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-rw-r--r--src/Persistent_cohomology/example/performance_rips_persistence.cpp168
1 files changed, 85 insertions, 83 deletions
diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
index 077c2b07..0e912d57 100644
--- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
@@ -1,49 +1,51 @@
- /* 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): Clément Maria
- *
- * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France)
- *
- * 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
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include "gudhi/reader_utils.h"
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/distance_functions.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Persistent_cohomology.h"
-#include "gudhi/Persistent_cohomology/Multi_field.h"
-#include "gudhi/Hasse_complex.h"
+/* 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): Clément Maria
+ *
+ * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ * 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
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Persistent_cohomology/Multi_field.h>
+#include <gudhi/Hasse_complex.h>
#include <chrono>
+#include <string>
+#include <vector>
using namespace Gudhi;
using namespace Gudhi::persistent_cohomology;
/* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */
template< typename FilteredComplex>
-void timing_persistence( FilteredComplex & cpx
- , int p );
+void timing_persistence(FilteredComplex & cpx
+ , int p);
/* Compute multi-field persistent homology of the complex cpx with coefficients in
* Z/rZ for all prime number r in [p;q].*/
template< typename FilteredComplex>
-void timing_persistence( FilteredComplex & cpx
- , int p
- , int q );
+void timing_persistence(FilteredComplex & cpx
+ , int p
+ , int q);
/* Timings for the computation of persistent homology with different
* representations of a Rips complex and different coefficient fields. The
@@ -59,111 +61,111 @@ void timing_persistence( FilteredComplex & cpx
* We present also timings for the computation of multi-field persistent
* homology in all fields Z/rZ for r prime between 2 and 1223.
*/
-int main (int argc, char * argv[])
-{
+int main(int argc, char * argv[]) {
std::chrono::time_point<std::chrono::system_clock> start, end;
int enlapsed_sec;
- std::string filepoints = "../examples/Kl.txt";
- Filtration_value threshold = 0.3;
- int dim_max = 3;
- int p = 2;
- int q = 1223;
+ std::string filepoints = "../examples/Kl.txt";
+ Filtration_value threshold = 0.3;
+ int dim_max = 3;
+ int p = 2;
+ int q = 1223;
-// Extract the points from the file filepoints
+ // Extract the points from the file filepoints
typedef std::vector<double> Point_t;
std::vector< Point_t > points;
- read_points( filepoints, points );
+ read_points(filepoints, points);
-// Compute the proximity graph of the points
+ // Compute the proximity graph of the points
start = std::chrono::system_clock::now();
- Graph_t prox_graph = compute_proximity_graph( points, threshold
- , euclidean_distance<Point_t> );
+ Graph_t prox_graph = compute_proximity_graph(points, threshold
+ , euclidean_distance<Point_t>);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
+ enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
std::cout << "Compute Rips graph in " << enlapsed_sec << " sec.\n";
-// Construct the Rips complex in a Simplex Tree
- Simplex_tree<> st;
+ // Construct the Rips complex in a Simplex Tree
+ Simplex_tree<> st;
start = std::chrono::system_clock::now();
- st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree
- st.expansion( dim_max ); // expand the graph until dimension dim_max
+ // insert the proximity graph in the simplex tree
+ st.insert_graph(prox_graph);
+ // expand the graph until dimension dim_max
+ st.expansion(dim_max);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
+ enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
std::cout << "Compute Rips complex in " << enlapsed_sec << " sec.\n";
std::cout << " - dimension = " << st.dimension() << std::endl;
std::cout << " - number of simplices = " << st.num_simplices() << std::endl;
-// Sort the simplices in the order of the filtration
+ // Sort the simplices in the order of the filtration
start = std::chrono::system_clock::now();
st.initialize_filtration();
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
+ enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
std::cout << "Order the simplices of the filtration in " << enlapsed_sec << " sec.\n";
-// Convert the simplex tree into a hasse diagram
+ // Convert the simplex tree into a hasse diagram
start = std::chrono::system_clock::now();
Hasse_complex<> hcpx(st);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
+ enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
std::cout << "Convert the simplex tree into a Hasse diagram in " << enlapsed_sec << " sec.\n";
std::cout << "Timings when using a simplex tree: \n";
- timing_persistence(st,p);
- timing_persistence(st,q);
- timing_persistence(st,p,q);
+ timing_persistence(st, p);
+ timing_persistence(st, q);
+ timing_persistence(st, p, q);
std::cout << "Timings when using a Hasse complex: \n";
- timing_persistence(hcpx,p);
- timing_persistence(hcpx,q);
- timing_persistence(hcpx,p,q);
+ timing_persistence(hcpx, p);
+ timing_persistence(hcpx, q);
+ timing_persistence(hcpx, p, q);
return 0;
}
-
template< typename FilteredComplex>
void
-timing_persistence( FilteredComplex & cpx
- , int p )
-{
+timing_persistence(FilteredComplex & cpx
+ , int p) {
std::chrono::time_point<std::chrono::system_clock> start, end;
int enlapsed_sec;
- Persistent_cohomology< FilteredComplex, Field_Zp > pcoh (cpx);
- pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
-
+ Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(p);
+
start = std::chrono::system_clock::now();
-
- pcoh.compute_persistent_cohomology( INFINITY );
-
+
+ pcoh.compute_persistent_cohomology(INFINITY);
+
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
- std::cout << " Compute persistent homology in Z/"<<p<<"Z in " << enlapsed_sec << " sec.\n";
+ enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
+ std::cout << " Compute persistent homology in Z/" << p << "Z in " << enlapsed_sec << " sec.\n";
}
template< typename FilteredComplex>
void
-timing_persistence( FilteredComplex & cpx
- , int p
- , int q )
-{
+timing_persistence(FilteredComplex & cpx
+ , int p
+ , int q) {
std::chrono::time_point<std::chrono::system_clock> start, end;
int enlapsed_sec;
- Persistent_cohomology< FilteredComplex, Multi_field > pcoh (cpx);
- pcoh.init_coefficients( p, q ); //initilizes the coefficient field for homology
+ Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(p, q);
// compute persistent homology, disgarding persistent features of life shorter than min_persistence
start = std::chrono::system_clock::now();
- pcoh.compute_persistent_cohomology( INFINITY );
+ pcoh.compute_persistent_cohomology(INFINITY);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
+ enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
std::cout << " Compute multi-field persistent homology in all coefficient fields Z/pZ "
- << "with p in ["<<p<<";"<<q<<"] in " << enlapsed_sec << " sec.\n";
+ << "with p in [" << p << ";" << q << "] in " << enlapsed_sec << " sec.\n";
}
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-01 07:49:36 +0000