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git-svn-id: http://igraph.rubyforge.org/svn/trunk@58 71f48855-0bbf-4aa5-930d-4df415e86613

This commit is contained in:
alexgutteridge 2007-11-14 05:17:37 +00:00
parent 30cb189900
commit 15a0198d62
6 changed files with 843 additions and 46 deletions
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161
ext/cIGraph.c
View File

@ -171,6 +171,18 @@ VALUE cIGraph_initialize(int argc, VALUE *argv, VALUE self){
void Init_igraph(){ void Init_igraph(){
//Modules
VALUE cIGraph_connectivity;
VALUE cIGraph_mincuts;
VALUE cIGraph_layout;
VALUE cIGraph_clique;
VALUE cIGraph_indyver;
VALUE cIGraph_isomor;
VALUE cIGraph_motifs;
VALUE cIGraph_sorting;
VALUE cIGraph_filewrite;
VALUE cIGraph_community;
igraph_i_set_attribute_table(&cIGraph_attribute_table); igraph_i_set_attribute_table(&cIGraph_attribute_table);
igraph_set_error_handler(cIGraph_error_handler); igraph_set_error_handler(cIGraph_error_handler);
igraph_set_warning_handler(cIGraph_warning_handler); igraph_set_warning_handler(cIGraph_warning_handler);
@ -226,6 +238,13 @@ void Init_igraph(){
rb_define_const(cIGraph, "TREE_IN", INT2NUM(1)); rb_define_const(cIGraph, "TREE_IN", INT2NUM(1));
rb_define_const(cIGraph, "TREE_UNDIRECTED", INT2NUM(2)); rb_define_const(cIGraph, "TREE_UNDIRECTED", INT2NUM(2));
rb_define_const(cIGraph, "VCONN_NEI_ERROR", INT2NUM(0));
rb_define_const(cIGraph, "VCONN_NEI_INFINITY", INT2NUM(1));
rb_define_const(cIGraph, "VCONN_NEI_IGNORE", INT2NUM(2));
rb_define_const(cIGraph, "SPINCOMM_UPDATE_SIMPLE", INT2NUM(0));
rb_define_const(cIGraph, "SPINCOMM_UPDATE_CONFIG", INT2NUM(1));
rb_define_singleton_method(cIGraph, "adjacency", cIGraph_adjacency, 2); /* in cIGraph_generators_deterministic.c */ rb_define_singleton_method(cIGraph, "adjacency", cIGraph_adjacency, 2); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph, "star", cIGraph_star, 3); /* in cIGraph_generators_deterministic.c */ rb_define_singleton_method(cIGraph, "star", cIGraph_star, 3); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph, "lattice", cIGraph_lattice, 4); /* in cIGraph_generators_deterministic.c */ rb_define_singleton_method(cIGraph, "lattice", cIGraph_lattice, 4); /* in cIGraph_generators_deterministic.c */
@ -348,52 +367,128 @@ void Init_igraph(){
rb_define_method(cIGraph, "cocitation", cIGraph_cocitation, 1); /* in cIGraph_other_ops.c */ rb_define_method(cIGraph, "cocitation", cIGraph_cocitation, 1); /* in cIGraph_other_ops.c */
rb_define_method(cIGraph, "get_adjacency", cIGraph_get_adjacency, 1); /* in cIGraph_other_ops.c */ rb_define_method(cIGraph, "get_adjacency", cIGraph_get_adjacency, 1); /* in cIGraph_other_ops.c */
rb_define_method(cIGraph, "cliques", cIGraph_cliques, 2); /* in cIGraph_cliques.c */ //cliques
rb_define_method(cIGraph, "largest_cliques", cIGraph_largest_cliques, 0); /* in cIGraph_cliques.c */ cIGraph_clique = rb_define_module_under(cIGraph, "Cliques");
rb_define_method(cIGraph, "maximal_cliques", cIGraph_maximal_cliques, 0); /* in cIGraph_cliques.c */ rb_include_module(cIGraph, cIGraph_clique);
rb_define_method(cIGraph, "clique_number", cIGraph_clique_number, 0); /* in cIGraph_cliques.c */
rb_define_method(cIGraph, "independent_vertex_sets", cIGraph_independent_vertex_sets, 2); /* in cIGraph_independent_vertex_sets.c */ rb_define_method(cIGraph_clique, "cliques", cIGraph_cliques, 2); /* in cIGraph_cliques.c */
rb_define_method(cIGraph, "largest_independent_vertex_sets", cIGraph_largest_independent_vertex_sets, 0); /* in cIGraph_independent_vertex_sets.c */ rb_define_method(cIGraph_clique, "largest_cliques", cIGraph_largest_cliques, 0); /* in cIGraph_cliques.c */
rb_define_method(cIGraph, "maximal_independent_vertex_sets", cIGraph_maximal_independent_vertex_sets, 0); /* in cIGraph_independent_vertex_sets.c */ rb_define_method(cIGraph_clique, "maximal_cliques", cIGraph_maximal_cliques, 0); /* in cIGraph_cliques.c */
rb_define_method(cIGraph, "independence_number", cIGraph_independence_number, 0); /* in cIGraph_independent_vertex_sets.c */ rb_define_method(cIGraph_clique, "clique_number", cIGraph_clique_number, 0); /* in cIGraph_cliques.c */
rb_define_method(cIGraph, "isomorphic", cIGraph_isomorphic, 1); /* in cIGraph_isomorphism.c */ //Motifs
rb_define_method(cIGraph, "isomorphic_vf2", cIGraph_isomorphic_vf2, 1); /* in cIGraph_isomorphism.c */ cIGraph_indyver = rb_define_module_under(cIGraph, "IndependentVertexSets");
rb_define_method(cIGraph, "isoclass", cIGraph_isoclass, 0); /* in cIGraph_isomorphism.c */ rb_include_module(cIGraph, cIGraph_indyver);
rb_define_method(cIGraph, "isoclass_subgraph", cIGraph_isoclass_subgraph, 1); /* in cIGraph_isomorphism.c */
rb_define_method(cIGraph_indyver, "independent_vertex_sets", cIGraph_independent_vertex_sets, 2); /* in cIGraph_independent_vertex_sets.c */
rb_define_method(cIGraph_indyver, "largest_independent_vertex_sets", cIGraph_largest_independent_vertex_sets, 0); /* in cIGraph_independent_vertex_sets.c */
rb_define_method(cIGraph_indyver, "maximal_independent_vertex_sets", cIGraph_maximal_independent_vertex_sets, 0); /* in cIGraph_independent_vertex_sets.c */
rb_define_method(cIGraph_indyver, "independence_number", cIGraph_independence_number, 0); /* in cIGraph_independent_vertex_sets.c */
//Motifs
cIGraph_isomor = rb_define_module_under(cIGraph, "Isomorphism");
rb_include_module(cIGraph, cIGraph_isomor);
rb_define_method(cIGraph_isomor, "isomorphic", cIGraph_isomorphic, 1); /* in cIGraph_isomorphism.c */
rb_define_method(cIGraph_isomor, "isomorphic_vf2", cIGraph_isomorphic_vf2, 1); /* in cIGraph_isomorphism.c */
rb_define_method(cIGraph_isomor, "isoclass", cIGraph_isoclass, 0); /* in cIGraph_isomorphism.c */
rb_define_method(cIGraph_isomor, "isoclass_subgraph", cIGraph_isoclass_subgraph, 1); /* in cIGraph_isomorphism.c */
rb_define_singleton_method(cIGraph, "isoclass_create", cIGraph_isoclass_create, 3); /* in cIGraph_isomorphism.c */ rb_define_singleton_method(cIGraph, "isoclass_create", cIGraph_isoclass_create, 3); /* in cIGraph_isomorphism.c */
rb_define_method(cIGraph, "motifs_randesu", cIGraph_motifs_randesu, 2); /* in cIGraph_motif.c */ //Motifs
rb_define_method(cIGraph, "motifs_randesu_no", cIGraph_motifs_randesu_no, 2); /* in cIGraph_motif.c */ cIGraph_motifs = rb_define_module_under(cIGraph, "Motifs");
rb_define_method(cIGraph, "motifs_randesu_estimate", cIGraph_motifs_randesu_estimate, 4); /* in cIGraph_motif.c */ rb_include_module(cIGraph, cIGraph_motifs);
rb_define_method(cIGraph, "topological_sorting", cIGraph_topological_sorting, 1); /* in cIGraph_topological_sort.c */ rb_define_method(cIGraph_motifs, "motifs_randesu", cIGraph_motifs_randesu, 2); /* in cIGraph_motif.c */
rb_define_method(cIGraph_motifs, "motifs_randesu_no", cIGraph_motifs_randesu_no, 2); /* in cIGraph_motif.c */
rb_define_method(cIGraph_motifs, "motifs_randesu_estimate", cIGraph_motifs_randesu_estimate, 4); /* in cIGraph_motif.c */
//File write
cIGraph_sorting = rb_define_module_under(cIGraph, "Sorting");
rb_include_module(cIGraph, cIGraph_sorting);
rb_define_method(cIGraph_sorting, "topological_sorting", cIGraph_topological_sorting, 1); /* in cIGraph_topological_sort.c */
//File read
rb_define_singleton_method(cIGraph, "read_graph_edgelist", cIGraph_read_graph_edgelist, 2); /* in cIGraph_file.c */ rb_define_singleton_method(cIGraph, "read_graph_edgelist", cIGraph_read_graph_edgelist, 2); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph, "read_graph_graphml", cIGraph_read_graph_graphml, 2); /* in cIGraph_file.c */ rb_define_singleton_method(cIGraph, "read_graph_graphml", cIGraph_read_graph_graphml, 2); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph, "read_graph_pajek", cIGraph_read_graph_pajek, 2); /* in cIGraph_file.c */ rb_define_singleton_method(cIGraph, "read_graph_ncol", cIGraph_read_graph_ncol, 5); /* in cIGraph_file.c */
rb_define_method(cIGraph, "write_graph_edgelist", cIGraph_write_graph_edgelist, 1); /* in cIGraph_file.c */ rb_define_singleton_method(cIGraph, "read_graph_lgl", cIGraph_read_graph_lgl, 3); /* in cIGraph_file.c */
rb_define_method(cIGraph, "write_graph_graphml", cIGraph_write_graph_graphml, 1); /* in cIGraph_file.c */ rb_define_singleton_method(cIGraph, "read_graph_dimacs", cIGraph_read_graph_dimacs, 2); /* in cIGraph_file.c */
rb_define_method(cIGraph, "write_graph_pajek", cIGraph_write_graph_pajek, 1); /* in cIGraph_file.c */ rb_define_singleton_method(cIGraph, "read_graph_graphdb", cIGraph_read_graph_graphdb, 2); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph, "read_graph_gml", cIGraph_read_graph_gml, 1); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph, "read_graph_pajek", cIGraph_read_graph_pajek, 2); /* in cIGraph_file.c */
//File write
cIGraph_filewrite = rb_define_module_under(cIGraph, "FileWrite");
rb_include_module(cIGraph, cIGraph_filewrite);
rb_define_method(cIGraph, "layout_random", cIGraph_layout_random, 0); /* in cIGraph_layout.c */ rb_define_method(cIGraph_filewrite, "write_graph_edgelist", cIGraph_write_graph_edgelist, 1); /* in cIGraph_file.c */
rb_define_method(cIGraph, "layout_circle", cIGraph_layout_circle, 0); /* in cIGraph_layout.c */ rb_define_method(cIGraph_filewrite, "write_graph_graphml", cIGraph_write_graph_graphml, 1); /* in cIGraph_file.c */
rb_define_method(cIGraph, "layout_fruchterman_reingold", cIGraph_layout_fruchterman_reingold, 6); /* in cIGraph_layout.c */ rb_define_method(cIGraph_filewrite, "write_graph_gml", cIGraph_write_graph_gml, 1); /* in cIGraph_file.c */
rb_define_method(cIGraph, "layout_kamada_kawai", cIGraph_layout_kamada_kawai, 5); /* in cIGraph_layout.c */ rb_define_method(cIGraph_filewrite, "write_graph_ncol", cIGraph_write_graph_ncol, 3); /* in cIGraph_file.c */
rb_define_method(cIGraph, "layout_reingold_tilford", cIGraph_layout_reingold_tilford, 1); /* in cIGraph_layout.c */ rb_define_method(cIGraph_filewrite, "write_graph_lgl", cIGraph_write_graph_lgl, 4); /* in cIGraph_file.c */
rb_define_method(cIGraph, "layout_reingold_tilford_circular", cIGraph_layout_reingold_tilford_circular, 1); /* in cIGraph_layout.c */ rb_define_method(cIGraph_filewrite, "write_graph_dimacs", cIGraph_write_graph_dimacs, 4); /* in cIGraph_file.c */
rb_define_method(cIGraph, "layout_grid_fruchterman_reingold", cIGraph_layout_grid_fruchterman_reingold, 7); /* in cIGraph_layout.c */ rb_define_method(cIGraph_filewrite, "write_graph_pajek", cIGraph_write_graph_pajek, 1); /* in cIGraph_file.c */
rb_define_method(cIGraph, "layout_lgl", cIGraph_layout_lgl, 7); /* in cIGraph_layout.c */
rb_define_method(cIGraph, "layout_random_3d", cIGraph_layout_random_3d, 0); /* in cIGraph_layout3d.c */ //Layouts
rb_define_method(cIGraph, "layout_sphere", cIGraph_layout_sphere, 0); /* in cIGraph_layout3d.c */ cIGraph_layout = rb_define_module_under(cIGraph, "Layout");
rb_define_method(cIGraph, "layout_fruchterman_reingold_3d", cIGraph_layout_fruchterman_reingold_3d, 6); /* in cIGraph_layout3d.c */ rb_include_module(cIGraph, cIGraph_layout);
rb_define_method(cIGraph, "layout_kamada_kawai_3d", cIGraph_layout_kamada_kawai_3d, 5); /* in cIGraph_layout3d.c */
rb_define_method(cIGraph_layout, "layout_random", cIGraph_layout_random, 0); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_circle", cIGraph_layout_circle, 0); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_fruchterman_reingold", cIGraph_layout_fruchterman_reingold, 6); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_kamada_kawai", cIGraph_layout_kamada_kawai, 5); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_reingold_tilford", cIGraph_layout_reingold_tilford, 1); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_reingold_tilford_circular", cIGraph_layout_reingold_tilford_circular, 1); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_grid_fruchterman_reingold", cIGraph_layout_grid_fruchterman_reingold, 7); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_lgl", cIGraph_layout_lgl, 7); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_random_3d", cIGraph_layout_random_3d, 0); /* in cIGraph_layout3d.c */
rb_define_method(cIGraph_layout, "layout_sphere", cIGraph_layout_sphere, 0); /* in cIGraph_layout3d.c */
rb_define_method(cIGraph_layout, "layout_fruchterman_reingold_3d", cIGraph_layout_fruchterman_reingold_3d, 6); /* in cIGraph_layout3d.c */
rb_define_method(cIGraph_layout, "layout_kamada_kawai_3d", cIGraph_layout_kamada_kawai_3d, 5); /* in cIGraph_layout3d.c */
rb_define_singleton_method(cIGraph, "layout_merge_dla", cIGraph_layout_merge_dla, 2); /* in cIGraph_layout.c */ rb_define_singleton_method(cIGraph, "layout_merge_dla", cIGraph_layout_merge_dla, 2); /* in cIGraph_layout.c */
//Min cuts
cIGraph_mincuts = rb_define_module_under(cIGraph, "MinimumCuts");
rb_include_module(cIGraph, cIGraph_mincuts);
rb_define_method(cIGraph_mincuts, "maxflow_value", cIGraph_maxflow_value, 3); /* in cIGraph_min_cuts.c */
rb_define_method(cIGraph_mincuts, "st_mincut_value", cIGraph_st_mincut_value, 3); /* in cIGraph_min_cuts.c */
rb_define_method(cIGraph_mincuts, "mincut_value", cIGraph_mincut_value, 1); /* in cIGraph_min_cuts.c */
rb_define_method(cIGraph_mincuts, "mincut", cIGraph_mincut, 1); /* in cIGraph_min_cuts.c */
//Connectivity
cIGraph_connectivity = rb_define_module_under(cIGraph, "Connectivity");
rb_include_module(cIGraph, cIGraph_connectivity);
rb_define_method(cIGraph_connectivity, "st_edge_connectivity", cIGraph_st_edge_connectivity, 2); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "edge_connectivity", cIGraph_edge_connectivity, 0); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "st_vertex_connectivity", cIGraph_st_vertex_connectivity, 3); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "vertex_connectivity", cIGraph_vertex_connectivity, 0); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "edge_disjoint_paths", cIGraph_edge_disjoint_paths, 2); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "vertex_disjoint_paths", cIGraph_vertex_disjoint_paths, 2); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "adhesion", cIGraph_adhesion, 0); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "cohesion", cIGraph_cohesion, 0); /* in cIGraph_connectivity.c */
//Community
cIGraph_community = rb_define_module_under(cIGraph, "Community");
rb_include_module(cIGraph, cIGraph_community);
rb_define_method(cIGraph_community, "modularity", cIGraph_modularity, 1); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_to_membership", cIGraph_community_to_membership, 2); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_spinglass", cIGraph_community_spinglass, 8); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_spinglass_single", cIGraph_community_spinglass_single, 5); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_leading_eigenvector", cIGraph_community_leading_eigenvector, 1); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_leading_eigenvector_naive", cIGraph_community_leading_eigenvector_naive, 1); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_leading_eigenvector_step", cIGraph_community_leading_eigenvector_step, 2); /* in cIGraph_community.c */ //rb_define_method(cIGraph_community, "community_walktrap", cIGraph_community_walktrap, 2); /* in cIGraph_community.c */
//rb_define_method(cIGraph_community, "community_edge_betweenness", cIGraph_community_edge_betweenness, 1); /* in cIGraph_community.c */
//rb_define_method(cIGraph_community, "community_eb_get_merges", cIGraph_community_eb_get_merges, 1); /* in cIGraph_community.c */
//rb_define_method(cIGraph_community, "community_fastgreedy", cIGraph_community_fastgreedy, 0); /* in cIGraph_community.c */
//Matrix class //Matrix class
cIGraphMatrix = rb_define_class("IGraphMatrix", rb_cObject); cIGraphMatrix = rb_define_class("IGraphMatrix", rb_cObject);

48
ext/cIGraph.h
View File

@ -200,8 +200,17 @@ VALUE cIGraph_motifs_randesu_estimate(VALUE self, VALUE size, VALUE cuts,
//File handling //File handling
VALUE cIGraph_read_graph_edgelist (VALUE self, VALUE file, VALUE mode); VALUE cIGraph_read_graph_edgelist (VALUE self, VALUE file, VALUE mode);
VALUE cIGraph_write_graph_edgelist(VALUE self, VALUE file); VALUE cIGraph_write_graph_edgelist(VALUE self, VALUE file);
VALUE cIGraph_read_graph_ncol (VALUE self, VALUE file, VALUE predefnames, VALUE names, VALUE weights, VALUE directed);
VALUE cIGraph_write_graph_ncol (VALUE self, VALUE file, VALUE names, VALUE weights);
VALUE cIGraph_read_graph_lgl (VALUE self, VALUE file, VALUE names, VALUE weights);
VALUE cIGraph_write_graph_lgl (VALUE self, VALUE file, VALUE names, VALUE weights, VALUE isolates);
VALUE cIGraph_read_graph_dimacs (VALUE self, VALUE file, VALUE directed);
VALUE cIGraph_write_graph_dimacs (VALUE self, VALUE file, VALUE source, VALUE target, VALUE capacity);
VALUE cIGraph_read_graph_graphdb (VALUE self, VALUE file, VALUE directed);
VALUE cIGraph_read_graph_graphml (VALUE self, VALUE file, VALUE index); VALUE cIGraph_read_graph_graphml (VALUE self, VALUE file, VALUE index);
VALUE cIGraph_write_graph_graphml (VALUE self, VALUE file); VALUE cIGraph_write_graph_graphml (VALUE self, VALUE file);
VALUE cIGraph_read_graph_gml (VALUE self, VALUE file);
VALUE cIGraph_write_graph_gml (VALUE self, VALUE file);
VALUE cIGraph_read_graph_pajek (VALUE self, VALUE file); VALUE cIGraph_read_graph_pajek (VALUE self, VALUE file);
VALUE cIGraph_write_graph_pajek (VALUE self, VALUE file); VALUE cIGraph_write_graph_pajek (VALUE self, VALUE file);
@ -260,6 +269,45 @@ VALUE cIGraph_layout_kamada_kawai_3d (VALUE self,
VALUE cIGraph_layout_merge_dla(VALUE self, VALUE graphs, VALUE layouts); VALUE cIGraph_layout_merge_dla(VALUE self, VALUE graphs, VALUE layouts);
//Min cuts
VALUE cIGraph_maxflow_value (VALUE self, VALUE source, VALUE target, VALUE capacity);
VALUE cIGraph_st_mincut_value(VALUE self, VALUE source, VALUE target, VALUE capacity);
VALUE cIGraph_mincut_value (VALUE self, VALUE capacity);
VALUE cIGraph_mincut (VALUE self, VALUE capacity);
//Connectivity
VALUE cIGraph_st_edge_connectivity (VALUE self, VALUE source, VALUE target);
VALUE cIGraph_edge_connectivity (VALUE self);
VALUE cIGraph_st_vertex_connectivity(VALUE self, VALUE source, VALUE target, VALUE neighbours);
VALUE cIGraph_vertex_connectivity (VALUE self);
VALUE cIGraph_edge_disjoint_paths (VALUE self, VALUE source, VALUE target);
VALUE cIGraph_vertex_disjoint_paths (VALUE self, VALUE source, VALUE target);
VALUE cIGraph_adhesion(VALUE self);
VALUE cIGraph_cohesion(VALUE self);
//Community
VALUE cIGraph_modularity (VALUE self, VALUE groups);
VALUE cIGraph_community_to_membership (VALUE self, VALUE merge,
VALUE steps);
VALUE cIGraph_community_spinglass (VALUE self, VALUE weights,
VALUE spins,
VALUE parupdate,
VALUE starttemp,
VALUE stoptemp,
VALUE coolfact,
VALUE update_rule,
VALUE gamma);
VALUE cIGraph_community_spinglass_single (VALUE self, VALUE weights,
VALUE vertex,
VALUE spins,
VALUE update_rule,
VALUE gamma);
VALUE cIGraph_community_leading_eigenvector (VALUE self, VALUE steps);
VALUE cIGraph_community_leading_eigenvector_naive(VALUE self, VALUE steps);
VALUE cIGraph_community_leading_eigenvector_step (VALUE self,
VALUE membership,
VALUE steps);
//Attributes //Attributes
int cIGraph_attribute_init(igraph_t *graph, int cIGraph_attribute_init(igraph_t *graph,
igraph_vector_ptr_t *attr); igraph_vector_ptr_t *attr);

36
ext/cIGraph_attribute_handler.c
View File

@ -497,9 +497,9 @@ igraph_bool_t cIGraph_attribute_has_attr(const igraph_t *graph,
VALUE obj; VALUE obj;
switch (type) { switch (type) {
case IGRAPH_ATTRIBUTE_GRAPH: attrnum=0; break; case IGRAPH_ATTRIBUTE_GRAPH: attrnum = 2; break;
case IGRAPH_ATTRIBUTE_VERTEX: attrnum=1; break; case IGRAPH_ATTRIBUTE_VERTEX: attrnum = 0; break;
case IGRAPH_ATTRIBUTE_EDGE: attrnum=2; break; case IGRAPH_ATTRIBUTE_EDGE: attrnum = 1; break;
default: return 0; break; default: return 0; break;
} }
@ -507,14 +507,14 @@ igraph_bool_t cIGraph_attribute_has_attr(const igraph_t *graph,
if (attrnum != 2) if (attrnum != 2)
obj = RARRAY(obj)->ptr[0]; obj = RARRAY(obj)->ptr[0];
if(rb_funcall(obj,rb_intern("include?"), 1, rb_str_new2(name))){ if(TYPE(obj) == T_HASH && rb_funcall(obj,rb_intern("include?"), 1, rb_str_new2(name))){
res = 1; res = 1;
} }
#ifdef DEBUG #ifdef DEBUG
printf("Leaving cIGraph_attribute_has_attr\n"); printf("Leaving cIGraph_attribute_has_attr\n");
#endif #endif
return res; return res;
} }
@ -533,9 +533,9 @@ int cIGraph_attribute_get_type(const igraph_t *graph,
VALUE val; VALUE val;
switch (elemtype) { switch (elemtype) {
case IGRAPH_ATTRIBUTE_GRAPH: attrnum=0; break; case IGRAPH_ATTRIBUTE_GRAPH: attrnum = 2; break;
case IGRAPH_ATTRIBUTE_VERTEX: attrnum=1; break; case IGRAPH_ATTRIBUTE_VERTEX: attrnum = 0; break;
case IGRAPH_ATTRIBUTE_EDGE: attrnum=2; break; case IGRAPH_ATTRIBUTE_EDGE: attrnum = 1; break;
default: return 0; break; default: return 0; break;
} }
@ -543,7 +543,9 @@ int cIGraph_attribute_get_type(const igraph_t *graph,
if (attrnum != 2) if (attrnum != 2)
obj = RARRAY(obj)->ptr[0]; obj = RARRAY(obj)->ptr[0];
if(rb_funcall(obj,rb_intern("includes"), rb_str_new2(name))){ rb_funcall(obj,rb_intern("include?"), 1, rb_str_new2(name));
if(rb_funcall(obj,rb_intern("include?"), 1, rb_str_new2(name))){
val = rb_hash_aref(obj,rb_str_new2(name)); val = rb_hash_aref(obj,rb_str_new2(name));
if (TYPE(val) == T_STRING){ if (TYPE(val) == T_STRING){
*type = IGRAPH_ATTRIBUTE_STRING; *type = IGRAPH_ATTRIBUTE_STRING;
@ -552,7 +554,9 @@ int cIGraph_attribute_get_type(const igraph_t *graph,
} else { } else {
*type = IGRAPH_ATTRIBUTE_PY_OBJECT; *type = IGRAPH_ATTRIBUTE_PY_OBJECT;
} }
} } else {
*type = IGRAPH_ATTRIBUTE_PY_OBJECT;
}
#ifdef DEBUG #ifdef DEBUG
printf("Leaving cIGraph_attribute_get_type\n"); printf("Leaving cIGraph_attribute_get_type\n");
@ -736,7 +740,7 @@ int cIGraph_get_string_edge_attr(const igraph_t *graph,
#endif #endif
VALUE array = ((VALUE*)graph->attr)[1]; VALUE array = ((VALUE*)graph->attr)[1];
VALUE val, vertex; VALUE val, edge;
igraph_eit_t it; igraph_eit_t it;
int i=0; int i=0;
@ -745,10 +749,16 @@ int cIGraph_get_string_edge_attr(const igraph_t *graph,
IGRAPH_CHECK(igraph_strvector_resize(value, IGRAPH_EIT_SIZE(it))); IGRAPH_CHECK(igraph_strvector_resize(value, IGRAPH_EIT_SIZE(it)));
while(!IGRAPH_EIT_END(it)){ while(!IGRAPH_EIT_END(it)){
vertex = RARRAY(array)->ptr[(int)IGRAPH_EIT_GET(it)]; edge = RARRAY(array)->ptr[(int)IGRAPH_EIT_GET(it)];
val = rb_hash_aref(vertex,rb_str_new2(name));
val = rb_hash_aref(edge,rb_str_new2(name));
if(val == Qnil) if(val == Qnil)
val = rb_str_new2(""); val = rb_str_new2("");
//Fix for floats when required by ncol write
val = rb_funcall(val,rb_intern("to_s"),0);
igraph_strvector_set(value,i,RSTRING(val)->ptr); igraph_strvector_set(value,i,RSTRING(val)->ptr);
IGRAPH_EIT_NEXT(it); IGRAPH_EIT_NEXT(it);
i++; i++;

451
ext/cIGraph_file.c
View File

@ -89,6 +89,414 @@ VALUE cIGraph_write_graph_edgelist(VALUE self, VALUE file){
} }
VALUE cIGraph_read_graph_ncol(VALUE self, VALUE file, VALUE predefnames, VALUE names, VALUE weights, VALUE directed){
VALUE string;
FILE *stream;
VALUE new_graph;
VALUE v_ary;
VALUE e_ary;
VALUE new_ary;
igraph_t *graph;
igraph_strvector_t names_vec;
igraph_bool_t directed_b = 0;
igraph_bool_t weights_b = 0;
igraph_bool_t names_b = 0;
int i;
if(directed)
directed_b = 1;
if(names)
names_b = 1;
if(weights)
weights_b = 1;
new_graph = cIGraph_alloc(cIGraph);
Data_Get_Struct(new_graph, igraph_t, graph);
igraph_strvector_init(&names_vec,RARRAY(predefnames)->len);
for(i=0;i<RARRAY(predefnames)->len;i++){
igraph_strvector_set(&names_vec, i, RSTRING(RARRAY(predefnames)->ptr[i])->ptr);
}
string = rb_funcall(file, rb_intern("read"), 0);
stream = fmemopen(RSTRING(string)->ptr,RSTRING(string)->len, "r");
if (RARRAY(predefnames)->len == 0){
igraph_read_graph_ncol(graph, stream, NULL, names_b, weights_b, directed_b);
} else {
igraph_read_graph_ncol(graph, stream, &names_vec, names_b, weights_b, directed_b);
}
fclose(stream);
//Convert the Hash of names to Strings instead
if(names){
v_ary = ((VALUE*)graph->attr)[0];
new_ary = rb_ary_new();
for(i=0;i<RARRAY(v_ary)->len;i++){
rb_ary_push(new_ary, rb_hash_aref(RARRAY(v_ary)->ptr[i], rb_str_new2("name")));
}
((VALUE*)graph->attr)[0] = new_ary;
}
//Convert the Hash of weights to floats instead
if(weights){
e_ary = ((VALUE*)graph->attr)[1];
new_ary = rb_ary_new();
for(i=0;i<RARRAY(e_ary)->len;i++){
rb_ary_push(new_ary, rb_hash_aref(RARRAY(e_ary)->ptr[i], rb_str_new2("weight")));
}
((VALUE*)graph->attr)[1] = new_ary;
}
igraph_strvector_destroy(&names_vec);
return new_graph;
}
VALUE cIGraph_write_graph_ncol(VALUE self, VALUE file, VALUE names, VALUE weights){
char *buf;
size_t size;
FILE *stream;
igraph_t *graph;
int e, i;
VALUE v_ary;
VALUE e_ary;
VALUE new_v_ary;
VALUE new_e_ary;
VALUE vertex_h;
VALUE edge_h;
char *weights_b = "0";
char *names_b = "0";
if(names)
names_b = "name";
if(weights)
weights_b = "weight";
Data_Get_Struct(self, igraph_t, graph);
//Convert each object to it's String representation and each edge to
//it's Float
if(names){
v_ary = ((VALUE*)graph->attr)[0];
new_v_ary = rb_ary_new();
for(i=0;i<RARRAY(v_ary)->len;i++){
vertex_h = rb_hash_new();
rb_hash_aset(vertex_h, rb_str_new2("name"), StringValue(RARRAY(v_ary)->ptr[i]));
rb_ary_push(new_v_ary, vertex_h);
}
((VALUE*)graph->attr)[0] = new_v_ary;
}
if(weights){
e_ary = ((VALUE*)graph->attr)[1];
new_e_ary = rb_ary_new();
for(i=0;i<RARRAY(e_ary)->len;i++){
edge_h = rb_hash_new();
rb_hash_aset(edge_h, rb_str_new2("weight"), rb_funcall(RARRAY(e_ary)->ptr[i],rb_intern("to_f"),0));
rb_ary_push(new_e_ary, edge_h);
}
((VALUE*)graph->attr)[1] = new_e_ary;
}
stream = open_memstream(&buf,&size);
e = igraph_write_graph_ncol(graph, stream, names_b, weights_b);
fflush(stream);
rb_funcall(file, rb_intern("write"), 1, rb_str_new(buf,size));
fclose(stream);
//Replace initital vertices and edges
if(names){
((VALUE*)graph->attr)[0] = v_ary;
}
if(weights){
((VALUE*)graph->attr)[0] = e_ary;
}
return e;
}
VALUE cIGraph_read_graph_lgl(VALUE self, VALUE file, VALUE names, VALUE weights){
VALUE string;
FILE *stream;
VALUE new_graph;
VALUE v_ary;
VALUE e_ary;
VALUE new_ary;
igraph_t *graph;
igraph_bool_t weights_b = 0;
igraph_bool_t names_b = 0;
int i;
if(names)
names_b = 1;
if(weights)
weights_b = 1;
new_graph = cIGraph_alloc(cIGraph);
Data_Get_Struct(new_graph, igraph_t, graph);
string = rb_funcall(file, rb_intern("read"), 0);
stream = fmemopen(RSTRING(string)->ptr,RSTRING(string)->len, "r");
igraph_read_graph_lgl(graph, stream, names_b, weights_b);
fclose(stream);
//Convert the Hash of names to Strings instead
if(names){
v_ary = ((VALUE*)graph->attr)[0];
new_ary = rb_ary_new();
for(i=0;i<RARRAY(v_ary)->len;i++){
rb_ary_push(new_ary, rb_hash_aref(RARRAY(v_ary)->ptr[i], rb_str_new2("name")));
}
((VALUE*)graph->attr)[0] = new_ary;
}
//Convert the Hash of weights to floats instead
if(weights){
e_ary = ((VALUE*)graph->attr)[1];
new_ary = rb_ary_new();
for(i=0;i<RARRAY(e_ary)->len;i++){
rb_ary_push(new_ary, rb_hash_aref(RARRAY(e_ary)->ptr[i], rb_str_new2("weight")));
}
((VALUE*)graph->attr)[1] = new_ary;
}
return new_graph;
}
VALUE cIGraph_write_graph_lgl(VALUE self, VALUE file, VALUE names, VALUE weights, VALUE isolates){
char *buf;
size_t size;
FILE *stream;
igraph_t *graph;
int e, i;
VALUE v_ary;
VALUE e_ary;
VALUE new_v_ary;
VALUE new_e_ary;
VALUE vertex_h;
VALUE edge_h;
char *weights_b = "0";
char *names_b = "0";
igraph_bool_t isolates_b;
if(names)
names_b = "name";
if(weights)
weights_b = "weight";
if(isolates)
isolates_b = 1;
Data_Get_Struct(self, igraph_t, graph);
//Convert each object to it's String representation and each edge to
//it's Float
if(names){
v_ary = ((VALUE*)graph->attr)[0];
new_v_ary = rb_ary_new();
for(i=0;i<RARRAY(v_ary)->len;i++){
vertex_h = rb_hash_new();
rb_hash_aset(vertex_h, rb_str_new2("name"), StringValue(RARRAY(v_ary)->ptr[i]));
rb_ary_push(new_v_ary, vertex_h);
}
((VALUE*)graph->attr)[0] = new_v_ary;
}
if(weights){
e_ary = ((VALUE*)graph->attr)[1];
new_e_ary = rb_ary_new();
for(i=0;i<RARRAY(e_ary)->len;i++){
edge_h = rb_hash_new();
rb_hash_aset(edge_h, rb_str_new2("weight"), rb_funcall(RARRAY(e_ary)->ptr[i],rb_intern("to_f"),0));
rb_ary_push(new_e_ary, edge_h);
}
((VALUE*)graph->attr)[1] = new_e_ary;
}
stream = open_memstream(&buf,&size);
e = igraph_write_graph_lgl(graph, stream, names_b, weights_b, isolates);
fflush(stream);
rb_funcall(file, rb_intern("write"), 1, rb_str_new(buf,size));
fclose(stream);
//Replace initital vertices and edges
if(names){
((VALUE*)graph->attr)[0] = v_ary;
}
if(weights){
((VALUE*)graph->attr)[0] = e_ary;
}
return e;
}
VALUE cIGraph_read_graph_dimacs(VALUE self, VALUE file, VALUE directed){
VALUE string;
FILE *stream;
VALUE new_graph;
igraph_integer_t source;
igraph_integer_t target;
igraph_vector_t capacity;
igraph_t *graph;
igraph_bool_t directed_b = 0;
igraph_vs_t vs;
igraph_vit_t vit;
VALUE v_ary;
VALUE g_hsh;
int i;
int vid;
if(directed)
directed_b = 1;
igraph_vector_init(&capacity, 0);
new_graph = cIGraph_alloc(cIGraph);
Data_Get_Struct(new_graph, igraph_t, graph);
string = rb_funcall(file, rb_intern("read"), 0);
stream = fmemopen(RSTRING(string)->ptr,RSTRING(string)->len, "r");
igraph_read_graph_dimacs(graph, stream, &source, &target, &capacity, directed_b);
fclose(stream);
igraph_vs_all(&vs);
igraph_vit_create(graph, vs, &vit);
//Push Integer onto vertex array
v_ary = ((VALUE*)graph->attr)[0];
while (!IGRAPH_VIT_END(vit)) {
vid = IGRAPH_VIT_GET(vit);
rb_ary_push(v_ary,INT2NUM(vid));
IGRAPH_VIT_NEXT(vit);
}
g_hsh = ((VALUE*)graph->attr)[2];
rb_hash_aset(g_hsh, rb_str_new2("source"), INT2NUM(source));
rb_hash_aset(g_hsh, rb_str_new2("target"), INT2NUM(target));
rb_hash_aset(g_hsh, rb_str_new2("capacity"), rb_ary_new());
for(i=0;i<igraph_vector_size(&capacity);i++){
rb_ary_push(rb_hash_aref(g_hsh, rb_str_new2("capacity")), rb_float_new(VECTOR(capacity)[i]));
}
igraph_vit_destroy(&vit);
igraph_vs_destroy(&vs);
return new_graph;
}
VALUE cIGraph_write_graph_dimacs(VALUE self, VALUE file, VALUE source, VALUE target, VALUE capacity){
char *buf;
size_t size;
FILE *stream;
igraph_t *graph;
int e, i;
igraph_vector_t capacity_v;
Data_Get_Struct(self, igraph_t, graph);
igraph_vector_init(&capacity_v,0);
for(i=0;i<RARRAY(capacity)->len;i++){
igraph_vector_push_back(&capacity_v,NUM2DBL(RARRAY(capacity)->ptr[i]));
}
stream = open_memstream(&buf,&size);
e = igraph_write_graph_dimacs(graph, stream, NUM2INT(source), NUM2INT(target), &capacity_v);
fflush(stream);
rb_funcall(file, rb_intern("write"), 1, rb_str_new(buf,size));
fclose(stream);
return e;
}
VALUE cIGraph_read_graph_graphdb(VALUE self, VALUE file, VALUE directed){
VALUE string;
FILE *stream;
VALUE new_graph;
VALUE v_ary;
igraph_t *graph;
igraph_bool_t directed_b = 0;
igraph_vs_t vs;
igraph_vit_t vit;
int vid;
if(directed)
directed_b = 1;
new_graph = cIGraph_alloc(cIGraph);
Data_Get_Struct(new_graph, igraph_t, graph);
string = rb_funcall(file, rb_intern("read"), 0);
stream = fmemopen(RSTRING(string)->ptr,RSTRING(string)->len, "r");
igraph_read_graph_graphdb(graph, stream, directed_b);
fclose(stream);
igraph_vs_all(&vs);
igraph_vit_create(graph, vs, &vit);
//Push Integer onto vertex array
v_ary = ((VALUE*)graph->attr)[0];
while (!IGRAPH_VIT_END(vit)) {
vid = IGRAPH_VIT_GET(vit);
rb_ary_push(v_ary,INT2NUM(vid));
IGRAPH_VIT_NEXT(vit);
}
igraph_vit_destroy(&vit);
igraph_vs_destroy(&vs);
return new_graph;
}
/* call-seq: /* call-seq:
* IGraph.read_graph_graphml(file,index) -> IGraph * IGraph.read_graph_graphml(file,index) -> IGraph
* *
@ -155,6 +563,49 @@ VALUE cIGraph_write_graph_graphml(VALUE self, VALUE file){
} }
VALUE cIGraph_read_graph_gml(VALUE self, VALUE file){
VALUE string;
FILE *stream;
VALUE new_graph;
igraph_t *graph;
new_graph = cIGraph_alloc(cIGraph);
Data_Get_Struct(new_graph, igraph_t, graph);
string = rb_funcall(file, rb_intern("read"), 0);
stream = fmemopen(RSTRING(string)->ptr,RSTRING(string)->len, "r");
igraph_read_graph_gml(graph, stream);
fclose(stream);
return new_graph;
}
VALUE cIGraph_write_graph_gml(VALUE self, VALUE file){
char *buf;
size_t size;
FILE *stream;
igraph_t *graph;
int e;
Data_Get_Struct(self, igraph_t, graph);
stream = open_memstream(&buf,&size);
e = igraph_write_graph_gml(graph, stream, NULL, 0);
fflush(stream);
rb_funcall(file, rb_intern("write"), 1, rb_str_new(buf,size));
fclose(stream);
return e;
}
/* call-seq: /* call-seq:
* IGraph.read_graph_pajek(file) -> IGraph * IGraph.read_graph_pajek(file) -> IGraph
* *

190
test/tc_file_read_write.rb
View File

@ -21,6 +21,93 @@ class TestGraph < Test::Unit::TestCase
assert_equal "0 1\n2 3\n", s.read assert_equal "0 1\n2 3\n", s.read
end end
def test_ncol_read
g = nil
assert_nothing_raised{
g = IGraph.read_graph_ncol(StringIO.new("0 1\n2 3\n"),[],
false,false,false)
}
assert_instance_of IGraph, g
assert_equal 4, g.vcount
assert g.are_connected?(0,1)
assert_nothing_raised{
g = IGraph.read_graph_ncol(StringIO.new("A B\nC D\n"),[],
true,false,false)
}
assert_instance_of IGraph, g
assert_equal 4, g.vcount
assert g.are_connected?('A','B')
assert_nothing_raised{
g = IGraph.read_graph_ncol(StringIO.new("A B 1\nC D 2\n"),[],
true,true,false)
}
assert_instance_of IGraph, g
assert_equal 4, g.vcount
assert g.are_connected?('A','B')
assert_equal 1, g['A','B']
end
def test_ncol_write
g = IGraph.new(["A","B","C","D"],true,[1,2])
s = StringIO.new("")
str = g.write_graph_ncol(s,true,true)
s.rewind
assert_equal "A B 1.0\nC D 2.0\n", s.read
end
def test_lgl_read
g = nil
assert_nothing_raised{
g = IGraph.read_graph_lgl(StringIO.new("#A\nB\n#C\nD\n"),
false,false)
}
assert_instance_of IGraph, g
assert_equal 4, g.vcount
assert g.are_connected?(0,1)
assert_nothing_raised{
g = IGraph.read_graph_lgl(StringIO.new("#A\nB 1\n#C\nD 1\n"),
true,true)
}
assert_instance_of IGraph, g
assert_equal 4, g.vcount
assert g.are_connected?('A','B')
assert_equal 1, g['A','B']
end
def test_lgl_write
g = IGraph.new(["A","B","C","D"],true,[1,2])
s = StringIO.new("")
str = g.write_graph_lgl(s,true,true,false)
s.rewind
assert_equal "# A\nB 1.0\n# C\nD 2.0\n", s.read
end
def test_dimacs_read
g = nil
assert_nothing_raised{
s = StringIO.new("c com\np min 4 2\nn 1 s\nn 2 t\na 1 2 1\na 3 4 2\n")
g = IGraph.read_graph_dimacs(s,
false)
}
assert_instance_of IGraph, g
assert_equal 4, g.vcount
assert g.are_connected?(0,1)
assert_equal 0, g.attributes['source']
assert_equal 1, g.attributes['target']
assert_equal [1,2], g.attributes['capacity']
end
def test_dimacs_write
g = IGraph.new(["A","B","C","D"],true,[1,2])
s = StringIO.new("")
str = g.write_graph_dimacs(s,0,1,[1,2])
s.rewind
assert_equal "c created by igraph\np max 4 2\nn 1 s\nn 2 t\na 1 2 1\na 3 4 2\n", s.read
end
def test_graphml_read def test_graphml_read
g = nil g = nil
g = IGraph.read_graph_graphml(StringIO.new(Graphml),0) g = IGraph.read_graph_graphml(StringIO.new(Graphml),0)
@ -46,6 +133,28 @@ class TestGraph < Test::Unit::TestCase
assert_equal Graphml_out, s.read assert_equal Graphml_out, s.read
end end
def test_gml_read
g = IGraph.read_graph_gml(StringIO.new(Gml))
assert_instance_of IGraph, g
end
def test_gml_write
g = IGraph.new([{'id'=>0,'name'=>'a','type' => 4.0},
{'id'=>1,'name'=>'b','type' => 5},
{'id'=>2,'type' => 6},
{'id'=>3,'name'=>'d'}],
true,
[{'eid'=>'e1'},
{'eid'=>'e2'}])
g.attributes['date'] = 'Friday'
s = StringIO.new("")
str = g.write_graph_gml(s)
s.rewind
s = s.read
s = s.split(/\n/)[1..-1].join("\n")
assert_equal Gml_out, s
end
def test_pajek_read_write def test_pajek_read_write
g = nil g = nil
g = IGraph.read_graph_pajek(StringIO.new(Pajek),0) g = IGraph.read_graph_pajek(StringIO.new(Pajek),0)
@ -158,4 +267,85 @@ awing.org/xmlns/1.0/graphml.xsd">
2 3 2 2 3 2
} }
Gml = %q{graph [
comment "This is a sample graph"
directed 1
id 42
label "Hello, I am a graph"
node [
id 1
label "Node 1"
thisIsASampleAttribute 42
]
node [
id 2
label "node 2"
thisIsASampleAttribute 43
]
node [
id 3
label "node 3"
thisIsASampleAttribute 44
]
edge [
source 1
target 2
label "Edge from node 1 to node 2"
]
edge [
source 2
target 3
label "Edge from node 2 to node 3"
]
edge [
source 3
target 1
label "Edge from node 3 to node 1"
]
]
}
Gml_out = %q{Version 1
graph
[
directed 0
date "Friday"
node
[
id 0
name "a"
type 4
]
node
[
id 1
name "b"
type 5
]
node
[
id 2
name ""
type 6
]
node
[
id 3
name "d"
type nan
]
edge
[
source 0
target 1
eid "e1"
]
edge
[
source 2
target 3
eid "e2"
]
]}
end end

3
test/test_all.rb
View File

@ -9,7 +9,9 @@ require 'tc_add_delete'
require 'tc_basic_query' require 'tc_basic_query'
require 'tc_basic_properties' require 'tc_basic_properties'
require 'tc_centrality' require 'tc_centrality'
require 'tc_community'
require 'tc_components' require 'tc_components'
require 'tc_connectivity'
require 'tc_copy' require 'tc_copy'
require 'tc_cores' require 'tc_cores'
require 'tc_dijkstra' require 'tc_dijkstra'
@ -24,6 +26,7 @@ require 'tc_iterators'
require 'tc_layout' require 'tc_layout'
require 'tc_layout3d' require 'tc_layout3d'
require 'tc_matrix' require 'tc_matrix'
require 'tc_mincuts'
require 'tc_motif' require 'tc_motif'
require 'tc_other_ops' require 'tc_other_ops'
require 'tc_randomisation' require 'tc_randomisation'