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-rw-r--r--src/Alpha_complex/utilities/CMakeLists.txt134
-rw-r--r--src/Alpha_complex/utilities/alpha_complex_persistence.cpp101
-rw-r--r--src/Alpha_complex/utilities/alphacomplex.md7
3 files changed, 152 insertions, 90 deletions
diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index 2ffbdde0..303bd0a6 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -1,78 +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)
+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")
+ 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")
- endif()
-
- install(TARGETS alpha_complex_persistence DESTINATION bin)
+ 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()
- 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)
+ install(TARGETS alpha_complex_persistence DESTINATION bin)
+ endif()
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
- 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")
+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_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_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_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")
+ 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")
- 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()
+ 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")
- 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")
+ 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()
- 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_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_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_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")
- install(TARGETS alpha_complex_3d_persistence DESTINATION bin)
-
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+ 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_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
index e17831d9..e86b34e2 100644
--- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
@@ -17,19 +17,82 @@
#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, bool &exact, bool &fast,
- std::string &output_file_diag, Filtration_value &alpha_square_max_value,
+ 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;
@@ -38,48 +101,34 @@ int main(int argc, char **argv) {
int coeff_field_characteristic;
Filtration_value min_persistence;
- program_options(argc, argv, off_file_points, exact_version, fast_version, 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 simplex;
+ 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>;
-
- // Init of an alpha complex from an OFF file
- Gudhi::alpha_complex::Alpha_complex<Fast_kernel> alpha_complex_from_file(off_file_points);
-
- if (!alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
- std::cerr << "Fast Alpha complex simplicial complex creation failed." << std::endl;
- exit(-1);
- }
+ 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>;
-
- // Init of an alpha complex from an OFF file
- Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);
-
- if (!alpha_complex_from_file.create_complex(simplex, alpha_square_max_value, exact_version)) {
- std::cerr << "Alpha complex simplicial complex creation failed." << std::endl;
- exit(-1);
- }
+ stree = create_simplex_tree<Kernel>(off_file_points, weight_file, exact_version, alpha_square_max_value);
}
// ----------------------------------------------------------------------------
// Display information about the alpha complex
// ----------------------------------------------------------------------------
- std::clog << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices()
- << " simplices - " << simplex.num_vertices() << " vertices." << std::endl;
+ std::clog << "Simplicial complex is of dimension " << stree.dimension() << " - " << stree.num_simplices()
+ << " simplices - " << stree.num_vertices() << " vertices." << std::endl;
- std::clog << "Simplex_tree dim: " << simplex.dimension() << 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(
- simplex);
+ stree);
// initializes the coefficient field for homology
pcoh.init_coefficients(coeff_field_characteristic);
@@ -98,7 +147,7 @@ int main(int argc, char **argv) {
}
void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast,
- std::string &output_file_diag, Filtration_value &alpha_square_max_value,
+ 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");
@@ -111,6 +160,8 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
"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::clog")(
"max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value)
diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index 527598a9..0d3c6027 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -46,6 +46,9 @@ 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.
@@ -58,6 +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#title20) documentation.
## alpha_complex_3d_persistence ##
generated by cgit v1.2.3 (git 2.39.1) at 2024-04-27 09:51:53 +0000