diff options
| author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-07-06 07:31:03 +0000 |
|---|---|---|
| committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-07-06 07:31:03 +0000 |
| commit | f233647cfacc8a7ac1c732474ef47e20e2a17527 (patch) | |
| tree | e66189128b9160b978de4772d47c6eaa391db65b | |
| parent | 73c3f473fa9d4dc6965607edd1ad748d26cfb86b (diff) | |
| parent | 2e7447cf1deb3a1ac08f2fe90cd780901da65016 (diff) | |
Merge last trunk modifications
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/graph_expansion_with_blocker_oracle@2588 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 551995fb34cfdc3c170ae5cfdaf2b249dcb03f8f
39 files changed, 330 insertions, 203 deletions
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index bd0c57ac..3d9add66 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,6 @@ set (GUDHI_MAJOR_VERSION 2) set (GUDHI_MINOR_VERSION 0) -set (GUDHI_PATCH_VERSION 0) +set (GUDHI_PATCH_VERSION 1.beta) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") diff --git a/data/persistence_diagram/first.pers b/data/persistence_diagram/first.pers new file mode 100644 index 00000000..193c60ba --- /dev/null +++ b/data/persistence_diagram/first.pers @@ -0,0 +1,5 @@ +# Simple persistence diagram
+2.7 3.7
+9.6 14.
+34.2 34.974
+3. inf
\ No newline at end of file diff --git a/data/persistence_diagram/second.pers b/data/persistence_diagram/second.pers new file mode 100644 index 00000000..6292fde6 --- /dev/null +++ b/data/persistence_diagram/second.pers @@ -0,0 +1,3 @@ +2.8 4.45
+9.5 14.1
+3.2 inf
\ No newline at end of file diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 4badcb91..5bf553e9 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -5,9 +5,9 @@ project(Alpha_complex_examples) # cmake -DCGAL_DIR=~/workspace/CGAL-4.7 .. if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp ) - target_link_libraries(Alpha_complex_example_from_points ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(Alpha_complex_example_from_points ${CGAL_LIBRARY}) add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp ) - target_link_libraries(Alpha_complex_example_from_off ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index d7f49b53..9e0b3b3c 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -5,7 +5,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) include(GUDHI_test_coverage) add_executable ( Alpha_complex_test_unit Alpha_complex_unit_test.cpp ) - target_link_libraries(Alpha_complex_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + target_link_libraries(Alpha_complex_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES}) endif() diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index 47f5e0c6..a0401619 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -2,7 +2,6 @@ cmake_minimum_required(VERSION 2.6) project(Bitmap_cubical_complex_examples) add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp ) -target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES}) endif() @@ -14,7 +13,6 @@ add_test(NAME Bitmap_cubical_complex_example_persistence_two_sphere COMMAND $<TA "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt") add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp ) -target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) target_link_libraries(Random_bitmap_cubical_complex ${TBB_LIBRARIES}) endif() @@ -22,7 +20,6 @@ add_test(NAME Bitmap_cubical_complex_example_random COMMAND $<TARGET_FILE:Random "2" "100" "100") add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp ) -target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES}) endif() diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt index b2895f85..02b026f2 100644 --- a/src/Bitmap_cubical_complex/test/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt @@ -4,7 +4,7 @@ project(Bitmap_cubical_complex_tests) include(GUDHI_test_coverage) add_executable ( Bitmap_cubical_complex_test_unit Bitmap_test.cpp ) -target_link_libraries(Bitmap_cubical_complex_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Bitmap_cubical_complex_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Bitmap_cubical_complex_test_unit ${TBB_LIBRARIES}) endif() diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 0534a2c4..dc1da31c 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -6,7 +6,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES}) target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES}) @@ -19,6 +19,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") + add_test(NAME Bottleneck_read_file_example + COMMAND $<TARGET_FILE:bottleneck_read_file_example> + "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers") + install(TARGETS bottleneck_read_file_example DESTINATION bin) install(TARGETS bottleneck_basic_example DESTINATION bin) install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin) diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp index bde05825..238d99ad 100644 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp @@ -20,9 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#define CGAL_HAS_THREADS - #include <gudhi/Bottleneck.h> +#include <gudhi/reader_utils.h> #include <iostream> #include <vector> #include <utility> // for pair @@ -30,43 +29,22 @@ #include <sstream> #include <string> -std::vector< std::pair<double, double> > read_diagram_from_file(const char* filename) { - std::ifstream in; - in.open(filename); - std::vector< std::pair<double, double> > result; - if (!in.is_open()) { - std::cerr << "File : " << filename << " do not exist. The program will now terminate \n"; - throw "File do not exist \n"; - } - - std::string line; - while (!in.eof()) { - getline(in, line); - if (line.length() != 0) { - std::stringstream lineSS; - lineSS << line; - double beginn, endd; - lineSS >> beginn; - lineSS >> endd; - result.push_back(std::make_pair(beginn, endd)); - } - } - in.close(); - return result; -} // read_diagram_from_file - int main(int argc, char** argv) { if (argc < 3) { std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " << "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" << " distance (set by default to zero). The program will now terminate \n"; + return -1; } - std::vector< std::pair< double, double > > diag1 = read_diagram_from_file(argv[1]); - std::vector< std::pair< double, double > > diag2 = read_diagram_from_file(argv[2]); + std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]); + std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]); + double tolerance = 0.; if (argc == 4) { tolerance = atof(argv[3]); } double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance); std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl; + + return 0; } diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index e1bbbbec..a165d472 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -5,7 +5,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) include(GUDHI_test_coverage) add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp ) - target_link_libraries(Bottleneck_distance_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + target_link_libraries(Bottleneck_distance_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Bottleneck_distance_test_unit ${TBB_LIBRARIES}) endif(TBB_FOUND) diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt index b2b38dea..83594c0e 100644 --- a/src/Contraction/example/CMakeLists.txt +++ b/src/Contraction/example/CMakeLists.txt @@ -5,10 +5,6 @@ project(Contraction_examples) add_executable(RipsContraction Rips_contraction.cpp) add_executable(GarlandHeckbert Garland_heckbert.cpp) -target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY}) -target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY}) - - add_test(NAME Contraction_example_tore3D_0.2 COMMAND $<TARGET_FILE:RipsContraction> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0.2") # TODO(DS) : These tests are too long under Windows diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp index 8b5a6a6c..f0cde95e 100644 --- a/src/Contraction/example/Garland_heckbert.cpp +++ b/src/Contraction/example/Garland_heckbert.cpp @@ -29,8 +29,8 @@ #include <gudhi/Edge_contraction.h> #include <gudhi/Skeleton_blocker.h> #include <gudhi/Off_reader.h> +#include <gudhi/Clock.h> -#include <boost/timer/timer.hpp> #include <iostream> #include "Garland_heckbert/Error_quadric.h" @@ -165,7 +165,7 @@ int main(int argc, char *argv[]) { int num_contractions = atoi(argv[3]); - boost::timer::auto_cpu_timer t; + Gudhi::Clock contraction_chrono("Time to simplify and enumerate simplices"); // constructs the contractor object with Garland Heckbert policies. Complex_contractor contractor(complex, @@ -182,6 +182,8 @@ int main(int argc, char *argv[]) { complex.num_edges() << " edges and " << complex.num_triangles() << " triangles." << std::endl; + std::cout << contraction_chrono; + // write simplified complex Gudhi::skeleton_blocker::Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex); diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp index 8289b1d3..501b0e87 100644 --- a/src/Contraction/example/Rips_contraction.cpp +++ b/src/Contraction/example/Rips_contraction.cpp @@ -23,8 +23,8 @@ #include <gudhi/Skeleton_blocker.h> #include <gudhi/Off_reader.h> #include <gudhi/Point.h> +#include <gudhi/Clock.h> -#include <boost/timer/timer.hpp> #include <iostream> struct Geometry_trait { @@ -68,7 +68,7 @@ int main(int argc, char *argv[]) { build_rips(complex, atof(argv[2])); - boost::timer::auto_cpu_timer t; + Gudhi::Clock contraction_chrono("Time to simplify and enumerate simplices"); std::cout << "Initial complex has " << complex.num_vertices() << " vertices and " << @@ -90,8 +90,7 @@ int main(int argc, char *argv[]) { complex.num_blockers() << " blockers and " << num_simplices << " simplices" << std::endl; - - std::cout << "Time to simplify and enumerate simplices:\n"; + std::cout << contraction_chrono; return EXIT_SUCCESS; } diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt index ea792c89..8b135ba1 100644 --- a/src/Persistent_cohomology/benchmark/CMakeLists.txt +++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt @@ -5,7 +5,7 @@ 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}) + target_link_libraries(performance_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if (TBB_FOUND) target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index a9884c49..f47de4c3 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -2,25 +2,23 @@ cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_examples) add_executable(plain_homology plain_homology.cpp) -target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY}) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) -target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY}) add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) -target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(rips_persistence rips_persistence.cpp) -target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) -target_link_libraries(rips_persistence_step_by_step ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp) -target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(persistence_from_file persistence_from_file.cpp) -target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(plain_homology ${TBB_LIBRARIES}) @@ -60,7 +58,7 @@ 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}) + ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if (TBB_FOUND) target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) @@ -72,11 +70,11 @@ endif(GMP_FOUND) if(CGAL_FOUND) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY}) add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp) - target_link_libraries(exact_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY}) add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) - target_link_libraries(weighted_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) @@ -97,13 +95,13 @@ if(CGAL_FOUND) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) target_link_libraries(alpha_complex_persistence - ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY}) add_executable(custom_persistence_sort custom_persistence_sort.cpp) - target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index 11e9a951..45f53eb9 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -4,9 +4,9 @@ project(Persistent_cohomology_tests) include(GUDHI_test_coverage) add_executable ( Persistent_cohomology_test_unit persistent_cohomology_unit_test.cpp ) -target_link_libraries(Persistent_cohomology_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Persistent_cohomology_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) add_executable ( Persistent_cohomology_test_betti_numbers betti_numbers_unit_test.cpp ) -target_link_libraries(Persistent_cohomology_test_betti_numbers ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Persistent_cohomology_test_betti_numbers ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Persistent_cohomology_test_unit ${TBB_LIBRARIES}) target_link_libraries(Persistent_cohomology_test_betti_numbers ${TBB_LIBRARIES}) @@ -22,7 +22,8 @@ gudhi_add_coverage_test(Persistent_cohomology_test_betti_numbers) if(GMPXX_FOUND AND GMP_FOUND) add_executable ( Persistent_cohomology_test_unit_multi_field persistent_cohomology_unit_test_multi_field.cpp ) - target_link_libraries(Persistent_cohomology_test_unit_multi_field ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + target_link_libraries(Persistent_cohomology_test_unit_multi_field + ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if (TBB_FOUND) target_link_libraries(Persistent_cohomology_test_unit_multi_field ${TBB_LIBRARIES}) endif(TBB_FOUND) diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index 712db16e..2940f164 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -3,17 +3,13 @@ project(Rips_complex_examples) # Point cloud add_executable ( Rips_complex_example_from_off example_rips_complex_from_off_file.cpp ) -target_link_libraries(Rips_complex_example_from_off ${Boost_SYSTEM_LIBRARY}) add_executable ( Rips_complex_example_one_skeleton_from_points example_one_skeleton_rips_from_points.cpp ) -target_link_libraries(Rips_complex_example_one_skeleton_from_points ${Boost_SYSTEM_LIBRARY}) # Distance matrix add_executable ( Rips_complex_example_one_skeleton_from_distance_matrix example_one_skeleton_rips_from_distance_matrix.cpp ) -target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix ${Boost_SYSTEM_LIBRARY}) add_executable ( Rips_complex_example_from_csv_distance_matrix example_rips_complex_from_csv_distance_matrix_file.cpp ) -target_link_libraries(Rips_complex_example_from_csv_distance_matrix ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) target_link_libraries(Rips_complex_example_from_off ${TBB_LIBRARIES}) diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt index 57f780f1..3da9c90d 100644 --- a/src/Rips_complex/test/CMakeLists.txt +++ b/src/Rips_complex/test/CMakeLists.txt @@ -4,7 +4,7 @@ project(Rips_complex_tests) include(GUDHI_test_coverage) add_executable ( Rips_complex_test_unit test_rips_complex.cpp ) -target_link_libraries(Rips_complex_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Rips_complex_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Rips_complex_test_unit ${TBB_LIBRARIES}) endif() diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index c414c019..8bc4ad53 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -26,7 +26,7 @@ install(TARGETS Simplex_tree_example_mini_simplex_tree DESTINATION bin) # An example with Simplex-tree using CGAL alpha_shapes_3 if(GMP_FOUND AND CGAL_FOUND) add_executable ( Simplex_tree_example_alpha_shapes_3_from_off example_alpha_shapes_3_simplex_tree_from_off_file.cpp ) - target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY}) + target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${GMP_LIBRARIES} ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${TBB_LIBRARIES}) endif() diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index 2408d937..fc34e6aa 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -4,7 +4,7 @@ project(Simplex_tree_tests) include(GUDHI_test_coverage) add_executable ( Simplex_tree_test_unit simplex_tree_unit_test.cpp ) -target_link_libraries(Simplex_tree_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Simplex_tree_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Simplex_tree_test_unit ${TBB_LIBRARIES}) endif() diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt index ce51ac39..de70f089 100644 --- a/src/Skeleton_blocker/example/CMakeLists.txt +++ b/src/Skeleton_blocker/example/CMakeLists.txt @@ -5,8 +5,6 @@ add_executable(Skeleton_blocker_example_from_simplices Skeleton_blocker_from_sim add_executable(Skeleton_blocker_example_iteration Skeleton_blocker_iteration.cpp) add_executable(Skeleton_blocker_example_link Skeleton_blocker_link.cpp) -target_link_libraries(Skeleton_blocker_example_iteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY}) - add_test(NAME Skeleton_blocker_example_from_simplices COMMAND $<TARGET_FILE:Skeleton_blocker_example_from_simplices>) add_test(NAME Skeleton_blocker_example_iteration COMMAND $<TARGET_FILE:Skeleton_blocker_example_iteration>) add_test(NAME Skeleton_blocker_example_link COMMAND $<TARGET_FILE:Skeleton_blocker_example_link>) diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp index 6a1bc480..08ff0264 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp @@ -21,8 +21,7 @@ */ #include <gudhi/Skeleton_blocker.h> - -#include <boost/timer/timer.hpp> +#include <gudhi/Clock.h> #include <stdio.h> #include <stdlib.h> @@ -47,8 +46,7 @@ Complex build_complete_complex(int n) { } int main(int argc, char *argv[]) { - boost::timer::auto_cpu_timer t; - + Gudhi::Clock skbl_chrono("Time to build the complete complex, enumerate simplices and Euler Characteristic"); const int n = 15; // build a full complex with n vertices and 2^n-1 simplices @@ -82,5 +80,6 @@ int main(int argc, char *argv[]) { std::cout << "Saw " << num_vertices << " vertices, " << num_edges << " edges and " << num_simplices << " simplices" << std::endl; std::cout << "The Euler Characteristic is " << euler << std::endl; + std::cout << skbl_chrono; return EXIT_SUCCESS; } diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt index 0887fcff..4a363294 100644 --- a/src/Skeleton_blocker/test/CMakeLists.txt +++ b/src/Skeleton_blocker/test/CMakeLists.txt @@ -4,11 +4,11 @@ project(Skeleton_blocker_tests) include(GUDHI_test_coverage) add_executable ( Skeleton_blocker_test_unit test_skeleton_blocker_complex.cpp ) -target_link_libraries(Skeleton_blocker_test_unit ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Skeleton_blocker_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) add_executable ( Skeleton_blocker_test_geometric_complex test_skeleton_blocker_geometric_complex.cpp ) -target_link_libraries(Skeleton_blocker_test_geometric_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Skeleton_blocker_test_geometric_complex ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) add_executable ( Skeleton_blocker_test_simplifiable test_skeleton_blocker_simplifiable.cpp ) -target_link_libraries(Skeleton_blocker_test_simplifiable ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Skeleton_blocker_test_simplifiable ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) # Do not forget to copy test files in current binary dir file(COPY "test2.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) diff --git a/src/Spatial_searching/test/CMakeLists.txt b/src/Spatial_searching/test/CMakeLists.txt index 2502ea5e..b9da7b4e 100644 --- a/src/Spatial_searching/test/CMakeLists.txt +++ b/src/Spatial_searching/test/CMakeLists.txt @@ -6,7 +6,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable( Spatial_searching_test_Kd_tree_search test_Kd_tree_search.cpp ) target_link_libraries(Spatial_searching_test_Kd_tree_search - ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) gudhi_add_coverage_test(Spatial_searching_test_Kd_tree_search) endif () diff --git a/src/Subsampling/include/gudhi/pick_n_random_points.h b/src/Subsampling/include/gudhi/pick_n_random_points.h index f0e3f1f1..8c90b6bf 100644 --- a/src/Subsampling/include/gudhi/pick_n_random_points.h +++ b/src/Subsampling/include/gudhi/pick_n_random_points.h @@ -52,7 +52,7 @@ typename OutputIterator> void pick_n_random_points(Point_container const &points, std::size_t final_size, OutputIterator output_it) { -#ifdef GUDHI_SUBS_PROFILING +#ifdef GUDHI_SUBSAMPLING_PROFILING Gudhi::Clock t; #endif @@ -72,7 +72,7 @@ void pick_n_random_points(Point_container const &points, for (int l : landmarks) *output_it++ = points[l]; -#ifdef GUDHI_SUBS_PROFILING +#ifdef GUDHI_SUBSAMPLING_PROFILING t.end(); std::cerr << "Random landmark choice took " << t.num_seconds() << " seconds." << std::endl; diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt index ef772be8..8729e394 100644 --- a/src/Tangential_complex/benchmark/CMakeLists.txt +++ b/src/Tangential_complex/benchmark/CMakeLists.txt @@ -3,8 +3,7 @@ project(Tangential_complex_benchmark) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable(Tangential_complex_benchmark benchmark_tc.cpp) - target_link_libraries(Tangential_complex_benchmark - ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(Tangential_complex_benchmark ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES}) endif(TBB_FOUND) diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index 45c7642b..16d1339d 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -3,9 +3,9 @@ project(Tangential_complex_examples) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable( Tangential_complex_example_basic example_basic.cpp ) - target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) + target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY}) add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) - target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) + target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt index fc710676..1948c8f6 100644 --- a/src/Tangential_complex/test/CMakeLists.txt +++ b/src/Tangential_complex/test/CMakeLists.txt @@ -5,7 +5,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) include(GUDHI_test_coverage) add_executable( Tangential_complex_test_TC test_tangential_complex.cpp ) - target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES}) endif() diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 1e18d024..cbc53902 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -2,7 +2,6 @@ cmake_minimum_required(VERSION 2.6) project(Witness_complex_examples) add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp ) -target_link_libraries(Witness_complex_example_nearest_landmark_table ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) target_link_libraries(Witness_complex_example_nearest_landmark_table ${TBB_LIBRARIES}) endif() @@ -14,17 +13,14 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) # CGAL and Eigen3 are required for Euclidean version of Witness if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) - target_link_libraries(Witness_complex_example_off ${Boost_SYSTEM_LIBRARY}) add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) - target_link_libraries(Witness_complex_example_strong_off ${Boost_SYSTEM_LIBRARY}) add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) - target_link_libraries(Witness_complex_example_sphere ${Boost_SYSTEM_LIBRARY}) add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp ) - target_link_libraries(Witness_complex_example_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp ) - target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES}) diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt index 152e2f2c..0b523eaf 100644 --- a/src/Witness_complex/test/CMakeLists.txt +++ b/src/Witness_complex/test/CMakeLists.txt @@ -4,7 +4,7 @@ project(Witness_complex_tests) include(GUDHI_test_coverage) add_executable ( Witness_complex_test_simple_witness_complex test_simple_witness_complex.cpp ) -target_link_libraries(Witness_complex_test_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Witness_complex_test_simple_witness_complex ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Witness_complex_test_simple_witness_complex ${TBB_LIBRARIES}) endif(TBB_FOUND) @@ -14,7 +14,7 @@ gudhi_add_coverage_test(Witness_complex_test_simple_witness_complex) # CGAL and Eigen3 are required for Euclidean version of Witness if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) add_executable ( Witness_complex_test_euclidean_simple_witness_complex test_euclidean_simple_witness_complex.cpp ) - target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${TBB_LIBRARIES}) endif(TBB_FOUND) diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 8cb01d3c..8f486118 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -1,6 +1,6 @@ # This files manage third party libraries required by GUDHI -find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread) +find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread) if(NOT Boost_FOUND) message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") @@ -99,6 +99,8 @@ add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) add_definitions(-DBOOST_ALL_NO_LIB) # problem with Visual Studio link on Boost program_options add_definitions( -DBOOST_ALL_DYN_LINK ) +# problem on Mac with boost_system and boost_thread +add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED ) INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) @@ -106,19 +108,6 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS}) message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) -macro( find_the_lib placeholder THE_LIBS ) - set (THE_LIB_WE_FOUND "NO") - foreach(THE_LIB ${THE_LIBS}) - if(EXISTS ${THE_LIB}) - get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE) - if (NOT THE_LIB_WE_FOUND) - set (THE_LIB_WE_FOUND "YES") - set(returnValue "${THE_LIB_WE}") - endif(NOT THE_LIB_WE_FOUND) - endif(EXISTS ${THE_LIB}) - endforeach(THE_LIB ${THE_LIBS}) -endmacro( find_the_lib ) - # Find the correct Python interpreter. # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance. find_package(Cython) diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h new file mode 100644 index 00000000..c145b271 --- /dev/null +++ b/src/common/doc/file_formats.h @@ -0,0 +1,54 @@ +/* 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 Jamin +* +* Copyright (C) 2017 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 +* 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/>. +*/ + +#ifndef DOC_COMMON_FILE_FORMAT_H_ +#define DOC_COMMON_FILE_FORMAT_H_ + +namespace Gudhi { + +/*! \page fileformats File formats + + \tableofcontents + + \section FileFormatsPers Persistence Diagram + + Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br> + Lines starting with `#` are ignored (comments).<br> + Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines): + \code{.unparsed} + [[field] dimension] birth death + \endcode + + Here is a simple sample file: + \code{.unparsed} + # Beautiful persistence diagram + 2 2.7 3.7 + 2 9.6 14. + 3 34.2 34.974 + 4 3. inf + \endcode + + Other sample files can be found in the `data/persistence_diagram` folder. +*/ +} // namespace Gudhi + +#endif // DOC_COMMON_FILE_FORMAT_H_ diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index af3c2c9d..afe865d4 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6) project(Common_examples) add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp ) -target_link_libraries(vector_double_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) +target_link_libraries(vector_double_off_reader ${CGAL_LIBRARY}) add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader> "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off") @@ -10,18 +10,19 @@ install(TARGETS vector_double_off_reader DESTINATION bin) if(CGAL_FOUND) add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp ) - target_link_libraries(cgal_3D_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(cgal_3D_off_reader ${CGAL_LIBRARY}) add_test(NAME Common_example_vector_cgal_3D_off_reader COMMAND $<TARGET_FILE:cgal_3D_off_reader> "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off") - # need CGAL 4.7and Eigen3 + install(TARGETS cgal_3D_off_reader DESTINATION bin) + + # need CGAL 4.7 and Eigen3 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp ) - target_link_libraries(cgal_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(cgal_off_reader ${CGAL_LIBRARY}) add_test(NAME Common_example_vector_cgal_off_reader COMMAND $<TARGET_FILE:cgal_off_reader> "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off") + install(TARGETS cgal_off_reader DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - install(TARGETS cgal_3D_off_reader DESTINATION bin) - install(TARGETS cgal_off_reader DESTINATION bin) endif() diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h index 77f196ca..b83de2f5 100644 --- a/src/common/include/gudhi/Clock.h +++ b/src/common/include/gudhi/Clock.h @@ -23,9 +23,9 @@ #ifndef CLOCK_H_ #define CLOCK_H_ -#include <boost/date_time/posix_time/posix_time.hpp> - +#include <iostream> #include <string> +#include <chrono> namespace Gudhi { @@ -33,20 +33,20 @@ class Clock { public: // Construct and start the timer Clock(const std::string& msg_ = std::string()) - : startTime(boost::posix_time::microsec_clock::local_time()), + : startTime(std::chrono::system_clock::now()), end_called(false), msg(msg_) { } // Restart the timer void begin() const { end_called = false; - startTime = boost::posix_time::microsec_clock::local_time(); + startTime = std::chrono::system_clock::now(); } // Stop the timer void end() const { end_called = true; - endTime = boost::posix_time::microsec_clock::local_time(); + endTime = std::chrono::system_clock::now(); } std::string message() const { @@ -62,7 +62,7 @@ class Clock { if (!clock.msg.empty()) stream << clock.msg << ": "; - stream << clock.num_seconds() << "s"; + stream << clock.num_seconds() << "s\n"; return stream; } @@ -71,15 +71,15 @@ class Clock { // - or now otherwise. In this case, the timer is not stopped. double num_seconds() const { if (!end_called) { - auto end = boost::posix_time::microsec_clock::local_time(); - return (end - startTime).total_milliseconds() / 1000.; + auto end = std::chrono::system_clock::now(); + return std::chrono::duration_cast<std::chrono::milliseconds>(end-startTime).count() / 1000.; } else { - return (endTime - startTime).total_milliseconds() / 1000.; + return std::chrono::duration_cast<std::chrono::milliseconds>(endTime-startTime).count() / 1000.; } } private: - mutable boost::posix_time::ptime startTime, endTime; + mutable std::chrono::time_point<std::chrono::system_clock> startTime, endTime; mutable bool end_called; std::string msg; }; diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 97a87edd..f1684d78 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -2,7 +2,7 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clement Maria, Pawel Dlotko + * Author(s): Clement Maria, Pawel Dlotko, Clement Jamin * * Copyright (C) 2014 INRIA * @@ -24,7 +24,9 @@ #define READER_UTILS_H_ #include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Debug_utils.h> +#include <boost/function_output_iterator.hpp> #include <boost/graph/adjacency_list.hpp> #include <iostream> @@ -92,7 +94,10 @@ template< typename Graph_t, typename Filtration_value, typename Vertex_handle > Graph_t read_graph(std::string file_name) { std::ifstream in_(file_name.c_str(), std::ios::in); if (!in_.is_open()) { - std::cerr << "Unable to open file " << file_name << std::endl; + std::string error_str("read_graph - Unable to open file "); + error_str.append(file_name); + std::cerr << error_str << std::endl; + throw std::invalid_argument(error_str); } typedef std::pair< Vertex_handle, Vertex_handle > Edge_t; @@ -295,4 +300,73 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from return result; } // read_lower_triangular_matrix_from_csv_file +/** +Reads a file containing persistence intervals. +Each line might contain 2, 3 or 4 values: [[field] dimension] birth death +The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);` +where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. +**/ +template <typename OutputIterator> +void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) { + + std::ifstream in(filename); + if (!in.is_open()) { + std::string error_str("read_persistence_intervals_and_dimension - Unable to open file "); + error_str.append(filename); + std::cerr << error_str << std::endl; + throw std::invalid_argument(error_str); + } + + while (!in.eof()) { + std::string line; + getline(in, line); + if (line.length() != 0 && line[0] != '#') { + double numbers[4]; + int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]); + if (n >= 2) { + //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1); + int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1); + *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]); + } + } + } +} // read_persistence_diagram_from_file + +/** +Reads a file containing persistence intervals. +Each line might contain 2, 3 or 4 values: [[field] dimension] birth death +The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>` +where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. +**/ +inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) { + + std::map<int, std::vector<std::pair<double, double>>> ret; + read_persistence_intervals_and_dimension( + filename, + boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); })); + return ret; +} // read_persistence_diagram_from_file + + +/** +Reads a file containing persistence intervals. +Each line might contain 2, 3 or 4 values: [[field] dimension] birth death +If `only_this_dim` = -1, dimension is ignored and all lines are returned. +If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` +(or where dimension is not specified) are returned. +The return value is an `std::vector<std::pair<birth, death>>` +where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. +**/ +inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) { + + std::vector<std::pair<double, double>> ret; + read_persistence_intervals_and_dimension( + filename, + boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); })); + return ret; +} // read_persistence_diagram_from_file + #endif // READER_UTILS_H_ diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt index c695fbf4..5aa426d7 100644 --- a/src/common/test/CMakeLists.txt +++ b/src/common/test/CMakeLists.txt @@ -4,10 +4,10 @@ project(Common_tests) include(GUDHI_test_coverage) add_executable ( Common_test_points_off_reader test_points_off_reader.cpp ) -target_link_libraries(Common_test_points_off_reader ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Common_test_points_off_reader ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) add_executable ( Common_test_distance_matrix_reader test_distance_matrix_reader.cpp ) -target_link_libraries(Common_test_distance_matrix_reader ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(Common_test_distance_matrix_reader ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) diff --git a/src/common/utilities/CMakeLists.txt b/src/common/utilities/CMakeLists.txt index c2e07e7e..b3e4b436 100644 --- a/src/common/utilities/CMakeLists.txt +++ b/src/common/utilities/CMakeLists.txt @@ -3,7 +3,6 @@ project(off_file_from_shape_generator) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) add_executable ( off_file_from_shape_generator off_file_from_shape_generator.cpp ) - target_link_libraries(off_file_from_shape_generator ${Boost_SYSTEM_LIBRARY}) add_test(NAME off_file_from_shape_generator_on_sphere_1000_3_15.2 COMMAND $<TARGET_FILE:off_file_from_shape_generator> "on" "sphere" "onSphere.off" "1000" "3" "15.2") add_test(NAME off_file_from_shape_generator_in_sphere_100_2 COMMAND $<TARGET_FILE:off_file_from_shape_generator> diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index d9f356f9..99badffb 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -1,20 +1,55 @@ cmake_minimum_required(VERSION 2.8) project(Cython) +function( add_gudhi_cython_lib THE_LIB ) + if(EXISTS ${THE_LIB}) + get_filename_component(THE_LIB_FILE_NAME ${THE_LIB} NAME_WE) + if(WIN32) + message("++ ${THE_LIB} => THE_LIB_FILE_NAME = ${THE_LIB_FILE_NAME}") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${THE_LIB_FILE_NAME}', " PARENT_SCOPE) + else(WIN32) + STRING(REGEX REPLACE "lib" "" UNIX_LIB_FILE_NAME ${THE_LIB_FILE_NAME}) + message("++ ${THE_LIB} => UNIX_LIB_FILE_NAME = ${UNIX_LIB_FILE_NAME}") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_LIB_FILE_NAME}', " PARENT_SCOPE) + endif(WIN32) + endif(EXISTS ${THE_LIB}) +endfunction( add_gudhi_cython_lib ) + if(CYTHON_FOUND) message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") - if(WIN32) - set( returnValue "" ) - find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY}) - set(BOOST_SYSTEM_LIB_NAME ${returnValue}) - else() - set(BOOST_SYSTEM_LIB_NAME "boost_system") - endif() - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") + + # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h + # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac). + # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h + # #if __has_feature(cxx_thread_local) || \ + # ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + # ( _MSC_VER >= 1900 ) + # #define CGAL_CAN_USE_CXX11_THREAD_LOCAL + # #endif + set(CGAL_CAN_USE_CXX11_THREAD_LOCAL " + int main() { + #ifndef __has_feature + #define __has_feature(x) 0 // Compatibility with non-clang compilers. + #endif + #if __has_feature(cxx_thread_local) || \ + ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + ( _MSC_VER >= 1900 ) + bool has_feature_thread_local = true; + #else + // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined + #endif + bool result = has_feature_thread_local; + } ") + check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + + if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + add_gudhi_cython_lib(${Boost_THREAD_LIBRARY}) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + endif() # Gudhi and CGAL compilation option if(MSVC) @@ -25,9 +60,9 @@ if(CYTHON_FOUND) if(CMAKE_COMPILER_IS_GNUCXX) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") endif(CMAKE_COMPILER_IS_GNUCXX) - if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + if (CMAKE_CXX_COMPILER_ID MATCHES Intel) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") - endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + endif(CMAKE_CXX_COMPILER_ID MATCHES Intel) if (DEBUG_TRACES) # For programs to be more verbose set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") @@ -114,25 +149,20 @@ if(CYTHON_FOUND) if(CGAL_HEADER_ONLY) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") else(CGAL_HEADER_ONLY) - if(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ") - else(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ") - endif(WIN32) + add_gudhi_cython_lib(${CGAL_LIBRARIES}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") + # If CGAL is not header only, CGAL library may link with boost system, + add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY}) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") endif(CGAL_HEADER_ONLY) # GMP and GMPXX are not required, but if present, CGAL will link with them. if(GMP_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") - if(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ") - else(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ") - endif(WIN32) - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") + add_gudhi_cython_lib(${GMP_LIBRARIES}) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") if(GMPXX_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ") + add_gudhi_cython_lib(${GMPXX_LIBRARIES}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") endif(GMPXX_FOUND) endif(GMP_FOUND) @@ -153,32 +183,33 @@ if(CYTHON_FOUND) if (TBB_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ") + add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY}) + add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") endif() + if(UNIX) + set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") + endif(UNIX) + # set sphinx-build in make files configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY) configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) - # Generate cythonize_gudhi.py file to cythonize Gudhi - configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY) + # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention + configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY) # Generate gudhi.pyx - Gudhi cython file configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY) add_custom_command( OUTPUT gudhi.so WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace") + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace") add_custom_target(cython ALL DEPENDS gudhi.so COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") - if(UNIX) - set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ ) - endif(UNIX) - # For installation purpose # TODO(VR) : files matching pattern mechanism is copying all cython directory install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING @@ -187,39 +218,52 @@ if(CYTHON_FOUND) PATTERN "*.pyd") # Test examples - add_test(NAME alpha_complex_from_points_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py") - set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - - add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) - set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - - add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" - -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - - add_test(NAME bottleneck_basic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py") - set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" + -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) + set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + add_test(NAME bottleneck_basic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py") + set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + add_test(NAME alpha_complex_from_points_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py") + set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) + set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} @@ -255,12 +299,6 @@ if(CYTHON_FOUND) COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py) set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - add_test(NAME witness_complex_from_nearest_landmark_table_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py) diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/setup.py.in index 5a97e9f3..c1a1717a 100644 --- a/src/cython/cythonize_gudhi.py.in +++ b/src/cython/setup.py.in @@ -36,13 +36,14 @@ gudhi = Extension( libraries=[@GUDHI_CYTHON_LIBRARIES@], library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@], include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@], + runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@], ) setup( name = 'gudhi', author='Vincent Rouvreau', author_email='gudhi-contact@lists.gforge.inria.fr', - version='0.1.0', + version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', ext_modules = cythonize(gudhi), ) |