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-rw-r--r--src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp127
1 files changed, 82 insertions, 45 deletions
diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
index a4ecf9da..293170f7 100644
--- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
@@ -20,6 +20,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
+#include <boost/program_options.hpp>
#include <boost/variant.hpp>
#include <gudhi/Simplex_tree.h>
@@ -42,7 +43,7 @@
#include <vector>
#include <cstdlib>
-#include "../utilities/alpha_complex_3d_helper.h"
+#include "alpha_complex_3d_helper.h"
// Traits
using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
@@ -60,10 +61,10 @@ using Weighted_point_3 = Gt::Weighted_point;
// filtration with alpha values needed type definition
using Alpha_value_type = Alpha_shape_3::FT;
using Object = CGAL::Object;
-using Dispatch = CGAL::Dispatch_output_iterator<
- CGAL::cpp11::tuple<Object, Alpha_value_type>,
- CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
- std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Dispatch =
+ CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
+ CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
+ std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
using Cell_handle = Alpha_shape_3::Cell_handle;
using Facet = Alpha_shape_3::Facet;
using Edge_3 = Alpha_shape_3::Edge;
@@ -74,48 +75,38 @@ using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = ST::Filtration_value;
using Simplex_tree_vertex = ST::Vertex_handle;
-using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >;
+using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<
- ST, Gudhi::persistent_cohomology::Field_Zp >;
-
-void usage(char * const progName) {
- std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_weight_file coeff_field_characteristic[integer " <<
- "> 0] min_persistence[float >= -1.0]\n";
- std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n";
- std::cerr << " path_to_weight_file is the path to the weights of your points cloud (one value per line.)\n";
- std::cerr << " Weights values are explained on CGAL documentation:\n";
- std::cerr << " https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0\n";
- std::cerr << " https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation\n";
- exit(-1);
-}
+using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
+using Persistent_cohomology =
+ Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
-int main(int argc, char * const argv[]) {
- // program args management
- if (argc != 5) {
- std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
- usage(argv[0]);
- }
+void program_options(int argc, char *argv[], std::string &off_file_points, std::string &weight_file,
+ std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence);
- int coeff_field_characteristic = atoi(argv[3]);
- Filtration_value min_persistence = strtof(argv[4], nullptr);
+int main(int argc, char **argv) {
+ std::string off_file_points;
+ std::string weight_file;
+ std::string output_file_diag;
+ int coeff_field_characteristic;
+ Filtration_value min_persistence;
+
+ program_options(argc, argv, off_file_points, weight_file, output_file_diag, coeff_field_characteristic,
+ min_persistence);
- // Read points from file
- std::string offInputFile(argv[1]);
// Read the OFF file (input file name given as parameter) and triangulate points
- Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
+ Gudhi::Points_3D_off_reader<Point_3> off_reader(off_file_points);
// Check the read operation was correct
if (!off_reader.is_valid()) {
- std::cerr << "Unable to read file " << offInputFile << std::endl;
- usage(argv[0]);
+ std::cerr << "Unable to read OFF file " << off_file_points << std::endl;
+ exit(-1);
}
// Retrieve the triangulation
std::vector<Point_3> lp = off_reader.get_point_cloud();
// Read weights information from file
- std::ifstream weights_ifstr(argv[2]);
+ std::ifstream weights_ifstr(weight_file);
std::vector<Weighted_point_3> wp;
if (weights_ifstr.good()) {
double weight = 0.0;
@@ -127,12 +118,12 @@ int main(int argc, char * const argv[]) {
index++;
}
if (index != lp.size()) {
- std::cerr << "Bad number of weights in file " << argv[2] << std::endl;
- usage(argv[0]);
+ std::cerr << "Bad number of weights in file " << weight_file << std::endl;
+ exit(-1);
}
} else {
- std::cerr << "Unable to read file " << argv[2] << std::endl;
- usage(argv[0]);
+ std::cerr << "Unable to read weights file " << weight_file << std::endl;
+ exit(-1);
}
// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
@@ -167,29 +158,29 @@ int main(int argc, char * const argv[]) {
Filtration_value filtration_max = 0.0;
for (auto object_iterator : the_objects) {
// Retrieve Alpha shape vertex list from object
- if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+ if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
count_cells++;
if (dim_max < 3) {
// Cell is of dim 3
dim_max = 3;
}
- } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
+ } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
vertex_list = from_facet<Vertex_list, Facet>(*facet);
count_facets++;
if (dim_max < 2) {
// Facet is of dim 2
dim_max = 2;
}
- } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+ } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
count_edges++;
if (dim_max < 1) {
// Edge_3 is of dim 1
dim_max = 1;
}
- } else if (const Alpha_shape_3::Vertex_handle * vertex =
- CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
+ } else if (const Alpha_shape_3::Vertex_handle *vertex =
+ CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
count_vertices++;
vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
}
@@ -215,7 +206,7 @@ int main(int argc, char * const argv[]) {
}
}
// Construction of the simplex_tree
- Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
+ Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator);
#ifdef DEBUG_TRACES
std::cout << "filtration = " << filtr << std::endl;
#endif // DEBUG_TRACES
@@ -236,7 +227,6 @@ int main(int argc, char * const argv[]) {
std::cout << "facets \t\t" << count_facets << std::endl;
std::cout << "cells \t\t" << count_cells << std::endl;
-
std::cout << "Information of the Simplex Tree: " << std::endl;
std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " ";
std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
@@ -265,3 +255,50 @@ int main(int argc, char * const argv[]) {
return 0;
}
+
+void program_options(int argc, char *argv[], std::string &off_file_points, std::string &weight_file,
+ std::string &output_file_diag, int &coeff_field_characteristic,
+ Filtration_value &min_persistence) {
+ namespace po = boost::program_options;
+ po::options_description hidden("Hidden options");
+ hidden.add_options()("input-file", po::value<std::string>(&off_file_points),
+ "Name of file containing a point set. Format is one point per line: X1 ... Xd ")(
+ "weight-file", po::value<std::string>(&weight_file),
+ "Name of file containing a point weights. Format is one weigt per line: W1\n...\nWn ");
+
+ po::options_description visible("Allowed options", 100);
+ visible.add_options()("help,h", "produce help message")(
+ "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
+ "Name of file in which the persistence diagram is written. Default print in std::cout")(
+ "field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
+ "Characteristic p of the coefficient field Z/pZ for computing homology.")(
+ "min-persistence,m", po::value<Filtration_value>(&min_persistence),
+ "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
+ "intervals");
+
+ po::positional_options_description pos;
+ pos.add("input-file", 1);
+ pos.add("weight-file", 2);
+
+ po::options_description all;
+ all.add(visible).add(hidden);
+
+ po::variables_map vm;
+ po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
+ po::notify(vm);
+
+ if (vm.count("help") || !vm.count("input-file") || !vm.count("weight-file")) {
+ std::cout << std::endl;
+ std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+ std::cout << "of a weighted 3D Alpha complex defined on a set of input points.\n \n";
+ std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+ std::cout << " p dim b d \n";
+ std::cout << "where dim is the dimension of the homological feature,\n";
+ std::cout << "b and d are respectively the birth and death of the feature and \n";
+ std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+ std::cout << "Usage: " << argv[0] << " [options] input-file weight-file" << std::endl << std::endl;
+ std::cout << visible << std::endl;
+ std::abort();
+ }
+}
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