summaryrefslogtreecommitdiff
path: root/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
diff options
context:
space:
mode:
Diffstat (limited to 'src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp')
-rw-r--r--src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp92
1 files changed, 39 insertions, 53 deletions
diff --git a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
index 6f2891fe..41cf915a 100644
--- a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp
@@ -1,5 +1,5 @@
-/* This file is part of the Gudhi Library. The Gudhi library
- * (Geometric Understanding in Higher Dimensions) is a generic C++
+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
* library for computational topology.
*
* Author(s): Pawel Dlotko, Vincent Rouvreau
@@ -31,24 +31,18 @@
#include <vector>
#include <limits> // infinity
-
// Types definition
using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = Simplex_tree::Filtration_value;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
using Correlation_matrix = std::vector<std::vector<Filtration_value>>;
-void program_options(int argc, char * argv[]
- , std::string & csv_matrix_file
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence);
+void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag,
+ Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence);
-int main(int argc, char * argv[]) {
+int main(int argc, char* argv[]) {
std::string csv_matrix_file;
std::string filediag;
Filtration_value threshold;
@@ -58,22 +52,20 @@ int main(int argc, char * argv[]) {
program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
- Correlation_matrix correlations = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
-
- //Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix:
- for ( size_t i = 0 ; i != correlations.size() ; ++i )
- {
- for ( size_t j = 0 ; j != correlations[i].size() ; ++j )
- {
- correlations[i][j] = 1-correlations[i][j];
- if ( correlations[i][j] < 0 )
- {
- std::cerr << "The input matrix is not a correlation matrix. \n";
- throw "The input matrix is not a correlation matrix. \n";
- }
- }
- }
-
+ Correlation_matrix correlations =
+ Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+
+ // Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix:
+ for (size_t i = 0; i != correlations.size(); ++i) {
+ for (size_t j = 0; j != correlations[i].size(); ++j) {
+ correlations[i][j] = 1 - correlations[i][j];
+ if (correlations[i][j] < 0) {
+ std::cerr << "The input matrix is not a correlation matrix. \n";
+ throw "The input matrix is not a correlation matrix. \n";
+ }
+ }
+ }
+
Rips_complex rips_complex_from_file(correlations, threshold);
// Construct the Rips complex in a Simplex Tree
@@ -104,33 +96,28 @@ int main(int argc, char * argv[]) {
return 0;
}
-void program_options(int argc, char * argv[]
- , std::string & csv_matrix_file
- , std::string & filediag
- , Filtration_value & threshold
- , int & dim_max
- , int & p
- , Filtration_value & min_persistence) {
+void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag,
+ Filtration_value& threshold, 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>(&csv_matrix_file),
- "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
+ hidden.add_options()(
+ "input-file", po::value<std::string>(&csv_matrix_file),
+ "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
po::options_description visible("Allowed options", 100);
- visible.add_options()
- ("help,h", "produce help message")
- ("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::cout")
- ("max-edge-length,r",
- po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
- "Maximal length of an edge for the Rips complex construction.")
- ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
- "Maximal dimension of the Rips complex we want to compute.")
- ("field-charac,p", po::value<int>(&p)->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");
+ visible.add_options()("help,h", "produce help message")(
+ "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::cout")(
+ "max-edge-length,r",
+ po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+ "Maximal length of an edge for the Rips complex construction.")(
+ "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+ "Maximal dimension of the Rips complex we want to compute.")(
+ "field-charac,p", po::value<int>(&p)->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);
@@ -139,8 +126,7 @@ void program_options(int argc, char * argv[]
all.add(visible).add(hidden);
po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).
- options(all).positional(pos).run(), 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")) {
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-29 03:59:29 +0000