/* call-seq:
* graph.decompose(mode,maxcomp=-1,minelem=1) -> Array
*
* Create separate graph for each component of a graph. Returns an Array
* of new IGraph object. mode specifies whether weakly and strongly connected
* components are returned. Right now only the former is implemented. maxcomp
* limits the number of components returned. Leave at the default -1 to return
* all components. minelements specifies the minimum number of vertices a
* component should contain before it is returned. Default 1 returns all
* components.
*/
VALUE cIGraph_decompose(int argc, VALUE *argv, VALUE self){
igraph_t *graph;
igraph_t *n_graph;
igraph_vector_ptr_t components;
VALUE mode,maxcomp, minelem, components_a;
VALUE n_graph_obj;
int i;
rb_scan_args(argc,argv,"12", &mode, &maxcomp, &minelem);
if(maxcomp == Qnil)
maxcomp = INT2NUM(-1);
if(minelem == Qnil)
minelem = INT2NUM(1);
igraph_vector_ptr_init(&components,0);
Data_Get_Struct(self, igraph_t, graph);
igraph_decompose(graph, &components, NUM2INT(mode), NUM2INT(maxcomp), NUM2INT(minelem));
components_a = rb_ary_new();
for(i=0; i<igraph_vector_ptr_size(&components); i++){
n_graph = VECTOR(components)[i];
n_graph_obj = Data_Wrap_Struct(cIGraph, cIGraph_mark, cIGraph_free, n_graph);
rb_ary_push(components_a,n_graph_obj);
}
igraph_vector_ptr_destroy(&components);
return components_a;
}
void LayoutBuilder::produce(AbstractPetriNetBuilder *builder){
if(!attrTableAttached){
igraph_i_set_attribute_table(&igraph_cattribute_table);
attrTableAttached = true;
}
size_t V = places.size() + transitions.size();
size_t E = inArcs.size() + outArcs.size();
igraph_t graph;
// Create a directed graph
igraph_empty(&graph, V, true);
// Create vector with all edges
igraph_vector_t edges;
igraph_vector_init(&edges, E * 2);
// Add edges to vector
int i = 0;
for(ArcIter it = inArcs.begin(); it != inArcs.end(); it++){
VECTOR(edges)[i++] = numberFromName(it->start);
VECTOR(edges)[i++] = numberFromName(it->end);
}
for(ArcIter it = outArcs.begin(); it != outArcs.end(); it++){
VECTOR(edges)[i++] = numberFromName(it->start);
VECTOR(edges)[i++] = numberFromName(it->end);
}
// Add the edges to graph
igraph_add_edges(&graph, &edges, 0);
// Delete the vector with edges
igraph_vector_destroy(&edges);
// Arrays to store result in
double posx[V];
double posy[V];
// Provide current positions, if they're used at all
if(startFromCurrentPositions){
int i = 0;
for(PlaceIter it = places.begin(); it != places.end(); it++){
posx[i] = it->x;
posy[i] = it->y;
igraph_cattribute_VAN_set(&graph, "id", i, i);
i++;
}
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++){
posx[i] = it->x;
posy[i] = it->y;
igraph_cattribute_VAN_set(&graph, "id", i, i);
i++;
}
}
// Decompose the graph, and layout subgraphs induvidually
igraph_vector_ptr_t subgraphs;
igraph_vector_ptr_init(&subgraphs, 0);
igraph_decompose(&graph, &subgraphs, IGRAPH_WEAK, -1, 0);
// Offset for places subgraphs
double offsetx = 0;
double offsety = 0;
// Layout, translate and extract results for each subgraph
for(int i = 0; i < igraph_vector_ptr_size(&subgraphs); i++){
//Get the subgraph
igraph_t* subgraph = (igraph_t*)VECTOR(subgraphs)[i];
// Allocate result matrix
igraph_matrix_t sublayout;
igraph_matrix_init(&sublayout, 0, 0);
// Vertex selector and iterator
igraph_vs_t vs;
igraph_vit_t vit;
// Select all and create iterator
igraph_vs_all(&vs);
igraph_vit_create(subgraph, vs, &vit);
// Initialize sublayout, using original positions
if(startFromCurrentPositions){
// Count vertices
int vertices = 0;
// Iterator over vertices to count them, hacked but it works
while(!IGRAPH_VIT_END(vit)){
vertices++;
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
// Resize sublayout
igraph_matrix_resize(&sublayout, vertices, 2);
// Iterator over vertices
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
int index = (int)igraph_cattribute_VAN(subgraph, "id", subindex);
MATRIX(sublayout, subindex, 0) = posx[index];
MATRIX(sublayout, subindex, 1) = posy[index];
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
}
igraph_layout_kamada_kawai(subgraph, &sublayout, 1000, ((double)V)/4.0, 10, 0.99, V*V, startFromCurrentPositions);
// Other layout algorithms with reasonable parameters
//igraph_layout_kamada_kawai(subgraph, &sublayout, 1000, ((double)V)/4.0, 10, 0.99, V*V, startFromCurrentPositions);
//igraph_layout_grid_fruchterman_reingold(subgraph, &sublayout, 500, V, V*V, 1.5, V*V*V, V*V/4, startFromCurrentPositions);
//igraph_layout_fruchterman_reingold(subgraph, &sublayout, 500, V, V*V, 1.5, V*V*V, startFromCurrentPositions, NULL);
//igraph_layout_lgl(subgraph, &sublayout, 150, V, V*V, 1.5, V*V*V, sqrt(V), -1);
//Find min and max values:
double minx = DBL_MAX,
miny = DBL_MAX,
maxx = -DBL_MAX,
maxy = -DBL_MAX;
//Iterator over all vertices
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
double x = MATRIX(sublayout, subindex, 0) * factor;
double y = MATRIX(sublayout, subindex, 1) * factor;
minx = minx < x ? minx : x;
miny = miny < y ? miny : y;
maxx = maxx > x ? maxx : x;
maxy = maxy > y ? maxy : y;
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
// Compute translation
double tx = margin - minx;
double ty = margin - miny;
// Decide whether to put it below or left of current content
if(maxx - minx + offsetx < maxy - miny + offsety){
tx += offsetx;
offsetx += maxx - minx + margin;
if(offsety < maxy - miny + margin)
offsety = maxy - miny + margin;
}else{
ty += offsety;
offsety += maxy - miny + margin;
if(offsetx < maxx - minx + margin)
offsetx = maxx - minx + margin;
}
// Translate and extract results
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
int index = (int)igraph_cattribute_VAN(subgraph, "id", subindex);
double x = MATRIX(sublayout, subindex, 0) * factor;
double y = MATRIX(sublayout, subindex, 1) * factor;
posx[index] = x + tx;
posy[index] = y + ty;
IGRAPH_VIT_NEXT(vit);
}
// Destroy iterator and selector
igraph_vit_destroy(&vit);
igraph_vs_destroy(&vs);
// Destroy the sublayout
igraph_matrix_destroy(&sublayout);
// Destroy subgraph
igraph_destroy(subgraph);
free(VECTOR(subgraphs)[i]);
}
// Remove the attributes
igraph_cattribute_remove_v(&graph, "id");
// Destroy the graph
igraph_destroy(&graph);
// Insert results
i = 0;
for(PlaceIter it = places.begin(); it != places.end(); it++){
it->x = posx[i];
it->y = posy[i];
i++;
}
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++){
it->x = posx[i];
it->y = posy[i];
i++;
}
// Produce variables
for(VarIter it = vars.begin(); it != vars.end(); it++)
builder->addVariable(it->name, it->initialValue, it->range);
for(BoolVarIter it = boolVars.begin(); it != boolVars.end(); it++)
builder->addBoolVariable(it->name, it->initialValue);
for(PlaceIter it = places.begin(); it != places.end(); it++)
builder->addPlace(it->name, it->tokens, it->x, it->y);
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++)
builder->addTransition(it->name, it->conditions, it->assignments, it->x, it->y);
for(ArcIter it = inArcs.begin(); it != inArcs.end(); it++)
builder->addInputArc(it->start, it->end, it->weight);
for(ArcIter it = outArcs.begin(); it != outArcs.end(); it++)
builder->addInputArc(it->start, it->end, it->weight);
//Reset builder state (just in case some idoit decides to reuse it!
vars.clear();
boolVars.clear();
places.clear();
transitions.clear();
inArcs.clear();
outArcs.clear();
}
int main(int argc, char** argv) {
int response;
igraph_t graph;
igraph_vector_ptr_t complist;
iclust_collection * collection = NULL;
time_t time_start, time_end;
/* turn on attribute handling */
igraph_i_set_attribute_table(&igraph_cattribute_table);
double minimal_weight;
unsigned int maximal_steps_delimieter;
char graphncol[1024], logconfig[1024];
Config *cfg = ConfigNew();
const char * configuration = getopt_configfile(argc, argv, "./graphtocluster.conf");
massert((ConfigReadFile(configuration, &cfg) == CONFIG_OK), "Configuration file is not readable");
ConfigReadString(cfg, "sources", "graphncol", graphncol, sizeof(graphncol), 0);
ConfigReadString(cfg, "sources", "logconfig", logconfig, sizeof(logconfig), 0);
ConfigReadDouble(cfg, "limits", "minimal_weight", &minimal_weight, 0);
ConfigReadUnsignedInt(cfg, "limits", "maximal_steps_delimieter", &maximal_steps_delimieter, 1);
massert((maximal_steps_delimieter > 0), "Delimiter can not be equal to zero");
ConfigFree(cfg);
logger_init(logconfig, "graphtocluster");
logger_info("File:\t configuration %s", configuration);
logger_info("File:\t configuration logger %s", logconfig);
logger_info("File:\t ncol graph source %s", graphncol);
logger_info("Min:\t edge weight %f", minimal_weight);
logger_info("Max:\t step delimeter %u", maximal_steps_delimieter);
FILE *graph_source = fopen(graphncol, "r");
response = igraph_read_graph_ncol(&graph, graph_source, NULL, true, IGRAPH_ADD_WEIGHTS_YES, 0);
massert((response == IGRAPH_SUCCESS), "Can not read a graph");
logger_info("Count:\t edges at start: %d", igraph_ecount(&graph));
fclose(graph_source);
time(&time_start);
igraph_edges_remove_by(&graph, "weight", minimal_weight, double_lt);
time(&time_end);
logger_info("Time:\t remove edges: %f", difftime(time_end, time_start));
logger_info("Count:\t edges after remove: %d", igraph_ecount(&graph));
response = igraph_vector_ptr_init(&complist, 0);
massert((response == IGRAPH_SUCCESS), "Can not initialize vector pointer");
response = igraph_decompose(&graph, &complist, IGRAPH_WEAK, -1, 0);
massert((response == IGRAPH_SUCCESS), "Can not decompose graph");
unsigned int n = igraph_vector_ptr_size(&complist);
collection = iclust_collection_new();
massert((collection != NULL), "Cluster collection object can not be empty");
time(&time_start);
for (unsigned int i = 0; i < n; i++) {
igraph_t *subgraph = VECTOR(complist)[i];
massert((subgraph != NULL), "Subgraph object can not be empty");
iclust_collection_fill_leading_eigenvector(collection, subgraph, (i + 1), maximal_steps_delimieter);
igraph_destroy(subgraph);
}
time(&time_end);
logger_info("Time:\t cluster: %f", difftime(time_end, time_start));
/* Sort collection by cluster id to be
* able to build a second column correct*/
time(&time_start);
iclust_collection_sort(collection);
time(&time_end);
logger_info("Time:\t cluster sorting: %f", difftime(time_end, time_start));
unsigned long cluster_index = 1, cluster = 0;
for (unsigned long i = 0; i < collection->length; i++) {
iclust_collection_element * element = collection->collection[i];
massert((element != NULL), "Cluster collection element object can not be empty");
if (element->cluster != cluster) {
cluster = element->cluster;
cluster_index = 0;
}
printf("%lu\t%lu\t%s\n", cluster, ++cluster_index, element->name);
}
iclust_collection_destroy(collection);
igraph_vector_ptr_destroy(&complist);
igraph_destroy(&graph);
logger_destroy();
return EXIT_SUCCESS;
}
