inline Rcpp::List
RipsDiagArbitDionysusPhat(const RealMatrix & X
, const int maxdimension
, const double maxscale
, const std::string & library
, const bool location
, const bool printProgress
) {
std::vector< std::vector< std::vector< double > > > persDgm;
std::vector< std::vector< std::vector< unsigned > > > persLoc;
std::vector< std::vector< std::vector< std::vector< unsigned > > > > persCycle;
PointContainer points = RcppToStl< PointContainer >(X, true);
//read_points2(infilename, points);
PairDistancesA distances(points);
GeneratorA rips(distances);
GeneratorA::Evaluator size(distances);
FltrRA f;
// Generate 2-skeleton of the Rips complex for epsilon = 50
rips.generate(maxdimension + 1, maxscale, make_push_back_functor(f));
if (printProgress) {
Rprintf("# Generated complex of size: %d \n", f.size());
}
// Sort the simplices with respect to distance
f.sort(GeneratorA::Comparison(distances));
// Compute the persistence diagram of the complex
if (library[0] == 'D') {
computePersistenceDionysus< PersistenceR >(f, size, maxdimension,
Rcpp::NumericVector(X.nrow()), location, printProgress,
persDgm, persLoc, persCycle);
}
if (library[0] == 'P') {
computePersistencePhat(f, size, maxdimension,
Rcpp::NumericVector(X.nrow()), location, printProgress,
persDgm, persLoc);
}
// Output persistent diagram
return Rcpp::List::create(
concatStlToRcpp< Rcpp::NumericMatrix >(persDgm, true, 3),
concatStlToRcpp< Rcpp::NumericMatrix >(persLoc, false, 2),
StlToRcppMatrixList< Rcpp::List, Rcpp::NumericMatrix >(persCycle));
}
