void get_segmentation(em::DensityMap *dmap, double apix,
double density_threshold, int num_means,
const std::string pdb_filename,
const std::string cmm_filename,
const std::string seg_filename,
const std::string txt_filename) {
IMP_LOG_VERBOSE("start setting trn_em" << std::endl);
IMP_NEW(DensityDataPoints, ddp, (dmap, density_threshold));
IMP_LOG_VERBOSE("initialize calculation of initial centers" << std::endl);
statistics::internal::VQClustering vq(ddp, num_means);
vq.run();
DataPointsAssignment assignment(ddp, &vq);
AnchorsData ad(assignment.get_centers(), *(assignment.get_edges()));
multifit::write_pdb(pdb_filename, assignment);
// also write cmm string into a file:
if (cmm_filename != "") {
write_cmm(cmm_filename, "anchor_graph", ad);
}
if (seg_filename != "") {
write_segments_as_mrc(dmap, assignment, apix, apix, density_threshold,
seg_filename);
}
if (txt_filename != "") {
write_txt(txt_filename, ad);
}
}
void Manifold::write_txt(const char* filename, bool MMA) const {
ofstream file;
file.open(filename, ios::out);
if (file.fail())
ibex_error("[manifold]: cannot create output file.\n");
// character to separate elements in a list
char s=MMA? ',' : ' ';
// character that ends a list
//char e=MMA? ' ' : '}';
if (MMA) file << "{{";
file << n << s << m << s << nb_ineq;
if (MMA) file << "},"; else file << '\n';
file << status;
if (MMA) file << ",{"; else file << '\n';
file << inner.size() << s << boundary.size() << s << unknown.size() << s << pending.size();
if (MMA) file << "},{"; else file << '\n';
file << time << s << nb_cells;
if (MMA) file << "}"; else file << '\n';
if (MMA) file << ",{";
bool first_sol=true;
for (vector<SolverOutputBox>::const_iterator it=inner.begin(); it!=inner.end(); it++) {
if (!first_sol && MMA) file << ','; else first_sol=false;
write_txt(file,*it,MMA);
}
for (vector<SolverOutputBox>::const_iterator it=boundary.begin(); it!=boundary.end(); it++) {
if (!first_sol && MMA) file << ','; else first_sol=false;
write_txt(file,*it,MMA);
}
for (vector<SolverOutputBox>::const_iterator it=unknown.begin(); it!=unknown.end(); it++) {
if (!first_sol && MMA) file << ','; else first_sol=false;
write_txt(file,*it,MMA);
}
for (vector<SolverOutputBox>::const_iterator it=pending.begin(); it!=pending.end(); it++) {
if (!first_sol && MMA) file << ','; else first_sol=false;
write_txt(file,*it,MMA);
}
if (MMA) file << '}';
if (MMA) file << "}\n";
file.close();
}
