diff options
author | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-06-10 18:32:40 +0000 |
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committer | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-06-10 18:32:40 +0000 |
commit | 956403526264a5dc25f289940f066da5dabc7cf4 (patch) | |
tree | 777627a8c9dfc82ae9f20d16d567ee29c03e8f29 /src/Persistent_cohomology | |
parent | 75a8bf8132d2bade9ccc31147db00bf29eeb7589 (diff) | |
parent | 2ecd97ff50b01f864944443b3a2a8ea0220d9b10 (diff) |
Rename namespaces according to convention
+ Missing Boost_THREAD_LIBRARY
+ Useless typename
+ Use TBB_LIBRARIES
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/fix_naming@1274 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 5c02ec481b62ef52b40d849e76e3d333e2ca4e7c
Diffstat (limited to 'src/Persistent_cohomology')
6 files changed, 36 insertions, 26 deletions
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index f85c50f9..a0af11c1 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -21,11 +21,11 @@ add_executable(persistence_from_file persistence_from_file.cpp) target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) - target_link_libraries(plain_homology ${TBB_RELEASE_LIBRARY}) - target_link_libraries(persistence_from_simple_simplex_tree ${TBB_RELEASE_LIBRARY}) - target_link_libraries(rips_persistence ${TBB_RELEASE_LIBRARY}) - target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_RELEASE_LIBRARY}) - target_link_libraries(persistence_from_file ${TBB_RELEASE_LIBRARY}) + target_link_libraries(plain_homology ${TBB_LIBRARIES}) + target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES}) + target_link_libraries(rips_persistence ${TBB_LIBRARIES}) + target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) + target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) endif() add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology) @@ -44,8 +44,8 @@ if(GMPXX_FOUND AND GMP_FOUND) 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_RELEASE_LIBRARY}) - target_link_libraries(performance_rips_persistence ${TBB_RELEASE_LIBRARY}) + target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES}) + target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) endif() 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) @@ -55,7 +55,7 @@ if(GMPXX_FOUND AND GMP_FOUND) target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) if (TBB_FOUND) - target_link_libraries(alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY}) + target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) endif() add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45) @@ -78,12 +78,12 @@ if(GMPXX_FOUND AND GMP_FOUND) target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) if (TBB_FOUND) - target_link_libraries(alpha_complex_persistence ${TBB_RELEASE_LIBRARY}) - target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY}) - target_link_libraries(custom_persistence_sort ${TBB_RELEASE_LIBRARY}) + target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) endif() add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2) - add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off 2 0) + add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0) add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort) else() diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp index 17fb84d2..cb181936 100644 --- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp @@ -30,7 +30,7 @@ int main(int argc, char **argv) { // Init of an alpha complex from an OFF file // ---------------------------------------------------------------------------- using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; - Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value); + Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value); // ---------------------------------------------------------------------------- // Display information about the alpha complex @@ -44,7 +44,7 @@ int main(int argc, char **argv) { std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl; // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alphacomplex::Alpha_complex<Kernel>, + Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alpha_complex::Alpha_complex<Kernel>, Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file); // initializes the coefficient field for homology pcoh.init_coefficients(coeff_field_characteristic); diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp index d591a0d0..9af38611 100644 --- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp +++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp @@ -37,7 +37,7 @@ using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<3> >; using Point = Kernel::Point_d; -using Alpha_complex = Gudhi::alphacomplex::Alpha_complex<Kernel>; +using Alpha_complex = Gudhi::alpha_complex::Alpha_complex<Kernel>; std::vector<Point> random_points() { // Instanciate a random point generator 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 b8e1097d..a199fea1 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -125,28 +125,28 @@ Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) { void usage(char * const progName) { std::cerr << "Usage: " << progName << - " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; exit(-1); } int main(int argc, char * const argv[]) { // program args management - if (argc != 4) { + if (argc != 5) { std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; usage(argv[0]); } int coeff_field_characteristic = 0; - int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); + int returnedScanValue = sscanf(argv[3], "%d", &coeff_field_characteristic); if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { - std::cerr << "Error: " << argv[2] << " is not correct\n"; + std::cerr << "Error: " << argv[3] << " is not correct\n"; usage(argv[0]); } Filtration_value min_persistence = 0.0; - returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); + returnedScanValue = sscanf(argv[4], "%lf", &min_persistence); if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; + std::cerr << "Error: " << argv[4] << " is not correct\n"; usage(argv[0]); } @@ -160,11 +160,21 @@ int main(int argc, char * const argv[]) { usage(argv[0]); } + // Read iso_cuboid_3 information from file + std::ifstream iso_cuboid_str(argv[2]); + double x_min, y_min, z_min, x_max, y_max, z_max; + if (iso_cuboid_str.good()) { + iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max; + } else { + std::cerr << "Unable to read file " << argv[2] << std::endl; + usage(argv[0]); + } + // Retrieve the triangulation std::vector<Point_3> lp = off_reader.get_point_cloud(); // Define the periodic cube - P3DT3 pdt(PK::Iso_cuboid_3(0, 0, 0, 1, 1, 1)); + P3DT3 pdt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); // Heuristic for inserting large point sets (if pts is reasonably large) pdt.insert(lp.begin(), lp.end(), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index ff6b38a6..31a86a2d 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -15,8 +15,8 @@ target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNI add_executable ( BettiNumbersUT betti_numbers_unit_test.cpp ) target_link_libraries(BettiNumbersUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) - target_link_libraries(PersistentCohomologyUT ${TBB_RELEASE_LIBRARY}) - target_link_libraries(BettiNumbersUT ${TBB_RELEASE_LIBRARY}) + target_link_libraries(PersistentCohomologyUT ${TBB_LIBRARIES}) + target_link_libraries(BettiNumbersUT ${TBB_LIBRARIES}) endif() # Unitary tests @@ -35,7 +35,7 @@ if(GMPXX_FOUND AND GMP_FOUND) add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp ) target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if (TBB_FOUND) - target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_RELEASE_LIBRARY}) + target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_LIBRARIES}) endif() # Unitary tests diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp index 194b3e74..5c54ed5f 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -43,7 +43,7 @@ std::string test_rips_persistence(int coefficient, int min_persistence) { st.initialize_filtration(); // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology<Simplex_tree<>, Field_Zp> pcoh(st); + Persistent_cohomology<Simplex_tree<>, Field_Zp> pcoh(st); pcoh.init_coefficients( coefficient ); // initializes the coefficient field for homology // Check infinite rips |