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-rw-r--r--src/Cech_complex/doc/Intro_cech_complex.h2
-rw-r--r--src/Cech_complex/include/gudhi/Cech_complex.h3
-rw-r--r--src/Cech_complex/utilities/CMakeLists.txt20
-rw-r--r--src/Cech_complex/utilities/cech_persistence.cpp69
-rw-r--r--src/Cech_complex/utilities/cechcomplex.md12
5 files changed, 80 insertions, 26 deletions
diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h
index 595fb64b..73093c07 100644
--- a/src/Cech_complex/doc/Intro_cech_complex.h
+++ b/src/Cech_complex/doc/Intro_cech_complex.h
@@ -17,7 +17,7 @@ namespace cech_complex {
/** \defgroup cech_complex Čech complex
*
- * \author Vincent Rouvreau
+ * \author Vincent Rouvreau, Hind montassif
*
* @{
*
diff --git a/src/Cech_complex/include/gudhi/Cech_complex.h b/src/Cech_complex/include/gudhi/Cech_complex.h
index 625f7c9c..dbdf5e93 100644
--- a/src/Cech_complex/include/gudhi/Cech_complex.h
+++ b/src/Cech_complex/include/gudhi/Cech_complex.h
@@ -1,11 +1,12 @@
/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
- * Author(s): Vincent Rouvreau
+ * Author(s): Vincent Rouvreau, Hind Montassif
*
* Copyright (C) 2018 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
+ * - 2022/02 Hind Montassif : Replace MiniBall with Sphere_circumradius
*/
#ifndef CECH_COMPLEX_H_
diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt
index e80a698e..64557cee 100644
--- a/src/Cech_complex/utilities/CMakeLists.txt
+++ b/src/Cech_complex/utilities/CMakeLists.txt
@@ -9,8 +9,24 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.0.1)
target_link_libraries(cech_persistence ${TBB_LIBRARIES})
endif()
- add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:cech_persistence>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
+ add_test(NAME Cech_complex_utility_from_rips_on_tore_3D_safe COMMAND $<TARGET_FILE:cech_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "safe.pers")
+ add_test(NAME Cech_complex_utility_from_rips_on_tore_3D_fast COMMAND $<TARGET_FILE:cech_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "fast.pers" "-f")
+ add_test(NAME Cech_complex_utility_from_rips_on_tore_3D_exact COMMAND $<TARGET_FILE:cech_persistence>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "exact.pers" "-e")
+
+ if (DIFF_PATH)
+ add_test(Cech_complex_utilities_diff_exact ${DIFF_PATH}
+ "exact.pers" "safe.pers")
+ set_tests_properties(Cech_complex_utilities_diff_exact PROPERTIES DEPENDS
+ "Cech_complex_utility_from_rips_on_tore_3D_safe;Cech_complex_utility_from_rips_on_tore_3D_exact")
+
+ add_test(Cech_complex_utilities_diff_fast ${DIFF_PATH}
+ "fast.pers" "safe.pers")
+ set_tests_properties(Cech_complex_utilities_diff_fast PROPERTIES DEPENDS
+ "Cech_complex_utility_from_rips_on_tore_3D_safe;Cech_complex_utility_from_rips_on_tore_3D_fast")
+ endif()
install(TARGETS cech_persistence DESTINATION bin)
endif()
diff --git a/src/Cech_complex/utilities/cech_persistence.cpp b/src/Cech_complex/utilities/cech_persistence.cpp
index 75d10c0f..e6419f3d 100644
--- a/src/Cech_complex/utilities/cech_persistence.cpp
+++ b/src/Cech_complex/utilities/cech_persistence.cpp
@@ -16,6 +16,7 @@
#include <boost/program_options.hpp>
#include <CGAL/Epeck_d.h> // For EXACT or SAFE version
+#include <CGAL/Epick_d.h> // For FAST version
#include <string>
#include <vector>
@@ -25,41 +26,66 @@
using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = Simplex_tree::Filtration_value;
-using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
-using Point = typename Kernel::Point_d;
-using Points_off_reader = Gudhi::Points_off_reader<Point>;
-using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
-void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
- Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence);
+void program_options(int argc, char* argv[], std::string& off_file_points, bool& exact, bool& fast,
+ std::string& filediag, Filtration_value& max_radius, int& dim_max, int& p,
+ Filtration_value& min_persistence);
+
+template<class Kernel>
+Simplex_tree create_simplex_tree(const std::string &off_file_points, bool exact_version,
+ Filtration_value max_radius, int dim_max) {
+ using Point = typename Kernel::Point_d;
+ using Points_off_reader = Gudhi::Points_off_reader<Point>;
+ using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>;
+
+ Simplex_tree stree;
+
+ Points_off_reader off_reader(off_file_points);
+ Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius, exact_version);
+ cech_complex_from_file.create_complex(stree, dim_max);
+
+ return stree;
+}
int main(int argc, char* argv[]) {
std::string off_file_points;
std::string filediag;
+ bool exact_version = false;
+ bool fast_version = false;
Filtration_value max_radius;
int dim_max;
int p;
Filtration_value min_persistence;
- program_options(argc, argv, off_file_points, filediag, max_radius, dim_max, p, min_persistence);
+ program_options(argc, argv, off_file_points, exact_version, fast_version, filediag, max_radius, dim_max, p,
+ min_persistence);
- Points_off_reader off_reader(off_file_points);
- Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius);
+ if ((exact_version) && (fast_version)) {
+ std::cerr << "You cannot set the exact and the fast version." << std::endl;
+ exit(-1);
+ }
- // Construct the Cech complex in a Simplex Tree
- Simplex_tree simplex_tree;
+ 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, exact_version, max_radius, dim_max);
+ } else {
+ using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
+ stree = create_simplex_tree<Kernel>(off_file_points, exact_version, max_radius, dim_max);
+ }
- cech_complex_from_file.create_complex(simplex_tree, dim_max);
- std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
- std::clog << " and has dimension " << simplex_tree.dimension() << " \n";
+ std::clog << "The complex contains " << stree.num_simplices() << " simplices \n";
+ std::clog << " and has dimension " << stree.dimension() << " \n";
// Sort the simplices in the order of the filtration
- simplex_tree.initialize_filtration();
+ stree.initialize_filtration();
// Compute the persistence diagram of the complex
- Persistent_cohomology pcoh(simplex_tree);
+ Persistent_cohomology pcoh(stree);
// initializes the coefficient field for homology
pcoh.init_coefficients(p);
@@ -77,8 +103,9 @@ int main(int argc, char* argv[]) {
return 0;
}
-void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
- Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence) {
+void program_options(int argc, char* argv[], std::string& off_file_points, bool& exact, bool& fast,
+ std::string& filediag, Filtration_value& max_radius, int& dim_max, int& p,
+ 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),
@@ -86,8 +113,12 @@ 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 Cech complex (default is false, not available if fast is set)")(
+ "fast,f", po::bool_switch(&fast),
+ "To activate fast version of Cech complex (default is false, not available if exact is set)")(
"output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
- "Name of file in which the persistence diagram is written. Default print in std::clog")(
+ "Name of file in which the persistence diagram is written. Default print in standard output")(
"max-radius,r",
po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()),
"Maximal length of an edge for the Cech complex construction.")(
diff --git a/src/Cech_complex/utilities/cechcomplex.md b/src/Cech_complex/utilities/cechcomplex.md
index 821e4dad..54c4e88d 100644
--- a/src/Cech_complex/utilities/cechcomplex.md
+++ b/src/Cech_complex/utilities/cechcomplex.md
@@ -26,18 +26,24 @@ a prime number).
**Usage**
-`cech_persistence [options] <OFF input file>`
+`cech_persistence [options] <input OFF file>`
+
+where
+`<input OFF file>` is the path to the input point cloud in
+[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF).
**Allowed options**
* `-h [ --help ]` Produce help message
* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
-* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Čech complex construction.
+* `-r [ --max-radius ]` (default = inf) Maximal radius for the Čech complex construction.
* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Čech complex we want to compute.
* `-p [ --field-charac ]` (default = 11) Characteristic p of the 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.
+* `-e [ --exact ]` for the exact computation version.
+* `-f [ --fast ]` for the fast computation version.
-Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value.
+Beware: this program may use a lot of RAM and take a lot of time if `max-radius` is set to a large value.
**Example 1 with Z/2Z coefficients**
generated by cgit v1.2.3 (git 2.39.1) at 2024-04-28 12:58:10 +0000