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authorvrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2016-09-30 14:24:41 +0000
committervrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2016-09-30 14:24:41 +0000
commit29499b02d1b6eafcc6419a0b6b4469152ea20a09 (patch)
treed8e5ef87e75ab8b572a69d7db1b47f12d3b5930f /src/Persistent_cohomology
parent1c1c3073e0612ee401a941008a6b13438b3429e2 (diff)
Fix compilation issues
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1596 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 343308ef914e6a6617890f49a55eb0bb8db15ee9
Diffstat (limited to 'src/Persistent_cohomology')
-rw-r--r--src/Persistent_cohomology/benchmark/CMakeLists.txt14
-rw-r--r--src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp (renamed from src/Persistent_cohomology/example/performance_rips_persistence.cpp)37
-rw-r--r--src/Persistent_cohomology/example/CMakeLists.txt4
-rw-r--r--src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp3
-rw-r--r--src/Persistent_cohomology/example/alpha_complex_persistence.cpp2
-rw-r--r--src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp1
-rw-r--r--src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp17
-rw-r--r--src/Persistent_cohomology/example/rips_multifield_persistence.cpp21
-rw-r--r--src/Persistent_cohomology/example/rips_persistence.cpp20
-rw-r--r--src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp50
-rw-r--r--src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp4
11 files changed, 99 insertions, 74 deletions
diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt
new file mode 100644
index 00000000..ea792c89
--- /dev/null
+++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt
@@ -0,0 +1,14 @@
+cmake_minimum_required(VERSION 2.6)
+project(Persistent_cohomology_benchmark)
+
+
+if(GMP_FOUND)
+ if(GMPXX_FOUND)
+ add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp )
+ target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+ if (TBB_FOUND)
+ target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
+ endif(TBB_FOUND)
+ file(COPY "${CMAKE_SOURCE_DIR}/data/points/Kl.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+ endif(GMPXX_FOUND)
+endif(GMP_FOUND)
diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
index b4d282ac..99fcad41 100644
--- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
@@ -20,20 +20,26 @@
* 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/Rips_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 <gudhi/Points_off_io.h>
#include <chrono>
#include <string>
#include <vector>
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
+// 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 Multi_field = Gudhi::persistent_cohomology::Multi_field;
+using Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
/* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */
template< typename FilteredComplex>
@@ -66,33 +72,30 @@ int main(int argc, char * argv[]) {
int elapsed_sec;
{
- std::string filepoints = "../../../data/points/Kl.txt";
+ std::string off_file_points = "Kl.off";
Filtration_value threshold = 0.27;
int dim_max = 3;
int p = 2;
int q = 1223;
- // Extract the points from the file filepoints
- typedef std::vector<double> Point_t;
- std::vector< Point_t > points;
- read_points(filepoints, points);
+ // Extract the points from the file off_file_points
+ Points_off_reader off_reader(off_file_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>);
+ Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
+ euclidean_distance<Point>);
end = std::chrono::system_clock::now();
elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n";
// Construct the Rips complex in a Simplex Tree
- Simplex_tree<Simplex_tree_options_fast_persistence> st;
+ Simplex_tree st;
start = std::chrono::system_clock::now();
// insert the proximity graph in the simplex tree
- st.insert_graph(prox_graph);
// expand the graph until dimension dim_max
- st.expansion(dim_max);
+ rips_complex_from_file.create_complex(st, dim_max);
end = std::chrono::system_clock::now();
elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
@@ -120,7 +123,7 @@ int main(int argc, char * argv[]) {
// Convert the simplex tree into a hasse diagram
start = std::chrono::system_clock::now();
- Hasse_complex<> hcpx(st);
+ Gudhi::Hasse_complex<> hcpx(st);
end = std::chrono::system_clock::now();
elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n";
@@ -152,7 +155,7 @@ timing_persistence(FilteredComplex & cpx
int elapsed_sec;
{
start = std::chrono::system_clock::now();
- Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
+ Gudhi::persistent_cohomology::Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
end = std::chrono::system_clock::now();
elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n";
@@ -186,7 +189,7 @@ timing_persistence(FilteredComplex & cpx
int elapsed_sec;
{
start = std::chrono::system_clock::now();
- Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
+ Gudhi::persistent_cohomology::Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
end = std::chrono::system_clock::now();
elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n";
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index d97d1b63..75f3c5d4 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -39,13 +39,9 @@ if(GMP_FOUND)
if(GMPXX_FOUND)
add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
- add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
- target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
if (TBB_FOUND)
target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
- target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
endif(TBB_FOUND)
-
add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
endif(GMPXX_FOUND)
endif(GMP_FOUND)
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index 48fbb91a..f7e8f800 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -64,6 +64,7 @@ typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
// gudhi type definition
typedef Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence> ST;
+typedef ST::Filtration_value Filtration_value;
typedef ST::Vertex_handle Simplex_tree_vertex;
typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
@@ -132,7 +133,7 @@ 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], "%lf", &min_persistence);
+ 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]);
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
index cb181936..24315144 100644
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -9,6 +9,8 @@
#include <string>
#include <limits> // for numeric_limits
+using Filtration_value = double;
+
void program_options(int argc, char * argv[]
, std::string & off_file_points
, std::string & output_file_diag
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 a199fea1..5184ef52 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -70,6 +70,7 @@ 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_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
index ba772f04..817aac4d 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -29,13 +29,12 @@
#include <utility>
#include <vector>
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-typedef Simplex_tree<> typeST;
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree</*Gudhi::Simplex_tree_options_fast_persistence*/>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using typeVectorVertex = std::vector< Simplex_tree::Vertex_handle >;
void usage(char * const progName) {
std::cerr << "Usage: " << progName << " coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
@@ -66,7 +65,7 @@ int main(int argc, char * const argv[]) {
// TEST OF INSERTION
std::cout << "********************************************************************" << std::endl;
std::cout << "TEST OF INSERTION" << std::endl;
- typeST st;
+ Simplex_tree st;
// ++ FIRST
std::cout << " - INSERT (0,1,2)" << std::endl;
@@ -166,7 +165,7 @@ int main(int argc, char * const argv[]) {
std::cout << "**************************************************************" << std::endl;
// Compute the persistence diagram of the complex
- persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st);
+ Persistent_cohomology pcoh(st);
// initializes the coefficient field for homology
pcoh.init_coefficients(coeff_field_characteristic);
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index d4a07bb6..f4adc7a9 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -25,14 +25,21 @@
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Persistent_cohomology/Multi_field.h>
+#include <gudhi/Points_off_io.h>
#include <boost/program_options.hpp>
#include <string>
#include <vector>
-
-typedef double Filtration_value;
+// 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 Multi_field = Gudhi::persistent_cohomology::Multi_field;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Multi_field >;
+using Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
void program_options(int argc, char * argv[]
, std::string & off_file_points
@@ -54,22 +61,22 @@ int main(int argc, char * argv[]) {
program_options(argc, argv, off_file_points, filediag, threshold, dim_max, min_p, max_p, min_persistence);
- Gudhi::rips_complex::Rips_complex<> rips_complex_from_file(off_file_points);
+ Points_off_reader off_reader(off_file_points);
+ Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
+ euclidean_distance<Point>);
// Construct the Rips complex in a Simplex Tree
- using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
Simplex_tree simplex_tree;
- if (rips_complex_from_file.create_complex(simplex_tree, threshold, dim_max, euclidean_distance<std::vector<double>>)) {
+ if (rips_complex_from_file.create_complex(simplex_tree, dim_max)) {
std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
std::cout << " and has dimension " << simplex_tree.dimension() << " \n";
// Sort the simplices in the order of the filtration
simplex_tree.initialize_filtration();
- using Multi_field = Gudhi::persistent_cohomology::Multi_field;
// Compute the persistence diagram of the complex
- Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Multi_field > pcoh(simplex_tree);
+ Persistent_cohomology pcoh(simplex_tree);
// initializes the coefficient field for homology
pcoh.init_coefficients(min_p, max_p);
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index e3ab5927..97bab14c 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -25,6 +25,7 @@
#include <gudhi/distance_functions.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
#include <boost/program_options.hpp>
@@ -32,7 +33,14 @@
#include <vector>
#include <limits> // infinity
-typedef double Filtration_value;
+// 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 Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
void program_options(int argc, char * argv[]
, std::string & off_file_points
@@ -52,22 +60,22 @@ int main(int argc, char * argv[]) {
program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
- Gudhi::rips_complex::Rips_complex<> rips_complex_from_file(off_file_points);
+ Points_off_reader off_reader(off_file_points);
+ Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
+ euclidean_distance<Point>);
// Construct the Rips complex in a Simplex Tree
- using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
Simplex_tree simplex_tree;
- if (rips_complex_from_file.create_complex(simplex_tree, threshold, dim_max, euclidean_distance<std::vector<double>>)) {
+ if (rips_complex_from_file.create_complex(simplex_tree, dim_max)) {
std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
std::cout << " and has dimension " << simplex_tree.dimension() << " \n";
// Sort the simplices in the order of the filtration
simplex_tree.initialize_filtration();
- using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
// Compute the persistence diagram of the complex
- Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp > pcoh(simplex_tree);
+ Persistent_cohomology pcoh(simplex_tree);
// initializes the coefficient field for homology
pcoh.init_coefficients(p);
diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index 4c6656f5..991ed4f0 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -21,12 +21,12 @@
* 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/Rips_complex.h>
#include <gudhi/Hasse_complex.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/distance_functions.h>
#include <boost/program_options.hpp>
@@ -44,14 +44,16 @@
// //
////////////////////////////////////////////////////////////////
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
-typedef double Filtration_value;
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<>;
+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 Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
void program_options(int argc, char * argv[]
- , std::string & filepoints
+ , std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
@@ -59,30 +61,22 @@ void program_options(int argc, char * argv[]
, Filtration_value & min_persistence);
int main(int argc, char * argv[]) {
- std::string filepoints;
+ std::string off_file_points;
std::string filediag;
Filtration_value threshold;
int dim_max;
int p;
Filtration_value min_persistence;
- program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence);
-
- // Extract the points from the file filepoints
- typedef std::vector<double> Point_t;
- std::vector< Point_t > points;
- read_points(filepoints, points);
+ program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
- // Compute the proximity graph of the points
- Graph_t prox_graph = compute_proximity_graph(points, threshold
- , euclidean_distance<Point_t>);
+ Points_off_reader off_reader(off_file_points);
+ Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
+ euclidean_distance<Point>);
// Construct the Rips complex in a Simplex Tree
- Simplex_tree<>& st = *new Simplex_tree<>;
- // insert the proximity graph in the simplex tree
- st.insert_graph(prox_graph);
- // expand the graph until dimension dim_max
- st.expansion(dim_max);
+ Simplex_tree& st = *new Simplex_tree;
+ rips_complex_from_file.create_complex(st, dim_max);
std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
std::cout << " and has dimension " << st.dimension() << " \n";
@@ -99,7 +93,7 @@ int main(int argc, char * argv[]) {
st.assign_key(sh, count++);
// Convert to a more convenient representation.
- Hasse_complex<> hcpx(st);
+ Gudhi::Hasse_complex<> hcpx(st);
#ifdef GUDHI_USE_TBB
ts.terminate();
@@ -109,7 +103,7 @@ int main(int argc, char * argv[]) {
delete &st;
// Compute the persistence diagram of the complex
- persistent_cohomology::Persistent_cohomology< Hasse_complex<>, Field_Zp > pcoh(hcpx);
+ Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Hasse_complex<>, Field_Zp > pcoh(hcpx);
// initializes the coefficient field for homology
pcoh.init_coefficients(p);
@@ -126,7 +120,7 @@ int main(int argc, char * argv[]) {
}
void program_options(int argc, char * argv[]
- , std::string & filepoints
+ , std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
@@ -135,7 +129,7 @@ void program_options(int argc, char * argv[]
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
hidden.add_options()
- ("input-file", po::value<std::string>(&filepoints),
+ ("input-file", po::value<std::string>(&off_file_points),
"Name of file containing a point set. Format is one point per line: X1 ... Xd ");
po::options_description visible("Allowed options", 100);
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
index 703682e1..1a6e3296 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
@@ -21,7 +21,7 @@ using namespace boost::unit_test;
typedef Simplex_tree<> typeST;
-std::string test_rips_persistence(int min_coefficient, int max_coefficient, int min_persistence) {
+std::string test_rips_persistence(int min_coefficient, int max_coefficient, double min_persistence) {
// file name is given as parameter from CMakeLists.txt
const std::string inputFile(framework::master_test_suite().argv[1]);
@@ -74,7 +74,7 @@ void test_rips_persistence_in_dimension(int min_dimension, int max_dimension) {
std::cout << "********************************************************************" << std::endl;
std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_MULTI_FIELD MIN_DIM=" << min_dimension << " MAX_DIM=" << max_dimension << " MIN_PERS=0" << std::endl;
- std::string str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, static_cast<Filtration_value> (0.0));
+ std::string str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, 0.0);
std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl;
BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found