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-rw-r--r--src/Alpha_complex/utilities/CMakeLists.txt124
-rw-r--r--src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp35
-rw-r--r--src/Alpha_complex/utilities/alpha_complex_persistence.cpp182
-rw-r--r--src/Alpha_complex/utilities/alphacomplex.md11
4 files changed, 228 insertions, 124 deletions
diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index 5295f3cd..303bd0a6 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -1,58 +1,82 @@
project(Alpha_complex_utilities)
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
- add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
- target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
- if (TBB_FOUND)
- target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
- endif(TBB_FOUND)
- add_test(NAME Alpha_complex_utilities_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45")
-
- install(TARGETS alpha_complex_persistence DESTINATION bin)
-
- add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
- target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
- if (TBB_FOUND)
- target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
- endif(TBB_FOUND)
-
- add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
- "-p" "2" "-m" "0.45" "-o" "safe.pers")
-
- add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
- "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e")
-
- add_test(NAME Alpha_complex_utilities_safe_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
- "-p" "2" "-m" "0.45" "-o" "fast.pers" "-f")
-
- if (DIFF_PATH)
- add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH}
- "exact.pers" "safe.pers")
- add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH}
- "fast.pers" "safe.pers")
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
+ if (TARGET Boost::program_options)
+ add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
+ target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options)
+
+ if (TBB_FOUND)
+ target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
+ endif(TBB_FOUND)
+ add_test(NAME Alpha_complex_utilities_safe_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "safe.pers")
+ add_test(NAME Alpha_complex_utilities_fast_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "fast.pers" "-f")
+ add_test(NAME Alpha_complex_utilities_exact_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e")
+ if (DIFF_PATH)
+ add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH}
+ "exact.pers" "safe.pers")
+ set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS
+ "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence")
+
+ add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH}
+ "fast.pers" "safe.pers")
+ set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS
+ "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence")
+ endif()
+
+ install(TARGETS alpha_complex_persistence DESTINATION bin)
endif()
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
+
+if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+ if (TARGET Boost::program_options)
+ add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
+ target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options)
+ if (TBB_FOUND)
+ target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
+ endif(TBB_FOUND)
- add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off"
- "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt"
- "-p" "2" "-m" "0")
+ add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
+ "-p" "2" "-m" "0.45" "-o" "safe_3d.pers")
- add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off"
- "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights"
- "-p" "2" "-m" "0")
+ add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
+ "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e")
- add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off"
- "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights"
- "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt"
- "-p" "2" "-m" "0" "-e")
+ add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
+ "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f")
- install(TARGETS alpha_complex_3d_persistence DESTINATION bin)
+ if (DIFF_PATH)
+ add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH}
+ "exact_3d.pers" "safe_3d.pers")
+ set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS
+ "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d")
+ add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH}
+ "fast_3d.pers" "safe_3d.pers")
+ set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS
+ "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d")
+ endif()
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+ add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off"
+ "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt"
+ "-p" "2" "-m" "0")
+
+ add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off"
+ "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights"
+ "-p" "2" "-m" "0")
+
+ add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off"
+ "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights"
+ "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt"
+ "-p" "2" "-m" "0" "-e")
+
+ install(TARGETS alpha_complex_3d_persistence DESTINATION bin)
+ endif()
+endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 2272576e..e65d8c6f 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -62,9 +62,9 @@ bool read_cuboid_file(const std::string &cuboid_file, double &x_min, double &y_m
}
template <typename AlphaComplex3d>
-std::vector<typename AlphaComplex3d::Point_3> read_off(const std::string &off_file_points) {
+std::vector<typename AlphaComplex3d::Bare_point_3> read_off(const std::string &off_file_points) {
// Read the OFF file (input file name given as parameter) and triangulate points
- Gudhi::Points_3D_off_reader<typename AlphaComplex3d::Point_3> off_reader(off_file_points);
+ Gudhi::Points_3D_off_reader<typename AlphaComplex3d::Bare_point_3> off_reader(off_file_points);
// Check the read operation was correct
if (!off_reader.is_valid()) {
std::cerr << "Unable to read OFF file " << off_file_points << std::endl;
@@ -222,10 +222,7 @@ int main(int argc, char **argv) {
break;
}
- // Sort the simplices in the order of the filtration
- simplex_tree.initialize_filtration();
-
- std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
+ std::clog << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
// Compute the persistence diagram of the complex
Persistent_cohomology pcoh(simplex_tree, true);
// initializes the coefficient field for homology
@@ -237,7 +234,7 @@ int main(int argc, char **argv) {
if (output_file_diag.empty()) {
pcoh.output_diagram();
} else {
- std::cout << "Result in file: " << output_file_diag << std::endl;
+ std::clog << "Result in file: " << output_file_diag << std::endl;
std::ofstream out(output_file_diag);
pcoh.output_diagram(out);
out.close();
@@ -266,7 +263,7 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
"cuboid-file,c", po::value<std::string>(&cuboid_file),
"Name of file describing the periodic domain. Format is:\n min_hx min_hy min_hz\n max_hx max_hy max_hz")(
"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")(
+ "Name of file in which the persistence diagram is written. Default print in standard output")(
"max-alpha-square-value,r",
po::value<Filtration_value>(&alpha_square_max_value)
->default_value(std::numeric_limits<Filtration_value>::infinity()),
@@ -288,18 +285,18 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
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 3D Alpha complex defined on a set of input points.\n";
- std::cout << "3D Alpha complex can be safe (by default) exact or fast, weighted and/or periodic\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.\n\n";
+ std::clog << std::endl;
+ std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
+ std::clog << "of a 3D Alpha complex defined on a set of input points.\n";
+ std::clog << "3D Alpha complex can be safe (by default) exact or fast, weighted and/or periodic\n\n";
+ std::clog << "The output diagram contains one bar per line, written with the convention: \n";
+ std::clog << " p dim b d \n";
+ std::clog << "where dim is the dimension of the homological feature,\n";
+ std::clog << "b and d are respectively the birth and death of the feature and \n";
+ std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients.\n\n";
- std::cout << "Usage: " << argv[0] << " [options] input-file weight-file\n\n";
- std::cout << visible << std::endl;
+ std::clog << "Usage: " << argv[0] << " [options] input-file weight-file\n\n";
+ std::clog << visible << std::endl;
exit(-1);
}
}
diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
index fab7bd30..29edbd8e 100644
--- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
@@ -11,76 +11,144 @@
#include <boost/program_options.hpp>
#include <CGAL/Epick_d.h>
+#include <CGAL/Epeck_d.h>
#include <gudhi/Alpha_complex.h>
#include <gudhi/Persistent_cohomology.h>
// to construct a simplex_tree from alpha complex
#include <gudhi/Simplex_tree.h>
+#include <gudhi/Points_off_io.h>
#include <iostream>
#include <string>
#include <limits> // for numeric_limits
+#include <vector>
+#include <fstream>
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
-void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
- Filtration_value &alpha_square_max_value, int &coeff_field_characteristic,
- Filtration_value &min_persistence);
+void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast,
+ std::string &weight_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value,
+ int &coeff_field_characteristic, Filtration_value &min_persistence);
+
+template<class Point_d>
+std::vector<Point_d> read_off(const std::string &off_file_points) {
+ Gudhi::Points_off_reader<Point_d> off_reader(off_file_points);
+ if (!off_reader.is_valid()) {
+ std::cerr << "Alpha_complex - Unable to read file " << off_file_points << "\n";
+ exit(-1); // ----- >>
+ }
+ return off_reader.get_point_cloud();
+}
+
+std::vector<double> read_weight_file(const std::string &weight_file) {
+ std::vector<double> weights;
+ // Read weights information from file
+ std::ifstream weights_ifstr(weight_file);
+ if (weights_ifstr.good()) {
+ double weight = 0.0;
+ // Attempt read the weight in a double format, return false if it fails
+ while (weights_ifstr >> weight) {
+ weights.push_back(weight);
+ }
+ } else {
+ std::cerr << "Unable to read weights file " << weight_file << std::endl;
+ exit(-1);
+ }
+ return weights;
+}
+
+template<class Kernel>
+Simplex_tree create_simplex_tree(const std::string &off_file_points, const std::string &weight_file,
+ bool exact_version, Filtration_value alpha_square_max_value) {
+ Simplex_tree stree;
+ auto points = read_off<typename Kernel::Point_d>(off_file_points);
+
+ if (weight_file != std::string()) {
+ std::vector<double> weights = read_weight_file(weight_file);
+ if (points.size() != weights.size()) {
+ std::cerr << "Alpha_complex - Inconsistency between number of points (" << points.size()
+ << ") and number of weights (" << weights.size() << ")" << "\n";
+ exit(-1); // ----- >>
+ }
+ // Init of an alpha complex from an OFF file
+ Gudhi::alpha_complex::Alpha_complex<Kernel, true> alpha_complex_from_file(points, weights);
+
+ if (!alpha_complex_from_file.create_complex(stree, alpha_square_max_value, exact_version)) {
+ std::cerr << "Alpha complex simplicial complex creation failed." << std::endl;
+ exit(-1);
+ }
+ } else {
+ // Init of an alpha complex from an OFF file
+ Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(points);
+
+ if (!alpha_complex_from_file.create_complex(stree, alpha_square_max_value, exact_version)) {
+ std::cerr << "Alpha complex simplicial complex creation failed." << std::endl;
+ exit(-1);
+ }
+ }
+ return stree;
+}
int main(int argc, char **argv) {
+ std::string weight_file;
std::string off_file_points;
std::string output_file_diag;
+ bool exact_version = false;
+ bool fast_version = false;
Filtration_value alpha_square_max_value;
int coeff_field_characteristic;
Filtration_value min_persistence;
- program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic,
- min_persistence);
+ program_options(argc, argv, off_file_points, exact_version, fast_version, weight_file, output_file_diag,
+ alpha_square_max_value, coeff_field_characteristic, min_persistence);
+ if ((exact_version) && (fast_version)) {
+ std::cerr << "You cannot set the exact and the fast version." << std::endl;
+ exit(-1);
+ }
+
+ Simplex_tree stree;
+ if (fast_version) {
+ // WARNING : CGAL::Epick_d is fast but not safe (unlike CGAL::Epeck_d)
+ // (i.e. when the points are on a grid)
+ using Fast_kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+ stree = create_simplex_tree<Fast_kernel>(off_file_points, weight_file, exact_version, alpha_square_max_value);
+ } else {
+ using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
+ stree = create_simplex_tree<Kernel>(off_file_points, weight_file, exact_version, alpha_square_max_value);
+ }
// ----------------------------------------------------------------------------
- // Init of an alpha complex from an OFF file
+ // Display information about the alpha complex
// ----------------------------------------------------------------------------
- using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
- Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);
-
- Simplex_tree simplex;
- if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
- // ----------------------------------------------------------------------------
- // Display information about the alpha complex
- // ----------------------------------------------------------------------------
- std::cout << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices()
- << " simplices - " << simplex.num_vertices() << " vertices." << std::endl;
-
- // Sort the simplices in the order of the filtration
- simplex.initialize_filtration();
-
- std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
- // Compute the persistence diagram of the complex
- Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh(
- simplex);
- // initializes the coefficient field for homology
- pcoh.init_coefficients(coeff_field_characteristic);
-
- pcoh.compute_persistent_cohomology(min_persistence);
-
- // Output the diagram in filediag
- if (output_file_diag.empty()) {
- pcoh.output_diagram();
- } else {
- std::cout << "Result in file: " << output_file_diag << std::endl;
- std::ofstream out(output_file_diag);
- pcoh.output_diagram(out);
- out.close();
- }
+ std::clog << "Simplicial complex is of dimension " << stree.dimension() << " - " << stree.num_simplices()
+ << " simplices - " << stree.num_vertices() << " vertices." << std::endl;
+
+ std::clog << "Simplex_tree dim: " << stree.dimension() << std::endl;
+ // Compute the persistence diagram of the complex
+ Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh(
+ stree);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(coeff_field_characteristic);
+
+ pcoh.compute_persistent_cohomology(min_persistence);
+
+ // Output the diagram in filediag
+ if (output_file_diag.empty()) {
+ pcoh.output_diagram();
+ } else {
+ std::clog << "Result in file: " << output_file_diag << std::endl;
+ std::ofstream out(output_file_diag);
+ pcoh.output_diagram(out);
+ out.close();
}
-
return 0;
}
-void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
- Filtration_value &alpha_square_max_value, int &coeff_field_characteristic,
- Filtration_value &min_persistence) {
+void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast,
+ std::string &weight_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value,
+ 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),
@@ -88,8 +156,14 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std::
po::options_description visible("Allowed options", 100);
visible.add_options()("help,h", "produce help message")(
+ "exact,e", po::bool_switch(&exact),
+ "To activate exact version of Alpha complex (default is false, not available if fast is set)")(
+ "fast,f", po::bool_switch(&fast),
+ "To activate fast version of Alpha complex (default is false, not available if exact is set)")(
+ "weight-file,w", po::value<std::string>(&weight_file)->default_value(std::string()),
+ "Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")(
"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")(
+ "Name of file in which the persistence diagram is written. Default print in standard output")(
"max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value)
->default_value(std::numeric_limits<Filtration_value>::infinity()),
"Maximal alpha square value for the Alpha complex construction.")(
@@ -110,17 +184,17 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std::
po::notify(vm);
if (vm.count("help") || !vm.count("input-file")) {
- std::cout << std::endl;
- std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
- std::cout << "of an 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" << std::endl << std::endl;
- std::cout << visible << std::endl;
+ std::clog << std::endl;
+ std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
+ std::clog << "of an Alpha complex defined on a set of input points.\n \n";
+ std::clog << "The output diagram contains one bar per line, written with the convention: \n";
+ std::clog << " p dim b d \n";
+ std::clog << "where dim is the dimension of the homological feature,\n";
+ std::clog << "b and d are respectively the birth and death of the feature and \n";
+ std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+ std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+ std::clog << visible << std::endl;
exit(-1);
}
}
diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index fcd16a3b..1e3b8fab 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -46,6 +46,11 @@ for the Alpha complex construction.
coefficient field Z/pZ for computing homology.
* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature
to be recorded. Enter a negative value to see zero length intervals.
+* `-w [ --weight-file ]` is the path to the file containing the weights of the
+points (one value per line).
+Default version is not weighted.
+* `-e [ --exact ]` for the exact computation version.
+* `-f [ --fast ]` for the fast computation version.
**Example**
@@ -56,6 +61,10 @@ to be recorded. Enter a negative value to see zero length intervals.
N.B.:
* Filtration values are alpha square values.
+* Weights values are explained on CGAL
+[dD Triangulations](https://doc.cgal.org/latest/Triangulation/index.html)
+and
+[Regular triangulation](https://doc.cgal.org/latest/Triangulation/index.html#TriangulationSecRT) documentation.
## alpha_complex_3d_persistence ##
@@ -122,6 +131,6 @@ N.B.:
* `alpha_complex_3d_persistence` only accepts OFF files in dimension 3.
* Filtration values are alpha square values.
* Weights values are explained on CGAL
-[Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0)
+[Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#Alpha_shapes_3Definitions)
and
[Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation.
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-24 22:50:29 +0000