool_t conn; IGRAPH_CHECK(igraph_is_connected(graph, &conn, IGRAPH_WEAK)); if (!conn) { IGRAPH_ERROR("Cannot work with unconnected graph", IGRAPH_EINVAL); } net = new network; net->node_list =new DL_Indexed_List<NNode*>(); net->link_list =new DL_Indexed_List<NLink*>(); net->cluster_list=new DL_Indexed_List<ClusterList<NNode*>*>(); /* Transform the igraph_t */ IGRAPH_CHECK(igraph_i_read_network(graph, weights, net, use_weights, 0)); prob=2.0*net->sum_weights/double(net->node_list->Size()) /double(net->node_list->Size()-1); pm=new PottsModel(net,(unsigned int)spins,update_rule); /* initialize the random number generator */ RNG_BEGIN(); /* to be exected, if we want to find the community around a particular node*/ /* the initial conf is needed, because otherwise, the degree of the nodes is not in the weight property, stupid!!! */ pm->assign_initial_conf(-1); snprintf(startnode, 255, "%li", (long int)vertex+1); pm->FindCommunityFromStart(gamma, prob, startnode, community, cohesion, adhesion, inner_links, outer_links); while (net->link_list->Size()) delete net->link_list->Pop(); while (net->node_list->Size()) delete net->node_list->Pop(); while (net->cluster_list->Size()) { cl_cur=net->cluster_list->Pop(); while (cl_cur->Size()) cl_cur->Pop(); delete cl_cur; } delete net->link_list; delete net->node_list; delete net->cluster_list; RNG_END(); delete net; delete pm; return 0; }
int igraph_i_community_spinglass_orig(const igraph_t *graph, const igraph_vector_t *weights, igraph_real_t *modularity, igraph_real_t *temperature, igraph_vector_t *membership, igraph_vector_t *csize, igraph_integer_t spins, igraph_bool_t parupdate, igraph_real_t starttemp, igraph_real_t stoptemp, igraph_real_t coolfact, igraph_spincomm_update_t update_rule, igraph_real_t gamma) { unsigned long changes, runs; igraph_bool_t use_weights=0; bool zeroT; double kT, acc, prob; ClusterList<NNode*> *cl_cur; network *net; PottsModel *pm; /* Check arguments */ if (spins < 2 || spins > 500) { IGRAPH_ERROR("Invalid number of spins", IGRAPH_EINVAL); } if (update_rule != IGRAPH_SPINCOMM_UPDATE_SIMPLE && update_rule != IGRAPH_SPINCOMM_UPDATE_CONFIG) { IGRAPH_ERROR("Invalid update rule", IGRAPH_EINVAL); } if (weights) { if (igraph_vector_size(weights) != igraph_ecount(graph)) { IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL); } use_weights=1; } if (coolfact < 0 || coolfact>=1.0) { IGRAPH_ERROR("Invalid cooling factor", IGRAPH_EINVAL); } if (gamma < 0.0) { IGRAPH_ERROR("Invalid gamme value", IGRAPH_EINVAL); } if (starttemp/stoptemp<1.0) { IGRAPH_ERROR("starttemp should be larger in absolute value than stoptemp", IGRAPH_EINVAL); } /* Check whether we have a single component */ igraph_bool_t conn; IGRAPH_CHECK(igraph_is_connected(graph, &conn, IGRAPH_WEAK)); if (!conn) { IGRAPH_ERROR("Cannot work with unconnected graph", IGRAPH_EINVAL); } net = new network; net->node_list =new DL_Indexed_List<NNode*>(); net->link_list =new DL_Indexed_List<NLink*>(); net->cluster_list=new DL_Indexed_List<ClusterList<NNode*>*>(); /* Transform the igraph_t */ IGRAPH_CHECK(igraph_i_read_network(graph, weights, net, use_weights, 0)); prob=2.0*net->sum_weights/double(net->node_list->Size()) /double(net->node_list->Size()-1); pm=new PottsModel(net,(unsigned int)spins,update_rule); /* initialize the random number generator */ RNG_BEGIN(); if ((stoptemp==0.0) && (starttemp==0.0)) zeroT=true; else zeroT=false; if (!zeroT) kT=pm->FindStartTemp(gamma, prob, starttemp); else kT=stoptemp; /* assign random initial configuration */ pm->assign_initial_conf(-1); runs=0; changes=1; while (changes>0 && (kT/stoptemp>1.0 || (zeroT && runs<150))) { IGRAPH_ALLOW_INTERRUPTION(); /* This is not clean.... */ runs++; if (!zeroT) { kT*=coolfact; if (parupdate) { changes=pm->HeatBathParallelLookup(gamma, prob, kT, 50); } else { acc=pm->HeatBathLookup(gamma, prob, kT, 50); if (acc<(1.0-1.0/double(spins))*0.01) { changes=0; } else { changes=1; } } } else { if (parupdate) { changes=pm->HeatBathParallelLookupZeroTemp(gamma, prob, 50); } else { acc=pm->HeatBathLookupZeroTemp(gamma, prob, 50); /* less than 1 percent acceptance ratio */ if (acc<(1.0-1.0/double(spins))*0.01) { changes=0; } else { changes=1; } } } } /* while loop */ pm->WriteClusters(modularity, temperature, csize, membership, kT, gamma); while (net->link_list->Size()) delete net->link_list->Pop(); while (net->node_list->Size()) delete net->node_list->Pop(); while (net->cluster_list->Size()) { cl_cur=net->cluster_list->Pop(); while (cl_cur->Size()) cl_cur->Pop(); delete cl_cur; } delete net->link_list; delete net->node_list; delete net->cluster_list; RNG_END(); delete net; delete pm; return 0; }
int igraph_layout_gem(const igraph_t *graph, igraph_matrix_t *res, igraph_bool_t use_seed, igraph_integer_t maxiter, igraph_real_t temp_max, igraph_real_t temp_min, igraph_real_t temp_init) { igraph_integer_t no_nodes = igraph_vcount(graph); igraph_vector_int_t perm; igraph_vector_float_t impulse_x, impulse_y, temp, skew_gauge; igraph_integer_t i; float temp_global; igraph_integer_t perm_pointer = 0; float barycenter_x = 0.0, barycenter_y = 0.0; igraph_vector_t phi; igraph_vector_t neis; const float elen_des2 = 128 * 128; const float gamma = 1/16.0; const float alpha_o = M_PI; const float alpha_r = M_PI / 3.0; const float sigma_o = 1.0 / 3.0; const float sigma_r = 1.0 / 2.0 / no_nodes; if (maxiter < 0) { IGRAPH_ERROR("Number of iterations must be non-negative in GEM layout", IGRAPH_EINVAL); } if (use_seed && (igraph_matrix_nrow(res) != no_nodes || igraph_matrix_ncol(res) != 2)) { IGRAPH_ERROR("Invalid start position matrix size in GEM layout", IGRAPH_EINVAL); } if (temp_max <= 0) { IGRAPH_ERROR("Maximum temperature should be positive in GEM layout", IGRAPH_EINVAL); } if (temp_min <= 0) { IGRAPH_ERROR("Minimum temperature should be positive in GEM layout", IGRAPH_EINVAL); } if (temp_init <= 0) { IGRAPH_ERROR("Initial temperature should be positive in GEM layout", IGRAPH_EINVAL); } if (temp_max < temp_init || temp_init < temp_min) { IGRAPH_ERROR("Minimum <= Initial <= Maximum temperature is required " "in GEM layout", IGRAPH_EINVAL); } if (no_nodes == 0) { return 0; } IGRAPH_CHECK(igraph_vector_float_init(&impulse_x, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &impulse_x); IGRAPH_CHECK(igraph_vector_float_init(&impulse_y, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &impulse_y); IGRAPH_CHECK(igraph_vector_float_init(&temp, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &temp); IGRAPH_CHECK(igraph_vector_float_init(&skew_gauge, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &skew_gauge); IGRAPH_CHECK(igraph_vector_int_init_seq(&perm, 0, no_nodes-1)); IGRAPH_FINALLY(igraph_vector_int_destroy, &perm); IGRAPH_VECTOR_INIT_FINALLY(&phi, no_nodes); IGRAPH_VECTOR_INIT_FINALLY(&neis, 10); RNG_BEGIN(); /* Initialization */ igraph_degree(graph, &phi, igraph_vss_all(), IGRAPH_ALL, IGRAPH_LOOPS); if (!use_seed) { const igraph_real_t width_half=no_nodes*100, height_half=width_half; IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 2)); for (i=0; i<no_nodes; i++) { MATRIX(*res, i, 0) = RNG_UNIF(-width_half, width_half); MATRIX(*res, i, 1) = RNG_UNIF(-height_half, height_half); barycenter_x += MATRIX(*res, i, 0); barycenter_y += MATRIX(*res, i, 1); VECTOR(phi)[i] *= (VECTOR(phi)[i] / 2.0 + 1.0); } } else { for (i=0; i<no_nodes; i++) { barycenter_x += MATRIX(*res, i, 0); barycenter_y += MATRIX(*res, i, 1); VECTOR(phi)[i] *= (VECTOR(phi)[i] / 2.0 + 1.0); } } igraph_vector_float_fill(&temp, temp_init); temp_global = temp_init * no_nodes; while (temp_global > temp_min * no_nodes && maxiter > 0) { /* choose a vertex v to update */ igraph_integer_t u, v, nlen, j; float px, py, pvx, pvy; if (!perm_pointer) { igraph_vector_int_shuffle(&perm); perm_pointer=no_nodes-1; } v=VECTOR(perm)[perm_pointer--]; /* compute v's impulse */ px = (barycenter_x/no_nodes - MATRIX(*res, v, 0)) * gamma * VECTOR(phi)[v]; py = (barycenter_y/no_nodes - MATRIX(*res, v, 1)) * gamma * VECTOR(phi)[v]; px += RNG_UNIF(-32.0, 32.0); py += RNG_UNIF(-32.0, 32.0); for (u = 0; u < no_nodes; u++) { float dx, dy, dist2; if (u == v) { continue; } dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0); dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1); dist2=dx * dx + dy * dy; if (dist2 != 0) { px += dx * elen_des2 / dist2; py += dy * elen_des2 / dist2; } } IGRAPH_CHECK(igraph_neighbors(graph, &neis, v, IGRAPH_ALL)); nlen=igraph_vector_size(&neis); for (j = 0; j < nlen; j++) { igraph_integer_t u=VECTOR(neis)[j]; float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0); float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1); float dist2= dx * dx + dy * dy; px -= dx * dist2 / (elen_des2 * VECTOR(phi)[v]); py -= dy * dist2 / (elen_des2 * VECTOR(phi)[v]); } /* update v's position and temperature */ if (px != 0 || py != 0) { float plen = sqrtf(px * px + py * py); px *= VECTOR(temp)[v] / plen; py *= VECTOR(temp)[v] / plen; MATRIX(*res, v, 0) += px; MATRIX(*res, v, 1) += py; barycenter_x += px; barycenter_y += py; } pvx=VECTOR(impulse_x)[v]; pvy=VECTOR(impulse_y)[v]; if (pvx != 0 || pvy != 0) { float beta = atan2f(pvy - py, pvx - px); float sin_beta = sinf(beta); float sign_sin_beta = (sin_beta > 0) ? 1 : ((sin_beta < 0) ? -1 : 0); float cos_beta = cosf(beta); float abs_cos_beta = fabsf(cos_beta); float old_temp=VECTOR(temp)[v]; if (sin(beta) >= sin(M_PI_2 + alpha_r / 2.0)) { VECTOR(skew_gauge)[v] += sigma_r * sign_sin_beta; } if (abs_cos_beta >= cosf(alpha_o / 2.0)) { VECTOR(temp)[v] *= sigma_o * cos_beta; } VECTOR(temp)[v] *= (1 - fabsf(VECTOR(skew_gauge)[v])); if (VECTOR(temp)[v] > temp_max) { VECTOR(temp)[v] = temp_max; } VECTOR(impulse_x)[v] = px; VECTOR(impulse_y)[v] = py; temp_global += VECTOR(temp)[v] - old_temp; } maxiter--; } /* while temp && iter */ RNG_END(); igraph_vector_destroy(&neis); igraph_vector_destroy(&phi); igraph_vector_int_destroy(&perm); igraph_vector_float_destroy(&skew_gauge); igraph_vector_float_destroy(&temp); igraph_vector_float_destroy(&impulse_y); igraph_vector_float_destroy(&impulse_x); IGRAPH_FINALLY_CLEAN(7); return 0; }
int igraph_forest_fire_game(igraph_t *graph, igraph_integer_t nodes, igraph_real_t fw_prob, igraph_real_t bw_factor, igraph_integer_t pambs, igraph_bool_t directed) { igraph_vector_long_t visited; long int no_of_nodes=nodes, actnode, i; igraph_vector_t edges; igraph_vector_t *inneis, *outneis; igraph_i_forest_fire_data_t data; igraph_dqueue_t neiq; long int ambs=pambs; igraph_real_t param_geom_out=1-fw_prob; igraph_real_t param_geom_in=1-fw_prob*bw_factor; if (fw_prob < 0) { IGRAPH_ERROR("Forest fire model: 'fw_prob' should be between non-negative", IGRAPH_EINVAL); } if (bw_factor < 0) { IGRAPH_ERROR("Forest fire model: 'bw_factor' should be non-negative", IGRAPH_EINVAL); } if (ambs < 0) { IGRAPH_ERROR("Number of ambassadors ('ambs') should be non-negative", IGRAPH_EINVAL); } if (fw_prob == 0 || ambs == 0) { IGRAPH_WARNING("'fw_prob or ambs is zero, creating empty graph"); IGRAPH_CHECK(igraph_empty(graph, nodes, directed)); return 0; } IGRAPH_VECTOR_INIT_FINALLY(&edges, 0); inneis=igraph_Calloc(no_of_nodes, igraph_vector_t); if (!inneis) { IGRAPH_ERROR("Cannot run forest fire model", IGRAPH_ENOMEM); } IGRAPH_FINALLY(igraph_free, inneis); outneis=igraph_Calloc(no_of_nodes, igraph_vector_t); if (!outneis) { IGRAPH_ERROR("Cannot run forest fire model", IGRAPH_ENOMEM); } IGRAPH_FINALLY(igraph_free, outneis); data.inneis=inneis; data.outneis=outneis; data.no_of_nodes=no_of_nodes; IGRAPH_FINALLY(igraph_i_forest_fire_free, &data); for (i=0; i<no_of_nodes; i++) { IGRAPH_CHECK(igraph_vector_init(inneis+i, 0)); IGRAPH_CHECK(igraph_vector_init(outneis+i, 0)); } IGRAPH_CHECK(igraph_vector_long_init(&visited, no_of_nodes)); IGRAPH_FINALLY(igraph_vector_long_destroy, &visited); IGRAPH_DQUEUE_INIT_FINALLY(&neiq, 10); RNG_BEGIN(); #define ADD_EDGE_TO(nei) \ if (VECTOR(visited)[(nei)] != actnode+1) { \ VECTOR(visited)[(nei)] = actnode+1; \ IGRAPH_CHECK(igraph_dqueue_push(&neiq, nei)); \ IGRAPH_CHECK(igraph_vector_push_back(&edges, actnode)); \ IGRAPH_CHECK(igraph_vector_push_back(&edges, nei)); \ IGRAPH_CHECK(igraph_vector_push_back(outneis+actnode, nei)); \ IGRAPH_CHECK(igraph_vector_push_back(inneis+nei, actnode)); \ } IGRAPH_PROGRESS("Forest fire: ", 0.0, NULL); for (actnode=1; actnode < no_of_nodes; actnode++) { IGRAPH_PROGRESS("Forest fire: ", 100.0*actnode/no_of_nodes, NULL); IGRAPH_ALLOW_INTERRUPTION(); /* We don't want to visit the current vertex */ VECTOR(visited)[actnode] = actnode+1; /* Choose ambassador(s) */ for (i=0; i<ambs; i++) { long int a=RNG_INTEGER(0, actnode-1); ADD_EDGE_TO(a); } while (!igraph_dqueue_empty(&neiq)) { long int actamb=(long int) igraph_dqueue_pop(&neiq); igraph_vector_t *outv=outneis+actamb; igraph_vector_t *inv=inneis+actamb; long int no_in=igraph_vector_size(inv); long int no_out=igraph_vector_size(outv); long int neis_out=(long int) RNG_GEOM(param_geom_out); long int neis_in=(long int) RNG_GEOM(param_geom_in); /* outgoing neighbors */ if (neis_out >= no_out) { for (i=0; i<no_out; i++) { long int nei=(long int) VECTOR(*outv)[i]; ADD_EDGE_TO(nei); } } else { long int oleft=no_out; for (i=0; i<neis_out && oleft > 0; ) { long int which=RNG_INTEGER(0, oleft-1); long int nei=(long int) VECTOR(*outv)[which]; VECTOR(*outv)[which] = VECTOR(*outv)[oleft-1]; VECTOR(*outv)[oleft-1] = nei; if (VECTOR(visited)[nei] != actnode+1) { ADD_EDGE_TO(nei); i++; } oleft--; } } /* incoming neighbors */ if (neis_in >= no_in) { for (i=0; i<no_in; i++) { long int nei=(long int) VECTOR(*inv)[i]; ADD_EDGE_TO(nei); } } else { long int ileft=no_in; for (i=0; i<neis_in && ileft > 0; ) { long int which=RNG_INTEGER(0, ileft-1); long int nei=(long int) VECTOR(*inv)[which]; VECTOR(*inv)[which] = VECTOR(*inv)[ileft-1]; VECTOR(*inv)[ileft-1] = nei; if (VECTOR(visited)[nei] != actnode+1) { ADD_EDGE_TO(nei); i++; } ileft--; } } } /* while neiq not empty */ } /* actnode < no_of_nodes */ #undef ADD_EDGE_TO RNG_END(); IGRAPH_PROGRESS("Forest fire: ", 100.0, NULL); igraph_dqueue_destroy(&neiq); igraph_vector_long_destroy(&visited); igraph_i_forest_fire_free(&data); igraph_free(outneis); igraph_free(inneis); IGRAPH_FINALLY_CLEAN(5); IGRAPH_CHECK(igraph_create(graph, &edges, nodes, directed)); igraph_vector_destroy(&edges); IGRAPH_FINALLY_CLEAN(1); return 0; }
int igraph_bipartite_game_gnp(igraph_t *graph, igraph_vector_bool_t *types, igraph_integer_t n1, igraph_integer_t n2, igraph_real_t p, igraph_bool_t directed, igraph_neimode_t mode) { int retval=0; igraph_vector_t edges, s; int i; if (p < 0.0 || p > 1.0) { IGRAPH_ERROR("Invalid connection probability", IGRAPH_EINVAL); } if (types) { IGRAPH_CHECK(igraph_vector_bool_resize(types, n1 + n2)); igraph_vector_bool_null(types); for (i=n1; i<n1+n2; i++) { VECTOR(*types)[i] = 1; } } if (p == 0 || n1 * n2 < 1) { IGRAPH_CHECK(retval=igraph_empty(graph, n1 + n2, directed)); } else if (p == 1.0) { IGRAPH_CHECK(retval=igraph_full_bipartite(graph, types, n1, n2, directed, mode)); } else { long int to, from, slen; double maxedges, last; if (!directed || mode != IGRAPH_ALL) { maxedges = n1 * n2; } else { maxedges = 2 * n1 * n2; } IGRAPH_VECTOR_INIT_FINALLY(&edges, 0); IGRAPH_VECTOR_INIT_FINALLY(&s, 0); IGRAPH_CHECK(igraph_vector_reserve(&s, (long) (maxedges*p*1.1))); RNG_BEGIN(); last=RNG_GEOM(p); while (last < maxedges) { IGRAPH_CHECK(igraph_vector_push_back(&s, last)); last += RNG_GEOM(p); last += 1; } RNG_END(); slen=igraph_vector_size(&s); IGRAPH_CHECK(igraph_vector_reserve(&edges, slen * 2)); for (i=0; i<slen; i++) { if (!directed || mode != IGRAPH_ALL) { to=(long) floor(VECTOR(s)[i]/n1); from=(long) (VECTOR(s)[i] - ((igraph_real_t) to) * n1); to += n1; } else { long int n1n2 = n1 * n2; if (VECTOR(s)[i] < n1n2) { to=(long) floor(VECTOR(s)[i]/n1); from=(long) (VECTOR(s)[i] - ((igraph_real_t) to) * n1); to += n1; } else { to=(long) floor( (VECTOR(s)[i]-n1n2) /n2); from=(long) (VECTOR(s)[i] - n1n2 - ((igraph_real_t) to) * n2); from += n1; } } if (mode != IGRAPH_IN) { igraph_vector_push_back(&edges, from); igraph_vector_push_back(&edges, to); } else { igraph_vector_push_back(&edges, to); igraph_vector_push_back(&edges, from); } } igraph_vector_destroy(&s); IGRAPH_FINALLY_CLEAN(1); IGRAPH_CHECK(retval=igraph_create(graph, &edges, n1+n2, directed)); igraph_vector_destroy(&edges); IGRAPH_FINALLY_CLEAN(1); } return retval; }
int igraph_layout_kamada_kawai_3d(const igraph_t *graph, igraph_matrix_t *res, igraph_bool_t use_seed, igraph_integer_t maxiter, igraph_real_t epsilon, igraph_real_t kkconst, const igraph_vector_t *weights, const igraph_vector_t *minx, const igraph_vector_t *maxx, const igraph_vector_t *miny, const igraph_vector_t *maxy, const igraph_vector_t *minz, const igraph_vector_t *maxz) { igraph_integer_t no_nodes=igraph_vcount(graph); igraph_integer_t no_edges=igraph_ecount(graph); igraph_real_t L, L0=sqrt(no_nodes); igraph_matrix_t dij, lij, kij; igraph_real_t max_dij; igraph_vector_t D1, D2, D3; igraph_integer_t i, j, m; if (maxiter < 0) { IGRAPH_ERROR("Number of iterations must be non-negatice in " "Kamada-Kawai layout", IGRAPH_EINVAL); } if (kkconst <= 0) { IGRAPH_ERROR("`K' constant must be positive in Kamada-Kawai layout", IGRAPH_EINVAL); } if (use_seed && (igraph_matrix_nrow(res) != no_nodes || igraph_matrix_ncol(res) != 3)) { IGRAPH_ERROR("Invalid start position matrix size in " "3d Kamada-Kawai layout", IGRAPH_EINVAL); } if (weights && igraph_vector_size(weights) != no_edges) { IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL); } if (minx && igraph_vector_size(minx) != no_nodes) { IGRAPH_ERROR("Invalid minx vector length", IGRAPH_EINVAL); } if (maxx && igraph_vector_size(maxx) != no_nodes) { IGRAPH_ERROR("Invalid maxx vector length", IGRAPH_EINVAL); } if (minx && maxx && !igraph_vector_all_le(minx, maxx)) { IGRAPH_ERROR("minx must not be greater than maxx", IGRAPH_EINVAL); } if (miny && igraph_vector_size(miny) != no_nodes) { IGRAPH_ERROR("Invalid miny vector length", IGRAPH_EINVAL); } if (maxy && igraph_vector_size(maxy) != no_nodes) { IGRAPH_ERROR("Invalid maxy vector length", IGRAPH_EINVAL); } if (miny && maxy && !igraph_vector_all_le(miny, maxy)) { IGRAPH_ERROR("miny must not be greater than maxy", IGRAPH_EINVAL); } if (minz && igraph_vector_size(minz) != no_nodes) { IGRAPH_ERROR("Invalid minz vector length", IGRAPH_EINVAL); } if (maxz && igraph_vector_size(maxz) != no_nodes) { IGRAPH_ERROR("Invalid maxz vector length", IGRAPH_EINVAL); } if (minz && maxz && !igraph_vector_all_le(minz, maxz)) { IGRAPH_ERROR("minz must not be greater than maxz", IGRAPH_EINVAL); } if (!use_seed) { if (minx || maxx || miny || maxy || minz || maxz) { const igraph_real_t width=sqrt(no_nodes), height=width, depth=width; IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 3)); RNG_BEGIN(); for (i=0; i<no_nodes; i++) { igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2; igraph_real_t x2=maxx ? VECTOR(*maxx)[i] : width/2; igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2; igraph_real_t y2=maxy ? VECTOR(*maxy)[i] : height/2; igraph_real_t z1=minz ? VECTOR(*minz)[i] : -depth/2; igraph_real_t z2=maxz ? VECTOR(*maxz)[i] : depth/2; if (!igraph_finite(x1)) { x1 = -width/2; } if (!igraph_finite(x2)) { x2 = width/2; } if (!igraph_finite(y1)) { y1 = -height/2; } if (!igraph_finite(y2)) { y2 = height/2; } if (!igraph_finite(z1)) { z1 = -depth/2; } if (!igraph_finite(z2)) { z2 = depth/2; } MATRIX(*res, i, 0) = RNG_UNIF(x1, x2); MATRIX(*res, i, 1) = RNG_UNIF(y1, y2); MATRIX(*res, i, 2) = RNG_UNIF(z1, z2); } RNG_END(); } else { igraph_layout_sphere(graph, res); } } if (no_nodes <= 1) { return 0; } IGRAPH_MATRIX_INIT_FINALLY(&dij, no_nodes, no_nodes); IGRAPH_MATRIX_INIT_FINALLY(&kij, no_nodes, no_nodes); IGRAPH_MATRIX_INIT_FINALLY(&lij, no_nodes, no_nodes); IGRAPH_CHECK(igraph_shortest_paths_dijkstra(graph, &dij, igraph_vss_all(), igraph_vss_all(), weights, IGRAPH_ALL)); max_dij = 0.0; for (i=0; i<no_nodes; i++) { for (j=i+1; j<no_nodes; j++) { if (!igraph_finite(MATRIX(dij, i, j))) { continue; } if (MATRIX(dij, i, j) > max_dij) { max_dij = MATRIX(dij, i, j); } } } for (i=0; i<no_nodes; i++) { for (j=0; j<no_nodes; j++) { if (MATRIX(dij, i, j) > max_dij) { MATRIX(dij, i, j) = max_dij; } } } L = L0 / max_dij; for (i=0; i<no_nodes; i++) { for (j=0; j<no_nodes; j++) { igraph_real_t tmp=MATRIX(dij, i, j) * MATRIX(dij, i, j); if (i==j) { continue; } MATRIX(kij, i, j) = kkconst / tmp; MATRIX(lij, i, j) = L * MATRIX(dij, i, j); } } /* Initialize delta */ IGRAPH_VECTOR_INIT_FINALLY(&D1, no_nodes); IGRAPH_VECTOR_INIT_FINALLY(&D2, no_nodes); IGRAPH_VECTOR_INIT_FINALLY(&D3, no_nodes); for (m=0; m<no_nodes; m++) { igraph_real_t myD1=0.0, myD2=0.0, myD3=0.0; for (i=0; i<no_nodes; i++) { if (i==m) { continue; } igraph_real_t dx=MATRIX(*res, m, 0) - MATRIX(*res, i, 0); igraph_real_t dy=MATRIX(*res, m, 1) - MATRIX(*res, i, 1); igraph_real_t dz=MATRIX(*res, m, 2) - MATRIX(*res, i, 2); igraph_real_t mi_dist=sqrt(dx * dx + dy * dy + dz * dz); myD1 += MATRIX(kij, m, i) * (dx - MATRIX(lij, m, i) * dx / mi_dist); myD2 += MATRIX(kij, m, i) * (dy - MATRIX(lij, m, i) * dy / mi_dist); myD3 += MATRIX(kij, m, i) * (dz - MATRIX(lij, m, i) * dz / mi_dist); } VECTOR(D1)[m] = myD1; VECTOR(D2)[m] = myD2; VECTOR(D3)[m] = myD3; } for (j=0; j<maxiter; j++) { igraph_real_t Ax=0.0, Ay=0.0, Az=0.0; igraph_real_t Axx=0.0, Axy=0.0, Axz=0.0, Ayy=0.0, Ayz=0.0, Azz=0.0; igraph_real_t max_delta, delta_x, delta_y, delta_z; igraph_real_t old_x, old_y, old_z, new_x, new_y, new_z; igraph_real_t detnum; /* Select maximal delta */ m=0; max_delta=-1; for (i=0; i<no_nodes; i++) { igraph_real_t delta=(VECTOR(D1)[i] * VECTOR(D1)[i] + VECTOR(D2)[i] * VECTOR(D2)[i] + VECTOR(D3)[i] * VECTOR(D3)[i]); if (delta > max_delta) { m=i; max_delta=delta; } } if (max_delta < epsilon) { break; } old_x=MATRIX(*res, m, 0); old_y=MATRIX(*res, m, 1); old_z=MATRIX(*res, m, 2); /* Calculate D1, D2 and D3, and other coefficients */ for (i=0; i<no_nodes; i++) { if (i==m) { continue; } igraph_real_t dx=old_x - MATRIX(*res, i, 0); igraph_real_t dy=old_y - MATRIX(*res, i, 1); igraph_real_t dz=old_z - MATRIX(*res, i, 2); igraph_real_t dist=sqrt(dx * dx + dy * dy + dz *dz); igraph_real_t den=dist * (dx * dx + dy * dy + dz * dz); igraph_real_t k_mi=MATRIX(kij, m, i); igraph_real_t l_mi=MATRIX(lij, m, i); Axx += k_mi * (1 - l_mi * (dy*dy + dz*dz) / den); Ayy += k_mi * (1 - l_mi * (dx*dx + dz*dz) / den); Azz += k_mi * (1 - l_mi * (dx*dx + dy*dy) / den); Axy += k_mi * l_mi * dx * dy / den; Axz += k_mi * l_mi * dx * dz / den; Ayz += k_mi * l_mi * dy * dz / den; } Ax = -VECTOR(D1)[m]; Ay = -VECTOR(D2)[m]; Az = -VECTOR(D3)[m]; /* Need to solve some linear equations, we just use Cramer's rule */ #define DET(a,b,c,d,e,f,g,h,i) ((a*e*i+b*f*g+c*d*h)-(c*e*g+b*d*i+a*f*h)) detnum = DET(Axx,Axy,Axz, Axy,Ayy,Ayz, Axz,Ayz,Azz); delta_x = DET(Ax ,Ay ,Az , Axy,Ayy,Ayz, Axz,Ayz,Azz) / detnum; delta_y = DET(Axx,Axy,Axz, Ax ,Ay ,Az , Axz,Ayz,Azz) / detnum; delta_z = DET(Axx,Axy,Axz, Axy,Ayy,Ayz, Ax ,Ay ,Az ) / detnum; new_x = old_x + delta_x; new_y = old_y + delta_y; new_z = old_z + delta_z; /* Limits, if given */ if (minx && new_x < VECTOR(*minx)[m]) { new_x = VECTOR(*minx)[m]; } if (maxx && new_x > VECTOR(*maxx)[m]) { new_x = VECTOR(*maxx)[m]; } if (miny && new_y < VECTOR(*miny)[m]) { new_y = VECTOR(*miny)[m]; } if (maxy && new_y > VECTOR(*maxy)[m]) { new_y = VECTOR(*maxy)[m]; } if (minz && new_z < VECTOR(*minz)[m]) { new_z = VECTOR(*minz)[m]; } if (maxz && new_z > VECTOR(*maxz)[m]) { new_z = VECTOR(*maxz)[m]; } /* Update delta, only with/for the affected node */ VECTOR(D1)[m] = VECTOR(D2)[m] = VECTOR(D3)[m] = 0.0; for (i=0; i<no_nodes; i++) { if (i==m) { continue; } igraph_real_t old_dx=old_x - MATRIX(*res, i, 0); igraph_real_t old_dy=old_y - MATRIX(*res, i, 1); igraph_real_t old_dz=old_z - MATRIX(*res, i, 2); igraph_real_t old_mi_dist=sqrt(old_dx * old_dx + old_dy * old_dy + old_dz * old_dz); igraph_real_t new_dx=new_x - MATRIX(*res, i, 0); igraph_real_t new_dy=new_y - MATRIX(*res, i, 1); igraph_real_t new_dz=new_z - MATRIX(*res, i, 2); igraph_real_t new_mi_dist=sqrt(new_dx * new_dx + new_dy * new_dy + new_dz * new_dz); VECTOR(D1)[i] -= MATRIX(kij, m, i) * (-old_dx + MATRIX(lij, m, i) * old_dx / old_mi_dist); VECTOR(D2)[i] -= MATRIX(kij, m, i) * (-old_dy + MATRIX(lij, m, i) * old_dy / old_mi_dist); VECTOR(D3)[i] -= MATRIX(kij, m, i) * (-old_dz + MATRIX(lij, m, i) * old_dz / old_mi_dist); VECTOR(D1)[i] += MATRIX(kij, m, i) * (-new_dx + MATRIX(lij, m, i) * new_dx / new_mi_dist); VECTOR(D2)[i] += MATRIX(kij, m, i) * (-new_dy + MATRIX(lij, m, i) * new_dy / new_mi_dist); VECTOR(D3)[i] += MATRIX(kij, m, i) * (-new_dz + MATRIX(lij, m, i) * new_dz / new_mi_dist); VECTOR(D1)[m] += MATRIX(kij, m, i) * (new_dx - MATRIX(lij, m, i) * new_dx / new_mi_dist); VECTOR(D2)[m] += MATRIX(kij, m, i) * (new_dy - MATRIX(lij, m, i) * new_dy / new_mi_dist); VECTOR(D3)[m] += MATRIX(kij, m, i) * (new_dz - MATRIX(lij, m, i) * new_dz / new_mi_dist); } /* Update coordinates*/ MATRIX(*res, m, 0) = new_x; MATRIX(*res, m, 1) = new_y; MATRIX(*res, m, 2) = new_z; } igraph_vector_destroy(&D3); igraph_vector_destroy(&D2); igraph_vector_destroy(&D1); igraph_matrix_destroy(&lij); igraph_matrix_destroy(&kij); igraph_matrix_destroy(&dij); IGRAPH_FINALLY_CLEAN(6); return 0; }
int igraph_layout_i_fr(const igraph_t *graph, igraph_matrix_t *res, igraph_bool_t use_seed, igraph_integer_t niter, igraph_real_t start_temp, const igraph_vector_t *weight, const igraph_vector_t *minx, const igraph_vector_t *maxx, const igraph_vector_t *miny, const igraph_vector_t *maxy) { igraph_integer_t no_nodes=igraph_vcount(graph); igraph_integer_t no_edges=igraph_ecount(graph); igraph_integer_t i; igraph_vector_float_t dispx, dispy; igraph_real_t temp=start_temp; igraph_real_t difftemp=start_temp / niter; float width=sqrtf(no_nodes), height=width; igraph_bool_t conn=1; float C; igraph_is_connected(graph, &conn, IGRAPH_WEAK); if (!conn) { C = no_nodes * sqrtf(no_nodes); } RNG_BEGIN(); if (!use_seed) { IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 2)); for (i=0; i<no_nodes; i++) { igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2; igraph_real_t x2=maxx ? VECTOR(*maxx)[i] : width/2; igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2; igraph_real_t y2=maxy ? VECTOR(*maxy)[i] : height/2; if (!igraph_finite(x1)) { x1 = -sqrt(no_nodes)/2; } if (!igraph_finite(x2)) { x2 = sqrt(no_nodes)/2; } if (!igraph_finite(y1)) { y1 = -sqrt(no_nodes)/2; } if (!igraph_finite(y2)) { y2 = sqrt(no_nodes)/2; } MATRIX(*res, i, 0) = RNG_UNIF(x1, x2); MATRIX(*res, i, 1) = RNG_UNIF(y1, y2); } } IGRAPH_CHECK(igraph_vector_float_init(&dispx, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &dispx); IGRAPH_CHECK(igraph_vector_float_init(&dispy, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &dispy); for (i=0; i<niter; i++) { igraph_integer_t v, u, e; /* calculate repulsive forces, we have a special version for unconnected graphs */ igraph_vector_float_null(&dispx); igraph_vector_float_null(&dispy); if (conn) { for (v=0; v<no_nodes; v++) { for (u=v+1; u<no_nodes; u++) { float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0); float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1); float dlen=dx * dx + dy * dy; if (dlen == 0) { dx = RNG_UNIF01() * 1e-9; dy = RNG_UNIF01() * 1e-9; dlen = dx * dx + dy * dy; } VECTOR(dispx)[v] += dx/dlen; VECTOR(dispy)[v] += dy/dlen; VECTOR(dispx)[u] -= dx/dlen; VECTOR(dispy)[u] -= dy/dlen; } } } else { for (v=0; v<no_nodes; v++) { for (u=v+1; u<no_nodes; u++) { float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0); float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1); float dlen, rdlen; dlen=dx * dx + dy * dy; if (dlen == 0) { dx = RNG_UNIF(0, 1e-6); dy = RNG_UNIF(0, 1e-6); dlen = dx * dx + dy * dy; } rdlen=sqrt(dlen); VECTOR(dispx)[v] += dx * (C-dlen * rdlen) / (dlen*C); VECTOR(dispy)[v] += dy * (C-dlen * rdlen) / (dlen*C); VECTOR(dispx)[u] -= dx * (C-dlen * rdlen) / (dlen*C); VECTOR(dispy)[u] -= dy * (C-dlen * rdlen) / (dlen*C); } } } /* calculate attractive forces */ for (e=0; e<no_edges; e++) { /* each edges is an ordered pair of vertices v and u */ igraph_integer_t v=IGRAPH_FROM(graph, e); igraph_integer_t u=IGRAPH_TO(graph, e); igraph_real_t dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0); igraph_real_t dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1); igraph_real_t w=weight ? VECTOR(*weight)[e] : 1.0; igraph_real_t dlen=sqrt(dx * dx + dy * dy) * w; VECTOR(dispx)[v] -= (dx * dlen); VECTOR(dispy)[v] -= (dy * dlen); VECTOR(dispx)[u] += (dx * dlen); VECTOR(dispy)[u] += (dy * dlen); } /* limit max displacement to temperature t and prevent from displacement outside frame */ for (v=0; v<no_nodes; v++) { igraph_real_t dx=VECTOR(dispx)[v] + RNG_UNIF01() * 1e-9; igraph_real_t dy=VECTOR(dispy)[v] + RNG_UNIF01() * 1e-9; igraph_real_t displen=sqrt(dx * dx + dy * dy); igraph_real_t mx=fabs(dx) < temp ? dx : temp; igraph_real_t my=fabs(dy) < temp ? dy : temp; if (displen > 0) { MATRIX(*res, v, 0) += (dx / displen) * mx; MATRIX(*res, v, 1) += (dy / displen) * my; } if (minx && MATRIX(*res, v, 0) < VECTOR(*minx)[v]) { MATRIX(*res, v, 0) = VECTOR(*minx)[v]; } if (maxx && MATRIX(*res, v, 0) > VECTOR(*maxx)[v]) { MATRIX(*res, v, 0) = VECTOR(*maxx)[v]; } if (miny && MATRIX(*res, v, 1) < VECTOR(*miny)[v]) { MATRIX(*res, v, 1) = VECTOR(*miny)[v]; } if (maxy && MATRIX(*res, v, 1) > VECTOR(*maxy)[v]) { MATRIX(*res, v, 1) = VECTOR(*maxy)[v]; } } temp -= difftemp; } RNG_END(); igraph_vector_float_destroy(&dispx); igraph_vector_float_destroy(&dispy); IGRAPH_FINALLY_CLEAN(2); return 0; }
int igraph_layout_kamada_kawai(const igraph_t *graph, igraph_matrix_t *res, igraph_bool_t use_seed, igraph_integer_t maxiter, igraph_real_t epsilon, igraph_real_t kkconst, const igraph_vector_t *weights, const igraph_vector_t *minx, const igraph_vector_t *maxx, const igraph_vector_t *miny, const igraph_vector_t *maxy) { igraph_integer_t no_nodes=igraph_vcount(graph); igraph_integer_t no_edges=igraph_ecount(graph); igraph_real_t L, L0=sqrt(no_nodes); igraph_matrix_t dij, lij, kij; igraph_real_t max_dij; igraph_vector_t D1, D2; igraph_integer_t i, j, m; if (maxiter < 0) { IGRAPH_ERROR("Number of iterations must be non-negatice in " "Kamada-Kawai layout", IGRAPH_EINVAL); } if (kkconst <= 0) { IGRAPH_ERROR("`K' constant must be positive in Kamada-Kawai layout", IGRAPH_EINVAL); } if (use_seed && (igraph_matrix_nrow(res) != no_nodes || igraph_matrix_ncol(res) != 2)) { IGRAPH_ERROR("Invalid start position matrix size in " "Kamada-Kawai layout", IGRAPH_EINVAL); } if (weights && igraph_vector_size(weights) != no_edges) { IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL); } if (minx && igraph_vector_size(minx) != no_nodes) { IGRAPH_ERROR("Invalid minx vector length", IGRAPH_EINVAL); } if (maxx && igraph_vector_size(maxx) != no_nodes) { IGRAPH_ERROR("Invalid maxx vector length", IGRAPH_EINVAL); } if (minx && maxx && !igraph_vector_all_le(minx, maxx)) { IGRAPH_ERROR("minx must not be greater than maxx", IGRAPH_EINVAL); } if (miny && igraph_vector_size(miny) != no_nodes) { IGRAPH_ERROR("Invalid miny vector length", IGRAPH_EINVAL); } if (maxy && igraph_vector_size(maxy) != no_nodes) { IGRAPH_ERROR("Invalid maxy vector length", IGRAPH_EINVAL); } if (miny && maxy && !igraph_vector_all_le(miny, maxy)) { IGRAPH_ERROR("miny must not be greater than maxy", IGRAPH_EINVAL); } if (!use_seed) { if (minx || maxx || miny || maxy) { const igraph_real_t width=sqrt(no_nodes), height=width; IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 2)); RNG_BEGIN(); for (i=0; i<no_nodes; i++) { igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2; igraph_real_t x2=maxx ? VECTOR(*maxx)[i] : width/2; igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2; igraph_real_t y2=maxy ? VECTOR(*maxy)[i] : height/2; if (!igraph_finite(x1)) { x1 = -width/2; } if (!igraph_finite(x2)) { x2 = width/2; } if (!igraph_finite(y1)) { y1 = -height/2; } if (!igraph_finite(y2)) { y2 = height/2; } MATRIX(*res, i, 0) = RNG_UNIF(x1, x2); MATRIX(*res, i, 1) = RNG_UNIF(y1, y2); } RNG_END(); } else { igraph_layout_circle(graph, res, /* order= */ igraph_vss_all()); } } if (no_nodes <= 1) { return 0; } IGRAPH_MATRIX_INIT_FINALLY(&dij, no_nodes, no_nodes); IGRAPH_MATRIX_INIT_FINALLY(&kij, no_nodes, no_nodes); IGRAPH_MATRIX_INIT_FINALLY(&lij, no_nodes, no_nodes); IGRAPH_CHECK(igraph_shortest_paths_dijkstra(graph, &dij, igraph_vss_all(), igraph_vss_all(), weights, IGRAPH_ALL)); max_dij = 0.0; for (i=0; i<no_nodes; i++) { for (j=i+1; j<no_nodes; j++) { if (!igraph_finite(MATRIX(dij, i, j))) { continue; } if (MATRIX(dij, i, j) > max_dij) { max_dij = MATRIX(dij, i, j); } } } for (i=0; i<no_nodes; i++) { for (j=0; j<no_nodes; j++) { if (MATRIX(dij, i, j) > max_dij) { MATRIX(dij, i, j) = max_dij; } } } L = L0 / max_dij; for (i=0; i<no_nodes; i++) { for (j=0; j<no_nodes; j++) { igraph_real_t tmp=MATRIX(dij, i, j) * MATRIX(dij, i, j); if (i==j) { continue; } MATRIX(kij, i, j) = kkconst / tmp; MATRIX(lij, i, j) = L * MATRIX(dij, i, j); } } /* Initialize delta */ IGRAPH_VECTOR_INIT_FINALLY(&D1, no_nodes); IGRAPH_VECTOR_INIT_FINALLY(&D2, no_nodes); for (m=0; m<no_nodes; m++) { igraph_real_t myD1=0.0, myD2=0.0; for (i=0; i<no_nodes; i++) { if (i==m) { continue; } igraph_real_t dx=MATRIX(*res, m, 0) - MATRIX(*res, i, 0); igraph_real_t dy=MATRIX(*res, m, 1) - MATRIX(*res, i, 1); igraph_real_t mi_dist=sqrt(dx * dx + dy * dy); myD1 += MATRIX(kij, m, i) * (dx - MATRIX(lij, m, i) * dx / mi_dist); myD2 += MATRIX(kij, m, i) * (dy - MATRIX(lij, m, i) * dy / mi_dist); } VECTOR(D1)[m] = myD1; VECTOR(D2)[m] = myD2; } for (j=0; j<maxiter; j++) { igraph_real_t myD1=0.0, myD2=0.0, A=0.0, B=0.0, C=0.0; igraph_real_t max_delta, delta_x, delta_y; igraph_real_t old_x, old_y, new_x, new_y; /* Select maximal delta */ m=0; max_delta=-1; for (i=0; i<no_nodes; i++) { igraph_real_t delta=(VECTOR(D1)[i] * VECTOR(D1)[i] + VECTOR(D2)[i] * VECTOR(D2)[i]); if (delta > max_delta) { m=i; max_delta=delta; } } if (max_delta < epsilon) { break; } old_x=MATRIX(*res, m, 0); old_y=MATRIX(*res, m, 1); /* Calculate D1 and D2, A, B, C */ for (i=0; i<no_nodes; i++) { if (i==m) { continue; } igraph_real_t dx=old_x - MATRIX(*res, i, 0); igraph_real_t dy=old_y - MATRIX(*res, i, 1); igraph_real_t dist=sqrt(dx * dx + dy * dy); igraph_real_t den=dist * (dx * dx + dy * dy); A += MATRIX(kij, m, i) * (1 - MATRIX(lij, m, i) * dy * dy / den); B += MATRIX(kij, m, i) * MATRIX(lij, m, i) * dx * dy / den; C += MATRIX(kij, m, i) * (1 - MATRIX(lij, m, i) * dx * dx / den); } myD1 = VECTOR(D1)[m]; myD2 = VECTOR(D2)[m]; /* Need to solve some linear equations */ delta_y = (B * myD1 - myD2 * A) / (C * A - B * B); delta_x = - (myD1 + B * delta_y) / A; new_x = old_x + delta_x; new_y = old_y + delta_y; /* Limits, if given */ if (minx && new_x < VECTOR(*minx)[m]) { new_x = VECTOR(*minx)[m]; } if (maxx && new_x > VECTOR(*maxx)[m]) { new_x = VECTOR(*maxx)[m]; } if (miny && new_y < VECTOR(*miny)[m]) { new_y = VECTOR(*miny)[m]; } if (maxy && new_y > VECTOR(*maxy)[m]) { new_y = VECTOR(*maxy)[m]; } /* Update delta, only with/for the affected node */ VECTOR(D1)[m] = VECTOR(D2)[m] = 0.0; for (i=0; i<no_nodes; i++) { if (i==m) { continue; } igraph_real_t old_dx=old_x - MATRIX(*res, i, 0); igraph_real_t old_dy=old_y - MATRIX(*res, i, 1); igraph_real_t old_mi_dist=sqrt(old_dx * old_dx + old_dy * old_dy); igraph_real_t new_dx=new_x - MATRIX(*res, i, 0); igraph_real_t new_dy=new_y - MATRIX(*res, i, 1); igraph_real_t new_mi_dist=sqrt(new_dx * new_dx + new_dy * new_dy); VECTOR(D1)[i] -= MATRIX(kij, m, i) * (-old_dx + MATRIX(lij, m, i) * old_dx / old_mi_dist); VECTOR(D2)[i] -= MATRIX(kij, m, i) * (-old_dy + MATRIX(lij, m, i) * old_dy / old_mi_dist); VECTOR(D1)[i] += MATRIX(kij, m, i) * (-new_dx + MATRIX(lij, m, i) * new_dx / new_mi_dist); VECTOR(D2)[i] += MATRIX(kij, m, i) * (-new_dy + MATRIX(lij, m, i) * new_dy / new_mi_dist); VECTOR(D1)[m] += MATRIX(kij, m, i) * (new_dx - MATRIX(lij, m, i) * new_dx / new_mi_dist); VECTOR(D2)[m] += MATRIX(kij, m, i) * (new_dy - MATRIX(lij, m, i) * new_dy / new_mi_dist); } /* Update coordinates*/ MATRIX(*res, m, 0) = new_x; MATRIX(*res, m, 1) = new_y; } igraph_vector_destroy(&D2); igraph_vector_destroy(&D1); igraph_matrix_destroy(&lij); igraph_matrix_destroy(&kij); igraph_matrix_destroy(&dij); IGRAPH_FINALLY_CLEAN(5); return 0; }
int igraph_i_community_spinglass_negative(const igraph_t *graph, const igraph_vector_t *weights, igraph_real_t *modularity, igraph_real_t *temperature, igraph_vector_t *membership, igraph_vector_t *csize, igraph_integer_t spins, igraph_bool_t parupdate, igraph_real_t starttemp, igraph_real_t stoptemp, igraph_real_t coolfact, igraph_spincomm_update_t update_rule, igraph_real_t gamma, /* igraph_matrix_t *adhesion, */ /* igraph_matrix_t *normalised_adhesion, */ /* igraph_real_t *polarization, */ igraph_real_t gamma_minus) { unsigned long changes, runs; igraph_bool_t use_weights=0; bool zeroT; double kT, acc; ClusterList<NNode*> *cl_cur; network *net; PottsModelN *pm; igraph_real_t d_n; igraph_real_t d_p; /* Check arguments */ if (parupdate) { IGRAPH_ERROR("Parallel spin update not implemented with " "negative gamma", IGRAPH_UNIMPLEMENTED); } if (spins < 2 || spins > 500) { IGRAPH_ERROR("Invalid number of spins", IGRAPH_EINVAL); } if (update_rule != IGRAPH_SPINCOMM_UPDATE_SIMPLE && update_rule != IGRAPH_SPINCOMM_UPDATE_CONFIG) { IGRAPH_ERROR("Invalid update rule", IGRAPH_EINVAL); } if (weights) { if (igraph_vector_size(weights) != igraph_ecount(graph)) { IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL); } use_weights=1; } if (coolfact < 0 || coolfact>=1.0) { IGRAPH_ERROR("Invalid cooling factor", IGRAPH_EINVAL); } if (gamma < 0.0) { IGRAPH_ERROR("Invalid gamma value", IGRAPH_EINVAL); } if (starttemp/stoptemp<1.0) { IGRAPH_ERROR("starttemp should be larger in absolute value than stoptemp", IGRAPH_EINVAL); } /* Check whether we have a single component */ igraph_bool_t conn; IGRAPH_CHECK(igraph_is_connected(graph, &conn, IGRAPH_WEAK)); if (!conn) { IGRAPH_ERROR("Cannot work with unconnected graph", IGRAPH_EINVAL); } igraph_vector_minmax(weights, &d_n, &d_p); if (d_n > 0) { d_n=0; } if (d_p < 0) { d_p=0; } d_n = -d_n; net = new network; net->node_list =new DL_Indexed_List<NNode*>(); net->link_list =new DL_Indexed_List<NLink*>(); net->cluster_list=new DL_Indexed_List<ClusterList<NNode*>*>(); /* Transform the igraph_t */ IGRAPH_CHECK(igraph_i_read_network(graph, weights, net, use_weights, 0)); bool directed = igraph_is_directed(graph); pm=new PottsModelN(net,(unsigned int)spins, directed); /* initialize the random number generator */ RNG_BEGIN(); if ((stoptemp==0.0) && (starttemp==0.0)) zeroT=true; else zeroT=false; //Begin at a high enough temperature kT=pm->FindStartTemp(gamma, gamma_minus, starttemp); /* assign random initial configuration */ pm->assign_initial_conf(true); runs=0; changes=1; acc = 0; while (changes>0 && (kT/stoptemp>1.0 || (zeroT && runs<150))) { IGRAPH_ALLOW_INTERRUPTION(); /* This is not clean.... */ runs++; kT = kT*coolfact; acc=pm->HeatBathLookup(gamma, gamma_minus, kT, 50); if (acc<(1.0-1.0/double(spins))*0.001) changes=0; else changes=1; } /* while loop */ /* These are needed, otherwise 'modularity' is not calculated */ igraph_matrix_t adhesion, normalized_adhesion; igraph_real_t polarization; IGRAPH_MATRIX_INIT_FINALLY(&adhesion, 0, 0); IGRAPH_MATRIX_INIT_FINALLY(&normalized_adhesion, 0, 0); pm->WriteClusters(modularity, temperature, csize, membership, &adhesion, &normalized_adhesion, &polarization, kT, d_p, d_n, gamma, gamma_minus); igraph_matrix_destroy(&normalized_adhesion); igraph_matrix_destroy(&adhesion); IGRAPH_FINALLY_CLEAN(2); while (net->link_list->Size()) delete net->link_list->Pop(); while (net->node_list->Size()) delete net->node_list->Pop(); while (net->cluster_list->Size()) { cl_cur=net->cluster_list->Pop(); while (cl_cur->Size()) cl_cur->Pop(); delete cl_cur; } RNG_END(); return 0; }
int igraph_layout_fruchterman_reingold_3d(const igraph_t *graph, igraph_matrix_t *res, igraph_bool_t use_seed, igraph_integer_t niter, igraph_real_t start_temp, const igraph_vector_t *weight, const igraph_vector_t *minx, const igraph_vector_t *maxx, const igraph_vector_t *miny, const igraph_vector_t *maxy, const igraph_vector_t *minz, const igraph_vector_t *maxz) { igraph_integer_t no_nodes=igraph_vcount(graph); igraph_integer_t no_edges=igraph_ecount(graph); igraph_integer_t i; igraph_vector_float_t dispx, dispy, dispz; igraph_real_t temp=start_temp; igraph_real_t difftemp=start_temp / niter; float width=sqrtf(no_nodes), height=width, depth=width; igraph_bool_t conn=1; float C; if (niter < 0) { IGRAPH_ERROR("Number of iterations must be non-negative in " "Fruchterman-Reingold layout", IGRAPH_EINVAL); } if (use_seed && (igraph_matrix_nrow(res) != no_nodes || igraph_matrix_ncol(res) != 3)) { IGRAPH_ERROR("Invalid start position matrix size in " "Fruchterman-Reingold layout", IGRAPH_EINVAL); } if (weight && igraph_vector_size(weight) != igraph_ecount(graph)) { IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL); } if (minx && igraph_vector_size(minx) != no_nodes) { IGRAPH_ERROR("Invalid minx vector length", IGRAPH_EINVAL); } if (maxx && igraph_vector_size(maxx) != no_nodes) { IGRAPH_ERROR("Invalid maxx vector length", IGRAPH_EINVAL); } if (minx && maxx && !igraph_vector_all_le(minx, maxx)) { IGRAPH_ERROR("minx must not be greater than maxx", IGRAPH_EINVAL); } if (miny && igraph_vector_size(miny) != no_nodes) { IGRAPH_ERROR("Invalid miny vector length", IGRAPH_EINVAL); } if (maxy && igraph_vector_size(maxy) != no_nodes) { IGRAPH_ERROR("Invalid maxy vector length", IGRAPH_EINVAL); } if (miny && maxy && !igraph_vector_all_le(miny, maxy)) { IGRAPH_ERROR("miny must not be greater than maxy", IGRAPH_EINVAL); } if (minz && igraph_vector_size(minz) != no_nodes) { IGRAPH_ERROR("Invalid minz vector length", IGRAPH_EINVAL); } if (maxz && igraph_vector_size(maxz) != no_nodes) { IGRAPH_ERROR("Invalid maxz vector length", IGRAPH_EINVAL); } if (minz && maxz && !igraph_vector_all_le(minz, maxz)) { IGRAPH_ERROR("minz must not be greater than maxz", IGRAPH_EINVAL); } igraph_is_connected(graph, &conn, IGRAPH_WEAK); if (!conn) { C = no_nodes * sqrtf(no_nodes); } RNG_BEGIN(); if (!use_seed) { IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 3)); for (i=0; i<no_nodes; i++) { igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2; igraph_real_t x2=maxx ? VECTOR(*maxx)[i] : width/2; igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2; igraph_real_t y2=maxy ? VECTOR(*maxy)[i] : height/2; igraph_real_t z1=minz ? VECTOR(*minz)[i] : -depth/2; igraph_real_t z2=maxz ? VECTOR(*maxz)[i] : depth/2; MATRIX(*res, i, 0) = RNG_UNIF(x1, x2); MATRIX(*res, i, 1) = RNG_UNIF(y1, y2); MATRIX(*res, i, 2) = RNG_UNIF(z1, z2); } } IGRAPH_CHECK(igraph_vector_float_init(&dispx, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &dispx); IGRAPH_CHECK(igraph_vector_float_init(&dispy, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &dispy); IGRAPH_CHECK(igraph_vector_float_init(&dispz, no_nodes)); IGRAPH_FINALLY(igraph_vector_float_destroy, &dispz); for (i=0; i<niter; i++) { igraph_integer_t v, u, e; /* calculate repulsive forces, we have a special version for unconnected graphs */ igraph_vector_float_null(&dispx); igraph_vector_float_null(&dispy); igraph_vector_float_null(&dispz); if (conn) { for (v=0; v<no_nodes; v++) { for (u=v+1; u<no_nodes; u++) { float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0); float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1); float dz=MATRIX(*res, v, 2) - MATRIX(*res, u, 2); float dlen=dx * dx + dy * dy + dz * dz; if (dlen == 0) { dx = RNG_UNIF01() * 1e-9; dy = RNG_UNIF01() * 1e-9; dz = RNG_UNIF01() * 1e-9; dlen = dx * dx + dy * dy + dz * dz; } VECTOR(dispx)[v] += dx/dlen; VECTOR(dispy)[v] += dy/dlen; VECTOR(dispz)[v] += dz/dlen; VECTOR(dispx)[u] -= dx/dlen; VECTOR(dispy)[u] -= dy/dlen; VECTOR(dispz)[u] -= dz/dlen; } } } else { for (v=0; v<no_nodes; v++) { for (u=v+1; u<no_nodes; u++) { float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0); float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1); float dz=MATRIX(*res, v, 2) - MATRIX(*res, u, 2); float dlen, rdlen; dlen=dx * dx + dy * dy + dz * dz; if (dlen == 0) { dx = RNG_UNIF01() * 1e-9; dy = RNG_UNIF01() * 1e-9; dz = RNG_UNIF01() * 1e-9; dlen = dx * dx + dy * dy + dz * dz; } rdlen=sqrt(dlen); VECTOR(dispx)[v] += dx * (C-dlen * rdlen) / (dlen*C); VECTOR(dispy)[v] += dy * (C-dlen * rdlen) / (dlen*C); VECTOR(dispy)[v] += dz * (C-dlen * rdlen) / (dlen*C); VECTOR(dispx)[u] -= dx * (C-dlen * rdlen) / (dlen*C); VECTOR(dispy)[u] -= dy * (C-dlen * rdlen) / (dlen*C); VECTOR(dispz)[u] -= dz * (C-dlen * rdlen) / (dlen*C); } } } /* calculate attractive forces */ for (e=0; e<no_edges; e++) { /* each edges is an ordered pair of vertices v and u */ igraph_integer_t v=IGRAPH_FROM(graph, e); igraph_integer_t u=IGRAPH_TO(graph, e); igraph_real_t dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0); igraph_real_t dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1); igraph_real_t dz=MATRIX(*res, v, 2) - MATRIX(*res, u, 2); igraph_real_t w=weight ? VECTOR(*weight)[e] : 1.0; igraph_real_t dlen=sqrt(dx * dx + dy * dy + dz * dz) * w; VECTOR(dispx)[v] -= (dx * dlen); VECTOR(dispy)[v] -= (dy * dlen); VECTOR(dispz)[v] -= (dz * dlen); VECTOR(dispx)[u] += (dx * dlen); VECTOR(dispy)[u] += (dy * dlen); VECTOR(dispz)[u] += (dz * dlen); } /* limit max displacement to temperature t and prevent from displacement outside frame */ for (v=0; v<no_nodes; v++) { igraph_real_t dx=VECTOR(dispx)[v] + RNG_UNIF01() * 1e-9; igraph_real_t dy=VECTOR(dispy)[v] + RNG_UNIF01() * 1e-9; igraph_real_t dz=VECTOR(dispz)[v] + RNG_UNIF01() * 1e-9; igraph_real_t displen=sqrt(dx * dx + dy * dy + dz * dz); igraph_real_t mx=fabs(dx) < temp ? dx : temp; igraph_real_t my=fabs(dy) < temp ? dy : temp; igraph_real_t mz=fabs(dz) < temp ? dz : temp; if (displen > 0) { MATRIX(*res, v, 0) += (dx / displen) * mx; MATRIX(*res, v, 1) += (dy / displen) * my; MATRIX(*res, v, 2) += (dz / displen) * mz; } if (minx && MATRIX(*res, v, 0) < VECTOR(*minx)[v]) { MATRIX(*res, v, 0) = VECTOR(*minx)[v]; } if (maxx && MATRIX(*res, v, 0) > VECTOR(*maxx)[v]) { MATRIX(*res, v, 0) = VECTOR(*maxx)[v]; } if (miny && MATRIX(*res, v, 1) < VECTOR(*miny)[v]) { MATRIX(*res, v, 1) = VECTOR(*miny)[v]; } if (maxy && MATRIX(*res, v, 1) > VECTOR(*maxy)[v]) { MATRIX(*res, v, 1) = VECTOR(*maxy)[v]; } if (minz && MATRIX(*res, v, 2) < VECTOR(*minz)[v]) { MATRIX(*res, v, 2) = VECTOR(*minz)[v]; } if (maxz && MATRIX(*res, v, 2) > VECTOR(*maxz)[v]) { MATRIX(*res, v, 2) = VECTOR(*maxz)[v]; } } temp -= difftemp; } RNG_END(); igraph_vector_float_destroy(&dispx); igraph_vector_float_destroy(&dispy); igraph_vector_float_destroy(&dispz); IGRAPH_FINALLY_CLEAN(3); return 0; }
int igraph_random_sample(igraph_vector_t *res, igraph_integer_t l, igraph_integer_t h, igraph_integer_t length) { igraph_real_t N=h-l+1; igraph_real_t n=length; int retval; igraph_real_t nreal=length; igraph_real_t ninv=1.0/nreal; igraph_real_t Nreal=N; igraph_real_t Vprime; igraph_real_t qu1=-n+1+N; igraph_real_t qu1real=-nreal+1.0+Nreal; igraph_real_t negalphainv=-13; igraph_real_t threshold=-negalphainv*n; igraph_real_t S; igraph_vector_clear(res); IGRAPH_CHECK(igraph_vector_reserve(res, length)); RNG_BEGIN(); Vprime=exp(log(RNG_UNIF01())*ninv); while (n>1 && threshold < N) { igraph_real_t X, U; igraph_real_t limit, t; igraph_real_t negSreal, y1, y2, top, bottom; igraph_real_t nmin1inv=1.0/(-1.0+nreal); while (1) { while(1) { X=Nreal*(-Vprime+1.0); S=floor(X); if (S==0) { S=1; } if (S <qu1) { break; } Vprime = exp(log(RNG_UNIF01())*ninv); } U=RNG_UNIF01(); negSreal=-S; y1=exp(log(U*Nreal/qu1real)*nmin1inv); Vprime=y1*(-X/Nreal+1.0)*(qu1real/(negSreal+qu1real)); if (Vprime <= 1.0) { break; } y2=1.0; top=-1.0+Nreal; if (-1+n > S) { bottom=-nreal+Nreal; limit=-S+N; } else { bottom=-1.0+negSreal+Nreal; limit=qu1; } for (t=-1+N; t>=limit; t--) { y2=(y2*top)/bottom; top=-1.0+top; bottom=-1.0+bottom; } if (Nreal/(-X+Nreal) >= y1*exp(log(y2)*nmin1inv)) { Vprime=exp(log(RNG_UNIF01())*nmin1inv); break; } Vprime=exp(log(RNG_UNIF01())*ninv); } l+=S; igraph_vector_push_back(res, l); /* allocated */ N=-S+(-1+N); Nreal=negSreal+(-1.0+Nreal); n=-1+n; nreal=-1.0+nreal; ninv=nmin1inv; qu1=-S+qu1; qu1real=negSreal+qu1real; threshold=threshold+negalphainv; } if (n>1) { retval=igraph_random_sample_alga(res, l, h, n); } else { retval=0; S=floor(N*Vprime); l+=S; igraph_vector_push_back(res, l); /* allocated */ } RNG_END(); return retval; }
int igraph_pagerank(const igraph_t *graph, igraph_vector_t *vector, igraph_real_t *value, const igraph_vs_t vids, igraph_bool_t directed, igraph_real_t damping, const igraph_vector_t *weights, igraph_arpack_options_t *options) { igraph_matrix_t values; igraph_matrix_t vectors; igraph_integer_t dirmode; igraph_vector_t outdegree; igraph_vector_t tmp; long int i; long int no_of_nodes=igraph_vcount(graph); long int no_of_edges=igraph_ecount(graph); options->n = igraph_vcount(graph); options->nev = 1; options->ncv = 3; options->which[0]='L'; options->which[1]='M'; options->start=1; /* no random start vector */ directed = directed && igraph_is_directed(graph); if (weights && igraph_vector_size(weights) != igraph_ecount(graph)) { IGRAPH_ERROR("Invalid length of weights vector when calculating " "PageRank scores", IGRAPH_EINVAL); } IGRAPH_MATRIX_INIT_FINALLY(&values, 0, 0); IGRAPH_MATRIX_INIT_FINALLY(&vectors, options->n, 1); if (directed) { dirmode=IGRAPH_IN; } else { dirmode=IGRAPH_ALL; } IGRAPH_VECTOR_INIT_FINALLY(&outdegree, options->n); IGRAPH_VECTOR_INIT_FINALLY(&tmp, options->n); RNG_BEGIN(); if (!weights) { igraph_adjlist_t adjlist; igraph_i_pagerank_data_t data = { graph, &adjlist, damping, &outdegree, &tmp }; IGRAPH_CHECK(igraph_degree(graph, &outdegree, igraph_vss_all(), directed ? IGRAPH_OUT : IGRAPH_ALL, /*loops=*/ 0)); /* Avoid division by zero */ for (i=0; i<options->n; i++) { if (VECTOR(outdegree)[i]==0) { VECTOR(outdegree)[i]=1; } MATRIX(vectors, i, 0) = VECTOR(outdegree)[i]; } IGRAPH_CHECK(igraph_adjlist_init(graph, &adjlist, dirmode)); IGRAPH_FINALLY(igraph_adjlist_destroy, &adjlist); IGRAPH_CHECK(igraph_arpack_rnsolve(igraph_i_pagerank, &data, options, 0, &values, &vectors)); igraph_adjlist_destroy(&adjlist); IGRAPH_FINALLY_CLEAN(1); } else { igraph_adjedgelist_t adjedgelist; igraph_i_pagerank_data2_t data = { graph, &adjedgelist, weights, damping, &outdegree, &tmp }; IGRAPH_CHECK(igraph_adjedgelist_init(graph, &adjedgelist, dirmode)); IGRAPH_FINALLY(igraph_adjedgelist_destroy, &adjedgelist); /* Weighted degree */ for (i=0; i<no_of_edges; i++) { long int from=IGRAPH_FROM(graph, i); long int to=IGRAPH_TO(graph, i); igraph_real_t weight=VECTOR(*weights)[i]; VECTOR(outdegree)[from] += weight; if (!directed) { VECTOR(outdegree)[to] += weight; } } /* Avoid division by zero */ for (i=0; i<options->n; i++) { if (VECTOR(outdegree)[i]==0) { VECTOR(outdegree)[i]=1; } MATRIX(vectors, i, 0) = VECTOR(outdegree)[i]; } IGRAPH_CHECK(igraph_arpack_rnsolve(igraph_i_pagerank2, &data, options, 0, &values, &vectors)); igraph_adjedgelist_destroy(&adjedgelist); IGRAPH_FINALLY_CLEAN(1); } RNG_END(); igraph_vector_destroy(&tmp); igraph_vector_destroy(&outdegree); IGRAPH_FINALLY_CLEAN(2); if (value) { *value=MATRIX(values, 0, 0); } if (vector) { long int i; igraph_vit_t vit; long int nodes_to_calc; igraph_real_t sum=0; for (i=0; i<no_of_nodes; i++) { sum += MATRIX(vectors, i, 0); } IGRAPH_CHECK(igraph_vit_create(graph, vids, &vit)); IGRAPH_FINALLY(igraph_vit_destroy, &vit); nodes_to_calc=IGRAPH_VIT_SIZE(vit); IGRAPH_CHECK(igraph_vector_resize(vector, nodes_to_calc)); for (IGRAPH_VIT_RESET(vit), i=0; !IGRAPH_VIT_END(vit); IGRAPH_VIT_NEXT(vit), i++) { VECTOR(*vector)[i] = MATRIX(vectors, (long int)IGRAPH_VIT_GET(vit), 0); VECTOR(*vector)[i] /= sum; } igraph_vit_destroy(&vit); IGRAPH_FINALLY_CLEAN(1); } if (options->info) { IGRAPH_WARNING("Non-zero return code from ARPACK routine!"); } igraph_matrix_destroy(&vectors); igraph_matrix_destroy(&values); IGRAPH_FINALLY_CLEAN(2); return 0; }