diff options
Diffstat (limited to 'src')
-rw-r--r-- | src/Persistent_cohomology/example/CMakeLists.txt | 6 | ||||
-rw-r--r-- | src/Simplex_tree/example/CMakeLists.txt | 16 | ||||
-rw-r--r-- | src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp (renamed from src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp) | 26 | ||||
-rw-r--r-- | src/Witness_complex/example/CMakeLists.txt | 3 | ||||
-rw-r--r-- | src/Witness_complex/example/witness_complex_from_file.cpp | 41 | ||||
-rw-r--r-- | src/cmake/modules/FindQGLViewer.cmake | 2 |
6 files changed, 38 insertions, 56 deletions
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 75f3c5d4..34a5ed71 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -31,9 +31,9 @@ endif() add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology) add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0) add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100) -add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100) -add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0) -add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) +add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100) +add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0) +add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100) if(GMP_FOUND) if(GMPXX_FOUND) diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index 9314a805..e5285591 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -5,8 +5,10 @@ add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of if (TBB_FOUND) target_link_libraries(simplex_tree_from_cliques_of_graph ${TBB_LIBRARIES}) endif() -add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2) -add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3) +add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph + ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_complex.fsc 2) +add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph + ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_complex.fsc 3) add_executable ( simple_simplex_tree simple_simplex_tree.cpp ) if (TBB_FOUND) @@ -20,10 +22,12 @@ add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree) # An example with Simplex-tree using CGAL alpha_shapes_3 if(GMP_FOUND AND CGAL_FOUND) - add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp ) - target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY}) + add_executable ( alpha_shapes_3_simplex_tree_from_off_file example_alpha_shapes_3_simplex_tree_from_off_file.cpp ) + target_link_libraries(alpha_shapes_3_simplex_tree_from_off_file ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) - target_link_libraries(simplex_tree_from_alpha_shapes_3 ${TBB_LIBRARIES}) + target_link_libraries(alpha_shapes_3_simplex_tree_from_off_file ${TBB_LIBRARIES}) endif() - add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000) + add_test(alpha_shapes_3_simplex_tree_from_off_file + ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_3_simplex_tree_from_off_file + ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off) endif() diff --git a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp index 49d358ab..ff2eebcb 100644 --- a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp +++ b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp @@ -20,8 +20,9 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/graph_simplicial_complex.h> #include <gudhi/Simplex_tree.h> +#include <gudhi/Points_3D_off_io.h> + #include <boost/variant.hpp> #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> @@ -118,24 +119,21 @@ int main(int argc, char * const argv[]) { // program args management if (argc != 2) { std::cerr << "Usage: " << argv[0] - << " path_to_file_graph \n"; + << " path_to_off_file \n"; return 0; } // Read points from file - std::string filegraph = argv[1]; - std::list<Point> lp; - std::ifstream is(filegraph.c_str()); - int n; - is >> n; -#ifdef DEBUG_TRACES - std::cout << "Reading " << n << " points " << std::endl; -#endif // DEBUG_TRACES - Point p; - for (; n > 0; n--) { - is >> p; - lp.push_back(p); + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader<Point> off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << argv[1] << std::endl; + return 0; } + // Retrieve the triangulation + std::vector<Point> lp = off_reader.get_point_cloud(); // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 4d67e0d0..857ec819 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -3,7 +3,8 @@ project(Witness_complex_examples) # A simple example add_executable( witness_complex_from_file witness_complex_from_file.cpp ) - add_test( witness_complex_from_bunny ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100) + add_test( witness_complex_from_bunny ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file + ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off 100) if(CGAL_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp index 392ad55d..6a203383 100644 --- a/src/Witness_complex/example/witness_complex_from_file.cpp +++ b/src/Witness_complex/example/witness_complex_from_file.cpp @@ -23,10 +23,10 @@ #include <sys/types.h> #include <sys/stat.h> +#include <gudhi/Points_off_io.h> #include <gudhi/Simplex_tree.h> #include <gudhi/Witness_complex.h> #include <gudhi/Landmark_choice_by_random_point.h> -#include <gudhi/reader_utils.h> #include <iostream> #include <fstream> @@ -37,49 +37,28 @@ typedef std::vector< int > typeVectorVertex; typedef std::vector< std::vector <double> > Point_Vector; -/** - * \brief Customized version of read_points - * which takes into account a possible nbP first line - * - */ -inline void -read_points_cust(std::string file_name, std::vector< std::vector< double > > & points) { - std::ifstream in_file(file_name.c_str(), std::ios::in); - if (!in_file.is_open()) { - std::cerr << "Unable to open file " << file_name << std::endl; - return; - } - std::string line; - double x; - while (getline(in_file, line)) { - std::vector< double > point; - std::istringstream iss(line); - while (iss >> x) { - point.push_back(x); - } - if (point.size() != 1) - points.push_back(point); - } - in_file.close(); -} - int main(int argc, char * const argv[]) { if (argc != 3) { std::cerr << "Usage: " << argv[0] - << " path_to_point_file nbL \n"; + << " path_to_point_file.off nbL \n"; return 0; } - std::string file_name = argv[1]; + std::string off_file_name = argv[1]; int nbL = atoi(argv[2]); clock_t start, end; // Construct the Simplex Tree Gudhi::Simplex_tree<> simplex_tree; + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_off_reader<std::vector <double>> off_reader(off_file_name); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << off_file_name << std::endl; + } // Read the point file - Point_Vector point_vector; - read_points_cust(file_name, point_vector); + Point_Vector point_vector = off_reader.get_point_cloud(); std::cout << "Successfully read " << point_vector.size() << " points.\n"; std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n"; diff --git a/src/cmake/modules/FindQGLViewer.cmake b/src/cmake/modules/FindQGLViewer.cmake index 65723d67..1f3dbc1f 100644 --- a/src/cmake/modules/FindQGLViewer.cmake +++ b/src/cmake/modules/FindQGLViewer.cmake @@ -15,7 +15,7 @@ find_path(QGLVIEWER_INCLUDE_DIR ) find_library(QGLVIEWER_LIBRARY_RELEASE - NAMES qglviewer-qt4 qglviewer QGLViewer QGLViewer2 + NAMES qglviewer-qt4 QGLViewer-qt4 qglviewer QGLViewer QGLViewer2 PATHS /usr/lib /usr/local/lib ENV QGLVIEWERROOT |