summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--data/points/grid_10_10_10_in_0_2.off127
-rw-r--r--data/points/grid_10_10_10_in_0_2.weights125
-rw-r--r--src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp11
-rw-r--r--src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp47
-rw-r--r--src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp4
-rw-r--r--src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp5
-rw-r--r--src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp8
7 files changed, 32 insertions, 295 deletions
diff --git a/data/points/grid_10_10_10_in_0_2.off b/data/points/grid_10_10_10_in_0_2.off
deleted file mode 100644
index 7618e065..00000000
--- a/data/points/grid_10_10_10_in_0_2.off
+++ /dev/null
@@ -1,127 +0,0 @@
-OFF
-125 0 0
-0 0 0
-0 0 0.2
-0 0 0.4
-0 0 0.6
-0 0 0.8
-0 0.2 0
-0 0.2 0.2
-0 0.2 0.4
-0 0.2 0.6
-0 0.2 0.8
-0 0.4 0
-0 0.4 0.2
-0 0.4 0.4
-0 0.4 0.6
-0 0.4 0.8
-0 0.6 0
-0 0.6 0.2
-0 0.6 0.4
-0 0.6 0.6
-0 0.6 0.8
-0 0.8 0
-0 0.8 0.2
-0 0.8 0.4
-0 0.8 0.6
-0 0.8 0.8
-0.2 0 0
-0.2 0 0.2
-0.2 0 0.4
-0.2 0 0.6
-0.2 0 0.8
-0.2 0.2 0
-0.2 0.2 0.2
-0.2 0.2 0.4
-0.2 0.2 0.6
-0.2 0.2 0.8
-0.2 0.4 0
-0.2 0.4 0.2
-0.2 0.4 0.4
-0.2 0.4 0.6
-0.2 0.4 0.8
-0.2 0.6 0
-0.2 0.6 0.2
-0.2 0.6 0.4
-0.2 0.6 0.6
-0.2 0.6 0.8
-0.2 0.8 0
-0.2 0.8 0.2
-0.2 0.8 0.4
-0.2 0.8 0.6
-0.2 0.8 0.8
-0.4 0 0
-0.4 0 0.2
-0.4 0 0.4
-0.4 0 0.6
-0.4 0 0.8
-0.4 0.2 0
-0.4 0.2 0.2
-0.4 0.2 0.4
-0.4 0.2 0.6
-0.4 0.2 0.8
-0.4 0.4 0
-0.4 0.4 0.2
-0.4 0.4 0.4
-0.4 0.4 0.6
-0.4 0.4 0.8
-0.4 0.6 0
-0.4 0.6 0.2
-0.4 0.6 0.4
-0.4 0.6 0.6
-0.4 0.6 0.8
-0.4 0.8 0
-0.4 0.8 0.2
-0.4 0.8 0.4
-0.4 0.8 0.6
-0.4 0.8 0.8
-0.6 0 0
-0.6 0 0.2
-0.6 0 0.4
-0.6 0 0.6
-0.6 0 0.8
-0.6 0.2 0
-0.6 0.2 0.2
-0.6 0.2 0.4
-0.6 0.2 0.6
-0.6 0.2 0.8
-0.6 0.4 0
-0.6 0.4 0.2
-0.6 0.4 0.4
-0.6 0.4 0.6
-0.6 0.4 0.8
-0.6 0.6 0
-0.6 0.6 0.2
-0.6 0.6 0.4
-0.6 0.6 0.6
-0.6 0.6 0.8
-0.6 0.8 0
-0.6 0.8 0.2
-0.6 0.8 0.4
-0.6 0.8 0.6
-0.6 0.8 0.8
-0.8 0 0
-0.8 0 0.2
-0.8 0 0.4
-0.8 0 0.6
-0.8 0 0.8
-0.8 0.2 0
-0.8 0.2 0.2
-0.8 0.2 0.4
-0.8 0.2 0.6
-0.8 0.2 0.8
-0.8 0.4 0
-0.8 0.4 0.2
-0.8 0.4 0.4
-0.8 0.4 0.6
-0.8 0.4 0.8
-0.8 0.6 0
-0.8 0.6 0.2
-0.8 0.6 0.4
-0.8 0.6 0.6
-0.8 0.6 0.8
-0.8 0.8 0
-0.8 0.8 0.2
-0.8 0.8 0.4
-0.8 0.8 0.6
-0.8 0.8 0.8
diff --git a/data/points/grid_10_10_10_in_0_2.weights b/data/points/grid_10_10_10_in_0_2.weights
deleted file mode 100644
index fea8f879..00000000
--- a/data/points/grid_10_10_10_in_0_2.weights
+++ /dev/null
@@ -1,125 +0,0 @@
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
-1e-6
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index a0db9b42..df96fcfd 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -39,6 +39,7 @@
#include <utility>
#include <list>
#include <vector>
+#include <cstdlib>
#include "alpha_complex_3d_helper.h"
@@ -78,7 +79,7 @@ using Persistent_cohomology =
void usage(const std::string& progName) {
std::cerr << "Usage: " << progName
- << " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+ << " path_to_the_OFF_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
exit(-1);
}
@@ -90,13 +91,7 @@ int main(int argc, char* const argv[]) {
}
int coeff_field_characteristic = atoi(argv[2]);
-
- Filtration_value min_persistence = 0.0;
- int returnedScanValue = sscanf(argv[3], "%f", &min_persistence);
- if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
- std::cerr << "Error: " << argv[3] << " is not correct\n";
- usage(argv[0]);
- }
+ Filtration_value min_persistence = strtof(argv[3], nullptr);
// Read points from file
std::string offInputFile(argv[1]);
diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
index 8a335075..b189e980 100644
--- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
@@ -4,7 +4,7 @@
*
* Author(s): Vincent Rouvreau
*
- * Copyright (C) 2014 INRIA Saclay (France)
+ * Copyright (C) 2014 INRIA
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -39,6 +39,7 @@
#include <utility>
#include <list>
#include <vector>
+#include <cstdlib>
#include "alpha_complex_3d_helper.h"
@@ -57,32 +58,33 @@ using Point_3 = Kernel::Point_3;
// 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;
using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Vertex_handle>;
+using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
// gudhi type definition
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 PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >;
+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: " << progName <<
- " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+void usage(const std::string& progName) {
+ std::cerr << "Usage: " << progName
+ << " path_to_the_OFF_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
exit(-1);
}
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
// program args management
if (argc != 4) {
std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
@@ -90,13 +92,7 @@ int main(int argc, char * const argv[]) {
}
int coeff_field_characteristic = atoi(argv[2]);
-
- Filtration_value min_persistence = 0.0;
- int returnedScanValue = sscanf(argv[3], "%f", &min_persistence);
- if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
- std::cerr << "Error: " << argv[3] << " is not correct\n";
- usage(argv[0]);
- }
+ Filtration_value min_persistence = strtof(argv[3], nullptr);
// Read points from file
std::string offInputFile(argv[1]);
@@ -143,28 +139,28 @@ 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 Vertex_handle * vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
+ } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
count_vertices++;
vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
}
@@ -213,7 +209,6 @@ 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;
@@ -233,7 +228,7 @@ int main(int argc, char * const argv[]) {
std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
// Compute the persistence diagram of the complex
- PCOH pcoh(simplex_tree);
+ Persistent_cohomology pcoh(simplex_tree, true);
// initializes the coefficient field for homology
pcoh.init_coefficients(coeff_field_characteristic);
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
index 33efbdc7..63731a4a 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -83,8 +83,8 @@ 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: " << progName << " path_to_file_graph path_to_iso_cuboid_3_file "
+void usage(const std::string& progName) {
+ std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_iso_cuboid_3_file "
"coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
exit(-1);
}
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 85b0ab34..96cc57e9 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -49,6 +49,7 @@
#include "alpha_complex_3d_helper.h"
+// Alpha_shape_3 templates type definitions
using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
// For CGAL < 4.11
@@ -102,8 +103,8 @@ 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: " << progName << " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > "
+void usage(const std::string& progName) {
+ std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file coeff_field_characteristic[integer > "
"0] min_persistence[float >= -1.0]\n";
exit(-1);
}
diff --git a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp
index ab2e29b4..a4a2a9f8 100644
--- a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp
@@ -86,8 +86,8 @@ 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: " << progName << " path_to_the_OFF_File path_to_weight_file path_to_the_cuboid_file "
+void usage(const std::string& progName) {
+ std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file path_to_the_cuboid_file "
"coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
exit(-1);
}
@@ -96,7 +96,6 @@ int main(int argc, char* const argv[]) {
// program args management
if (argc != 6) {
std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
- // file with points, file with weights, cuboid file, field characteristics, minimum persistence.
usage(argv[0]);
}
@@ -206,8 +205,7 @@ int main(int argc, char* const argv[]) {
// 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 Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
count_vertices++;
vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
}
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-02 13:13:26 +0000