diff options
Diffstat (limited to 'src')
70 files changed, 424 insertions, 682 deletions
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp index f8754345..122160a2 100644 --- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp +++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp @@ -30,6 +30,7 @@ #include <iostream> #include <sstream> #include <vector> +#include <string> int main(int argc, char** argv) { std::cout << "This program computes persistent homology, by using " << diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt index 170081ce..20a4e47b 100644 --- a/src/Bottleneck_distance/benchmark/CMakeLists.txt +++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt @@ -1,9 +1,9 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_benchmark) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) if (TBB_FOUND) target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES}) endif(TBB_FOUND) -endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +endif(NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index dc1da31c..eac617db 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -1,30 +1,38 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) 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_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES}) target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES}) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>) - add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck - 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) +endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) + +# Eigen3 and CGAL > 4.7.0 is required for alpha complex +# CGAL > 4.8.1 is required for bottleneck distance => +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck + 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") + + install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin) + if (TBB_FOUND) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) + endif(TBB_FOUND) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp index 1408681a..24d73c57 100644 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp @@ -25,21 +25,21 @@ #include <iostream> #include <vector> #include <utility> // for pair -#include <fstream> -#include <sstream> #include <string> +#include <limits> // for numeric_limits 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"; + 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 the smallest positive double value). If you set the error bound to 0, be" << + " aware this version is exact but expensive. The program will now terminate \n"; return -1; } std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]); std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]); - double tolerance = 0.; + double tolerance = std::numeric_limits<double>::min(); if (argc == 4) { tolerance = atof(argv[3]); } diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index bdc47578..a6b9b021 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -44,16 +44,16 @@ struct Square_query { typedef Internal_point Point_d; typedef double FT; bool contains(Point_d p) const { - return std::abs(p.x()-c.x())<=size && std::abs(p.y()-c.y())<=size; + return std::abs(p.x()-c.x()) <= size && std::abs(p.y()-c.y()) <= size; } - bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT,D> const&r) const { + bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT, D> const&r) const { return r.max_coord(0) >= c.x() - size && r.min_coord(0) <= c.x() + size && r.max_coord(1) >= c.y() - size && r.min_coord(1) <= c.y() + size; } - bool outer_range_contains(CGAL::Kd_tree_rectangle<FT,D> const&r) const { + bool outer_range_contains(CGAL::Kd_tree_rectangle<FT, D> const&r) const { return r.min_coord(0) >= c.x() - size && r.max_coord(0) <= c.x() + size && @@ -146,7 +146,7 @@ inline int Neighbors_finder::pull_near(int u_point_index) { // Is the query point near to a V point in the plane ? Internal_point u_point = g.get_u_point(u_point_index); auto neighbor = kd_t.search_any_point(Square_query{u_point, r}); - if(!neighbor) + if (!neighbor) return null_point_index(); tmp = neighbor->point_index; auto point = g.get_v_point(tmp); diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index a165d472..2676b82c 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -1,7 +1,7 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_tests) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) include(GUDHI_test_coverage) add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp ) @@ -12,4 +12,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) gudhi_add_coverage_test(Bottleneck_distance_test_unit) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Doxyfile b/src/Doxyfile index 6c01aefc..0ef81e5c 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -38,7 +38,7 @@ PROJECT_NAME = "GUDHI" # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = "2.0.1-rc1" +PROJECT_NUMBER = "2.0.1" # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index 57861946..374195d0 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -5,28 +5,6 @@ find_package(Qt5 COMPONENTS Widgets Xml OpenGL) find_package(QGLViewer) find_package(OpenGL) -if (CGAL_VERSION VERSION_EQUAL 4.8.0) - message(ERROR " GudhUI does not compile with CGAL 4.8.0. 4.8.1, 4.8.2 and 4.9 are OK.") -endif() - -if (NOT CGAL_FOUND) - message(ERROR " GudhUI requires CGAL and will not be compiled.") -endif() - -if (NOT Qt5_FOUND) - message(ERROR " GudhUI requires Qt5 and will not be compiled.") -endif() - -if (NOT OPENGL_FOUND) - message(ERROR " GudhUI requires OpenGL and will not be compiled.") -endif() - -if (NOT QGLVIEWER_FOUND) - message(ERROR " GudhUI requires QGLViewer and will not be compiled.") -endif() - - - if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0) set(CMAKE_AUTOMOC ON) @@ -37,8 +15,6 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_ SET(Boost_USE_MULTITHREAD OFF) include_directories (${QGLVIEWER_INCLUDE_DIR}) - ##################################################################### - add_executable ( GudhUI gui/gudhui.cpp gui/MainWindow.cpp @@ -52,14 +28,10 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_ target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL ) target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} ) target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ) -if (TBB_FOUND) - target_link_libraries( GudhUI ${TBB_LIBRARIES}) -endif() + if (TBB_FOUND) + target_link_libraries( GudhUI ${TBB_LIBRARIES}) + endif() install(TARGETS GudhUI DESTINATION bin) -############################################################################### - -else() - message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt5, and will not be compiled.") endif() diff --git a/src/Hasse_complex/include/gudhi/Hasse_complex.h b/src/Hasse_complex/include/gudhi/Hasse_complex.h index 8b06b771..e67f7609 100644 --- a/src/Hasse_complex/include/gudhi/Hasse_complex.h +++ b/src/Hasse_complex/include/gudhi/Hasse_complex.h @@ -30,6 +30,7 @@ #include <algorithm> #include <utility> // for pair #include <vector> +#include <limits> // for infinity value #ifdef GUDHI_USE_TBB #include <tbb/parallel_for.h> @@ -104,7 +105,6 @@ class Hasse_complex { Hasse_complex(Complex_ds & cpx) : complex_(cpx.num_simplices()) , vertices_() - , threshold_(cpx.filtration()) , num_vertices_() , dim_max_(cpx.dimension()) { int size = complex_.size(); @@ -125,7 +125,6 @@ class Hasse_complex { Hasse_complex() : complex_() , vertices_() - , threshold_(0) , num_vertices_(0) , dim_max_(-1) { } @@ -157,15 +156,11 @@ class Hasse_complex { Filtration_value filtration(Simplex_handle sh) { if (sh == null_simplex()) { - return filtration(); + return std::numeric_limits<Filtration_value>::infinity(); } return complex_[sh].filtration_; } - Filtration_value filtration() { - return threshold_; - } - int dimension(Simplex_handle sh) { if (complex_[sh].boundary_.empty()) return 0; return complex_[sh].boundary_.size() - 1; @@ -206,7 +201,6 @@ class Hasse_complex { std::vector< Hasse_simp, Gudhi::no_init_allocator<Hasse_simp> > complex_; std::vector<Simplex_handle> vertices_; - Filtration_value threshold_; size_t num_vertices_; int dim_max_; }; @@ -245,7 +239,6 @@ std::istream& operator>>(std::istream & is } hcpx.dim_max_ = max_dim; - hcpx.threshold_ = max_fil; return is; } diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index e17e5926..6400116b 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -189,10 +189,10 @@ and a weights file. \code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights 2 0.45 \endcode \code Simplex_tree dim: 3 -2 -0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 \endcode +2 0 -1 inf +2 1 -0.931784 0.000103311 +2 1 -0.906588 2.60165e-05 +2 2 -0.43556 0.0393798 \endcode \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with @@ -208,7 +208,8 @@ Simplex_tree dim: 3 \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. -\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 \endcode +\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off +../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 \endcode \code Periodic Delaunay computed. Simplex_tree dim: 3 3 0 0 inf diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index fd227b82..f63ff0f6 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -76,8 +76,9 @@ using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; void usage(const std::string& progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; exit(-1); } @@ -202,7 +203,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -216,7 +216,6 @@ int main(int argc, char * const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp index 8a335075..09561d03 100644 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -77,8 +77,9 @@ using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; exit(-1); } @@ -204,7 +205,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -218,7 +218,6 @@ int main(int argc, char * const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES 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 8928cfc2..8140a3c5 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -84,8 +84,16 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog ST, Gudhi::persistent_cohomology::Field_Zp >; void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" << + "integer > 0] min_persistence[float >= -1.0]\n" << + " path_to_OFF_file is the path to your points cloud in OFF format.\n" << + " path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" << + " x_min y_min z_min x_max y_max z_max\n" << + " In this example, the periodic cube will be " << + "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" << + " For more information, please refer to\n" << + " https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n"; + exit(-1); } @@ -221,7 +229,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -235,7 +242,6 @@ int main(int argc, char * const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp index 67235467..eafa3fd5 100644 --- a/src/Persistent_cohomology/example/persistence_from_file.cpp +++ b/src/Persistent_cohomology/example/persistence_from_file.cpp @@ -61,8 +61,7 @@ int main(int argc, char * argv[]) { simplex_tree_stream >> simplex_tree; std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() - << std::endl; + std::cout << " - dimension " << simplex_tree.dimension() << std::endl; /* std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; 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 7ca9410a..8214d66a 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -143,11 +143,10 @@ int main(int argc, char * const argv[]) { /* An edge [10,12,2] */ st.set_dimension(2); - st.set_filtration(0.4); std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; std::cout << "**************************************************************" << std::endl; diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp index 34b90933..72268511 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -81,8 +81,13 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog ST, Gudhi::persistent_cohomology::Field_Zp >; void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_weight_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; + std::cerr << " path_to_weight_file is the path to the weights of your points cloud (one value per line.)\n"; + std::cerr << " Weights values are explained on CGAL documentation:\n"; + std::cerr << " https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0\n"; + std::cerr << " https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation\n"; exit(-1); } @@ -115,6 +120,7 @@ int main(int argc, char * const argv[]) { if (weights_ifstr.good()) { double weight = 0.0; std::size_t index = 0; + wp.reserve(lp.size()); // Attempt read the weight in a double format, return false if it fails while ((weights_ifstr >> weight) && (index < lp.size())) { wp.push_back(Weighted_point_3(lp[index], weight)); @@ -130,7 +136,7 @@ int main(int argc, char * const argv[]) { } // 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); + Alpha_shape_3 as(wp.begin(), wp.end(), 0, Alpha_shape_3::GENERAL); #ifdef DEBUG_TRACES std::cout << "Alpha shape computed in GENERAL mode" << std::endl; #endif // DEBUG_TRACES @@ -222,7 +228,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -236,7 +241,6 @@ int main(int argc, char * const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp index f8174020..f53987b6 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -31,12 +31,11 @@ std::string test_rips_persistence(int coefficient, int min_persistence) { // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() - << " - filtration= " << st.filtration() << std::endl; + << std::endl; // Check BOOST_CHECK(st.num_simplices() == 98); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(st.filtration() == 1.89); // Sort the simplices in the order of the filtration st.initialize_filtration(); 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 3537cfa4..9e767943 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 @@ -31,12 +31,11 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, doub // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() - << " - filtration= " << st.filtration() << std::endl; + << std::endl; // Check BOOST_CHECK(st.num_simplices() == 58); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(st.filtration() == 0.4); // Sort the simplices in the order of the filtration st.initialize_filtration(); diff --git a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp index d0d3f038..86bfb8cb 100644 --- a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp +++ b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp @@ -65,8 +65,8 @@ int main(int argc, char * const argv[]) { }); std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n"; - std::cout << " - dimension " << simplexTree.dimension() << " - filtration " << simplexTree.filtration() << "\n"; + std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices"; + std::cout << " - dimension " << simplexTree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : simplexTree.filtration_simplex_range()) { std::cout << " " << "[" << simplexTree.filtration(f_simplex) << "] "; diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index 33face2a..09cda526 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -185,13 +185,12 @@ int main(int argc, char * const argv[]) { } // ++ GENERAL VARIABLE SET - simplexTree.set_filtration(FOURTH_FILTRATION_VALUE); // Max filtration value simplexTree.set_dimension(2); // Max dimension = 2 -> (2,1,0) std::cout << "********************************************************************\n"; // Display the Simplex_tree - Can not be done in the middle of 2 inserts std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n"; - std::cout << " - dimension " << simplexTree.dimension() << " - filtration " << simplexTree.filtration() << "\n"; + std::cout << " - dimension " << simplexTree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : simplexTree.filtration_simplex_range()) { std::cout << " " << "[" << simplexTree.filtration(f_simplex) << "] "; diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index a8c01f84..8ab3da41 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -289,7 +289,6 @@ class Simplex_tree { /** \brief Constructs an empty simplex tree. */ Simplex_tree() : null_vertex_(-1), - threshold_(0), root_(nullptr, null_vertex_), filtration_vect_(), dimension_(-1) { } @@ -297,7 +296,6 @@ class Simplex_tree { /** \brief User-defined copy constructor reproduces the whole tree structure. */ Simplex_tree(const Simplex_tree& simplex_source) : null_vertex_(simplex_source.null_vertex_), - threshold_(simplex_source.threshold_), root_(nullptr, null_vertex_ , simplex_source.root_.members_), filtration_vect_(), dimension_(simplex_source.dimension_) { @@ -323,12 +321,10 @@ class Simplex_tree { /** \brief User-defined move constructor moves the whole tree structure. */ Simplex_tree(Simplex_tree && old) : null_vertex_(std::move(old.null_vertex_)), - threshold_(std::move(old.threshold_)), root_(std::move(old.root_)), filtration_vect_(std::move(old.filtration_vect_)), dimension_(std::move(old.dimension_)) { old.dimension_ = -1; - old.threshold_ = 0; old.root_ = Siblings(nullptr, null_vertex_); } @@ -356,7 +352,6 @@ class Simplex_tree { /** \brief Checks if two simplex trees are equal. */ bool operator==(Simplex_tree& st2) { if ((null_vertex_ != st2.null_vertex_) || - (threshold_ != st2.threshold_) || (dimension_ != st2.dimension_)) return false; return rec_equal(&root_, &st2.root_); @@ -407,14 +402,14 @@ class Simplex_tree { /** \brief Returns the filtration value of a simplex. * - * Called on the null_simplex, returns INFINITY. + * Called on the null_simplex, it returns infinity. * If SimplexTreeOptions::store_filtration is false, returns 0. */ static Filtration_value filtration(Simplex_handle sh) { if (sh != null_simplex()) { return sh->second.filtration(); } else { - return INFINITY; + return std::numeric_limits<Filtration_value>::infinity(); } } @@ -427,11 +422,6 @@ class Simplex_tree { sh->second.assign_filtration(fv); } - /** \brief Returns an upper bound of the filtration values of the simplices. */ - Filtration_value filtration() const { - return threshold_; - } - /** \brief Returns a Simplex_handle different from all Simplex_handles * associated to the simplices in the simplicial complex. * @@ -757,11 +747,6 @@ class Simplex_tree { return &root_; } - /** Set an upper bound for the filtration values. */ - void set_filtration(Filtration_value fil) { - threshold_ = fil; - } - /** Set a dimension for the simplicial complex. */ void set_dimension(int dimension) { dimension_ = dimension; @@ -1331,8 +1316,6 @@ class Simplex_tree { private: Vertex_handle null_vertex_; - /** \brief Upper bound on the filtration values of the simplices.*/ - Filtration_value threshold_; /** \brief Total number of simplices in the complex, without the empty simplex.*/ /** \brief Set of simplex tree Nodes representing the vertices.*/ Siblings root_; @@ -1360,7 +1343,6 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T...> & st) { typedef Simplex_tree<T...> ST; std::vector<typename ST::Vertex_handle> simplex; typename ST::Filtration_value fil; - typename ST::Filtration_value max_fil = 0; int max_dim = -1; while (read_simplex(is, simplex, fil)) { // read all simplices in the file as a list of vertices @@ -1369,15 +1351,11 @@ std::istream& operator>>(std::istream & is, Simplex_tree<T...> & st) { if (max_dim < dim) { max_dim = dim; } - if (max_fil < fil) { - max_fil = fil; - } // insert every simplex in the simplex tree st.insert_simplex(simplex, fil); simplex.clear(); } st.set_dimension(max_dim); - st.set_filtration(max_fil); return is; } diff --git a/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp index bef82275..19ce3321 100644 --- a/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp @@ -65,8 +65,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_3, typeST, li std::cout << "********************************************************************\n"; std::cout << "simplex_tree_expansion_with_blockers_3\n"; std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << simplex_tree.num_simplices() << " simplices\n"; - std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() << "\n"; + std::cout << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; + std::cout << " - dimension " << simplex_tree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : simplex_tree.filtration_simplex_range()) { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; @@ -127,8 +127,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_2, typeST, li std::cout << "********************************************************************\n"; std::cout << "simplex_tree_expansion_with_blockers_2\n"; std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << simplex_tree.num_simplices() << " simplices\n"; - std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() << "\n"; + std::cout << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; + std::cout << " - dimension " << simplex_tree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : simplex_tree.filtration_simplex_range()) { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; @@ -169,8 +169,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion, typeST, list_of_tested_var std::cout << "********************************************************************\n"; std::cout << "simplex_tree_expansion_3\n"; std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << simplex_tree.num_simplices() << " simplices\n"; - std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() << "\n"; + std::cout << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; + std::cout << " - dimension " << simplex_tree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : simplex_tree.filtration_simplex_range()) { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; @@ -213,8 +213,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_2, typeST, list_of_tested_v std::cout << "********************************************************************\n"; std::cout << "simplex_tree_expansion_2\n"; std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << simplex_tree.num_simplices() << " simplices\n"; - std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() << "\n"; + std::cout << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; + std::cout << " - dimension " << simplex_tree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : simplex_tree.filtration_simplex_range()) { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index b06d7ec9..17ddc605 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -26,7 +26,6 @@ void test_empty_simplex_tree(typeST& tst) { typedef typename typeST::Vertex_handle Vertex_handle; const Vertex_handle DEFAULT_VERTEX_VALUE = Vertex_handle(- 1); BOOST_CHECK(tst.null_vertex() == DEFAULT_VERTEX_VALUE); - BOOST_CHECK(tst.filtration() == 0.0); BOOST_CHECK(tst.num_vertices() == (size_t) 0); BOOST_CHECK(tst.num_simplices() == (size_t) 0); typename typeST::Siblings* STRoot = tst.root(); @@ -98,12 +97,11 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_from_file, typeST, list_of_tested_var // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; // Check BOOST_CHECK(st.num_simplices() == 143353); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(AreAlmostTheSame(st.filtration(), 0.4)); int previous_size = 0; for (auto f_simplex : st.filtration_simplex_range()) { @@ -147,7 +145,6 @@ void test_simplex_tree_insert_returns_true(const typePairSimplexBool& returnValu } // Global variables -double max_fil = 0.0; int dim_max = -1; template<class typeST, class Filtration_value> @@ -158,15 +155,8 @@ void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, cons std::cout << " set_and_test_simplex_tree_dim_fil - dim_max=" << dim_max << std::endl; } - if (fil > max_fil) { - max_fil = fil; - simplexTree.set_filtration(max_fil); - std::cout << " set_and_test_simplex_tree_dim_fil - max_fil=" << max_fil - << std::endl; - } BOOST_CHECK(simplexTree.dimension() == dim_max); - BOOST_CHECK(AreAlmostTheSame(simplexTree.filtration(), max_fil)); // Another way to count simplices: size_t num_simp = 0; @@ -190,7 +180,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var const Filtration_value FOURTH_FILTRATION_VALUE = 0.4; // reset since we run the test several times dim_max = -1; - max_fil = 0.0; // TEST OF INSERTION std::cout << "********************************************************************" << std::endl; @@ -310,7 +299,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr)); BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !! BOOST_CHECK(st.dimension() == dim_max); - BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil)); // ++ ELEVENTH std::cout << " - INSERT (2,1,0) (already inserted)" << std::endl; @@ -325,7 +313,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr)); BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !! BOOST_CHECK(st.dimension() == dim_max); - BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil)); /* Inserted simplex: */ /* 1 */ @@ -365,7 +352,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var // Display the Simplex_tree - Can not be done in the middle of 2 inserts std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; for (auto f_simplex : st.filtration_simplex_range()) { std::cout << " " << "[" << st.filtration(f_simplex) << "] "; @@ -575,7 +562,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o // Display the Simplex_tree - Can not be done in the middle of 2 inserts std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; for (auto f_simplex : st.filtration_simplex_range()) { std::cout << " " << "[" << st.filtration(f_simplex) << "] "; @@ -756,7 +743,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(copy_move_on_simplex_tree, typeST, list_of_tested_ typeST st_empty; // Check st has been emptied by the move BOOST_CHECK(st == st_empty); - BOOST_CHECK(st.filtration() == 0); BOOST_CHECK(st.dimension() == -1); BOOST_CHECK(st.num_simplices() == 0); BOOST_CHECK(st.num_vertices() == (size_t)0); @@ -1149,4 +1135,4 @@ BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) { // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; -}
\ No newline at end of file +} diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h index 9a3c1b65..1ee5e92e 100644 --- a/src/Spatial_searching/doc/Intro_spatial_searching.h +++ b/src/Spatial_searching/doc/Intro_spatial_searching.h @@ -46,7 +46,7 @@ namespace spatial_searching { * * \section spatial_searching_examples Example * - * This example generates 500 random points, then performs radius search, and queries for nearest and farthest points using different methods. + * This example generates 500 random points, then performs all-near-neighbors searches, and queries for nearest and furthest neighbors using different methods. * * \include Spatial_searching/example_spatial_searching.cpp * diff --git a/src/Spatial_searching/example/example_spatial_searching.cpp b/src/Spatial_searching/example/example_spatial_searching.cpp index 9e6a8f32..034ad24a 100644 --- a/src/Spatial_searching/example/example_spatial_searching.cpp +++ b/src/Spatial_searching/example/example_spatial_searching.cpp @@ -24,34 +24,34 @@ int main(void) { // 10-nearest neighbor query std::cout << "10 nearest neighbors from points[20]:\n"; - auto knn_range = points_ds.query_k_nearest_neighbors(points[20], 10, true); + auto knn_range = points_ds.k_nearest_neighbors(points[20], 10, true); for (auto const& nghb : knn_range) std::cout << nghb.first << " (sq. dist. = " << nghb.second << ")\n"; // Incremental nearest neighbor query std::cout << "Incremental nearest neighbors:\n"; - auto inn_range = points_ds.query_incremental_nearest_neighbors(points[45]); + auto inn_range = points_ds.incremental_nearest_neighbors(points[45]); // Get the neighbors in distance order until we hit the first point for (auto ins_iterator = inn_range.begin(); ins_iterator->first != 0; ++ins_iterator) std::cout << ins_iterator->first << " (sq. dist. = " << ins_iterator->second << ")\n"; - // 10-farthest neighbor query - std::cout << "10 farthest neighbors from points[20]:\n"; - auto kfn_range = points_ds.query_k_farthest_neighbors(points[20], 10, true); + // 10-furthest neighbor query + std::cout << "10 furthest neighbors from points[20]:\n"; + auto kfn_range = points_ds.k_furthest_neighbors(points[20], 10, true); for (auto const& nghb : kfn_range) std::cout << nghb.first << " (sq. dist. = " << nghb.second << ")\n"; - // Incremental farthest neighbor query - std::cout << "Incremental farthest neighbors:\n"; - auto ifn_range = points_ds.query_incremental_farthest_neighbors(points[45]); + // Incremental furthest neighbor query + std::cout << "Incremental furthest neighbors:\n"; + auto ifn_range = points_ds.incremental_furthest_neighbors(points[45]); // Get the neighbors in distance reverse order until we hit the first point for (auto ifs_iterator = ifn_range.begin(); ifs_iterator->first != 0; ++ifs_iterator) std::cout << ifs_iterator->first << " (sq. dist. = " << ifs_iterator->second << ")\n"; - // Radius search - std::cout << "Radius search:\n"; + // All-near-neighbors search + std::cout << "All-near-neighbors search:\n"; std::vector<std::size_t> rs_result; - points_ds.radius_search(points[45], 0.5, std::back_inserter(rs_result)); + points_ds.all_near_neighbors(points[45], 0.5, std::back_inserter(rs_result)); K k; for (auto const& p_idx : rs_result) std::cout << p_idx << " (sq. dist. = " << k.squared_distance_d_object()(points[p_idx], points[45]) << ")\n"; diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h index f13a98f7..ef428002 100644 --- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h +++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h @@ -42,19 +42,19 @@ namespace spatial_searching { /** * \class Kd_tree_search Kd_tree_search.h gudhi/Kd_tree_search.h - * \brief Spatial tree data structure to perform (approximate) nearest and farthest neighbor search. + * \brief Spatial tree data structure to perform (approximate) nearest and furthest neighbor search. * * \ingroup spatial_searching * * \details * The class Kd_tree_search is a tree-based data structure, based on * <a target="_blank" href="http://doc.cgal.org/latest/Spatial_searching/index.html">CGAL dD spatial searching data structures</a>. - * It provides a simplified API to perform (approximate) nearest and farthest neighbor searches. Contrary to CGAL default behavior, the tree + * It provides a simplified API to perform (approximate) nearest and furthest neighbor searches. Contrary to CGAL default behavior, the tree * does not store the points themselves, but stores indices. * - * There are two types of queries: the <i>k-nearest or k-farthest neighbor query</i>, where <i>k</i> is fixed and the <i>k</i> nearest - * or farthest points are computed right away, - * and the <i>incremental nearest or farthest neighbor query</i>, where no number of neighbors is provided during the call, as the + * There are two types of queries: the <i>k-nearest or k-furthest neighbor query</i>, where <i>k</i> is fixed and the <i>k</i> nearest + * or furthest points are computed right away, + * and the <i>incremental nearest or furthest neighbor query</i>, where no number of neighbors is provided during the call, as the * neighbors will be computed incrementally when the iterator on the range is incremented. * * \tparam Search_traits must be a model of the <a target="_blank" @@ -96,7 +96,7 @@ class Kd_tree_search { typedef CGAL::Orthogonal_k_neighbor_search<STraits> K_neighbor_search; typedef typename K_neighbor_search::Tree Tree; typedef typename K_neighbor_search::Distance Distance; - /// \brief The range returned by a k-nearest or k-farthest neighbor search. + /// \brief The range returned by a k-nearest or k-furthest neighbor search. /// Its value type is `std::pair<std::size_t, FT>` where `first` is the index /// of a point P and `second` is the squared distance between P and the query point. typedef K_neighbor_search KNS_range; @@ -104,7 +104,7 @@ class Kd_tree_search { typedef CGAL::Orthogonal_incremental_neighbor_search< STraits, Distance, CGAL::Sliding_midpoint<STraits>, Tree> Incremental_neighbor_search; - /// \brief The range returned by an incremental nearest or farthest neighbor search. + /// \brief The range returned by an incremental nearest or furthest neighbor search. /// Its value type is `std::pair<std::size_t, FT>` where `first` is the index /// of a point P and `second` is the squared distance between P and the query point. typedef Incremental_neighbor_search INS_range; @@ -171,7 +171,7 @@ class Kd_tree_search { /// @param[in] sorted Indicates if the computed sequence of k-nearest neighbors needs to be sorted. /// @param[in] eps Approximation factor. /// @return A range (whose `value_type` is `std::size_t`) containing the k-nearest neighbors. - KNS_range query_k_nearest_neighbors( + KNS_range k_nearest_neighbors( Point const& p, unsigned int k, bool sorted = true, @@ -193,11 +193,11 @@ class Kd_tree_search { /// \brief Search incrementally for the nearest neighbors from a query point. /// @param[in] p The query point. /// @param[in] eps Approximation factor. - /// @return A range (whose `value_type` is `std::size_t`) containing the + /// @return A range (whose `value_type` is `std::size_t`) containing the /// neighbors sorted by their distance to p. /// All the neighbors are not computed by this function, but they will be /// computed incrementally when the iterator on the range is incremented. - INS_range query_incremental_nearest_neighbors(Point const& p, FT eps = FT(0)) const { + INS_range incremental_nearest_neighbors(Point const& p, FT eps = FT(0)) const { // Initialize the search structure, and search all N points // Note that we need to pass the Distance explicitly since it needs to // know the property map @@ -211,13 +211,13 @@ class Kd_tree_search { return search; } - /// \brief Search for the k-farthest points from a query point. + /// \brief Search for the k-furthest points from a query point. /// @param[in] p The query point. - /// @param[in] k Number of farthest points to search. - /// @param[in] sorted Indicates if the computed sequence of k-farthest neighbors needs to be sorted. + /// @param[in] k Number of furthest points to search. + /// @param[in] sorted Indicates if the computed sequence of k-furthest neighbors needs to be sorted. /// @param[in] eps Approximation factor. - /// @return A range (whose `value_type` is `std::size_t`) containing the k-farthest neighbors. - KNS_range query_k_farthest_neighbors( + /// @return A range (whose `value_type` is `std::size_t`) containing the k-furthest neighbors. + KNS_range k_furthest_neighbors( Point const& p, unsigned int k, bool sorted = true, @@ -236,14 +236,14 @@ class Kd_tree_search { return search; } - /// \brief Search incrementally for the farthest neighbors from a query point. + /// \brief Search incrementally for the furthest neighbors from a query point. /// @param[in] p The query point. /// @param[in] eps Approximation factor. - /// @return A range (whose `value_type` is `std::size_t`) + /// @return A range (whose `value_type` is `std::size_t`) /// containing the neighbors sorted by their distance to p. /// All the neighbors are not computed by this function, but they will be /// computed incrementally when the iterator on the range is incremented. - INS_range query_incremental_farthest_neighbors(Point const& p, FT eps = FT(0)) const { + INS_range incremental_furthest_neighbors(Point const& p, FT eps = FT(0)) const { // Initialize the search structure, and search all N points // Note that we need to pass the Distance explicitly since it needs to // know the property map @@ -264,12 +264,10 @@ class Kd_tree_search { /// Note: `it` is used this way: `*it++ = each_point`. /// @param[in] eps Approximation factor. template <typename OutputIterator> - void radius_search( - Point const& p, - FT radius, - OutputIterator it, - FT eps = FT(0)) const { - + void all_near_neighbors(Point const& p, + FT radius, + OutputIterator it, + FT eps = FT(0)) const { m_tree.search(it, Fuzzy_sphere(p, radius, eps, m_tree.traits())); } diff --git a/src/Spatial_searching/test/test_Kd_tree_search.cpp b/src/Spatial_searching/test/test_Kd_tree_search.cpp index f79114bc..8a8334c3 100644 --- a/src/Spatial_searching/test/test_Kd_tree_search.cpp +++ b/src/Spatial_searching/test/test_Kd_tree_search.cpp @@ -48,12 +48,12 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) { Points_ds points_ds(points); - // Test query_k_nearest_neighbors + // Test k_nearest_neighbors std::size_t closest_pt_index = - points_ds.query_k_nearest_neighbors(points[10], 1, false).begin()->first; + points_ds.k_nearest_neighbors(points[10], 1, false).begin()->first; BOOST_CHECK(closest_pt_index == 10); - auto kns_range = points_ds.query_k_nearest_neighbors(points[20], 10, true); + auto kns_range = points_ds.k_nearest_neighbors(points[20], 10, true); std::vector<std::size_t> knn_result; FT last_dist = -1.; @@ -63,12 +63,12 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) { last_dist = nghb.second; } - // Test query_incremental_nearest_neighbors + // Test incremental_nearest_neighbors closest_pt_index = - points_ds.query_incremental_nearest_neighbors(points[10]).begin()->first; + points_ds.incremental_nearest_neighbors(points[10]).begin()->first; BOOST_CHECK(closest_pt_index == 10); - auto inn_range = points_ds.query_incremental_nearest_neighbors(points[20]); + auto inn_range = points_ds.incremental_nearest_neighbors(points[20]); std::vector<std::size_t> inn_result; last_dist = -1.; @@ -83,8 +83,8 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) { // Same result for KNN and INN? BOOST_CHECK(knn_result == inn_result); - // Test query_k_farthest_neighbors - auto kfn_range = points_ds.query_k_farthest_neighbors(points[20], 10, true); + // Test k_furthest_neighbors + auto kfn_range = points_ds.k_furthest_neighbors(points[20], 10, true); std::vector<std::size_t> kfn_result; last_dist = kfn_range.begin()->second; @@ -94,8 +94,8 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) { last_dist = nghb.second; } - // Test query_k_farthest_neighbors - auto ifn_range = points_ds.query_incremental_farthest_neighbors(points[20]); + // Test k_furthest_neighbors + auto ifn_range = points_ds.incremental_furthest_neighbors(points[20]); std::vector<std::size_t> ifn_result; last_dist = ifn_range.begin()->second; @@ -110,10 +110,10 @@ BOOST_AUTO_TEST_CASE(test_Kd_tree_search) { // Same result for KFN and IFN? BOOST_CHECK(kfn_result == ifn_result); - // Test radius search + // Test all_near_neighbors Point rs_q(rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1), rd.get_double(-1., 1)); std::vector<std::size_t> rs_result; - points_ds.radius_search(rs_q, 0.5, std::back_inserter(rs_result)); + points_ds.all_near_neighbors(rs_q, 0.5, std::back_inserter(rs_result)); K k; for (auto const& p_idx : rs_result) BOOST_CHECK(k.squared_distance_d_object()(points[p_idx], rs_q) <= 0.5); diff --git a/src/Subsampling/include/gudhi/sparsify_point_set.h b/src/Subsampling/include/gudhi/sparsify_point_set.h index 507f8c79..7d3b97fb 100644 --- a/src/Subsampling/include/gudhi/sparsify_point_set.h +++ b/src/Subsampling/include/gudhi/sparsify_point_set.h @@ -83,7 +83,7 @@ sparsify_point_set( *output_it++ = *it_pt; - auto ins_range = points_ds.query_incremental_nearest_neighbors(*it_pt); + auto ins_range = points_ds.incremental_nearest_neighbors(*it_pt); // If another point Q is closer that min_squared_dist, mark Q to be dropped for (auto const& neighbor : ins_range) { diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index 9fa7c825..a5cefd6a 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1093,8 +1093,8 @@ class Tangential_complex { std::size_t num_inserted_points = 1; #endif // const int NUM_NEIGHBORS = 150; - // KNS_range ins_range = m_points_ds.query_k_nearest_neighbors(center_pt, NUM_NEIGHBORS); - INS_range ins_range = m_points_ds.query_incremental_nearest_neighbors(center_pt); + // KNS_range ins_range = m_points_ds.k_nearest_neighbors(center_pt, NUM_NEIGHBORS); + INS_range ins_range = m_points_ds.incremental_nearest_neighbors(center_pt); // While building the local triangulation, we keep the radius // of the sphere "star sphere" centered at "center_vertex" @@ -1203,7 +1203,7 @@ class Tangential_complex { Point center_point = compute_perturbed_point(i); // Among updated point, what is the closer from our center point? std::size_t closest_pt_index = - updated_pts_ds.query_k_nearest_neighbors(center_point, 1, false).begin()->first; + updated_pts_ds.k_nearest_neighbors(center_point, 1, false).begin()->first; typename K::Construct_weighted_point_d k_constr_wp = m_k.construct_weighted_point_d_object(); @@ -1315,11 +1315,10 @@ class Tangential_complex { m_k.compute_coordinate_d_object(); #ifdef GUDHI_TC_USE_ANOTHER_POINT_SET_FOR_TANGENT_SPACE_ESTIM - KNS_range kns_range = m_points_ds_for_tse.query_k_nearest_neighbors( - p, num_pts_for_pca, false); + KNS_range kns_range = m_points_ds_for_tse.k_nearest_neighbors(p, num_pts_for_pca, false); const Points &points_for_pca = m_points_for_tse; #else - KNS_range kns_range = m_points_ds.query_k_nearest_neighbors(p, num_pts_for_pca, false); + KNS_range kns_range = m_points_ds.k_nearest_neighbors(p, num_pts_for_pca, false); const Points &points_for_pca = m_points; #endif @@ -1413,11 +1412,10 @@ class Tangential_complex { const Point &p = m_points[*it_index]; #ifdef GUDHI_TC_USE_ANOTHER_POINT_SET_FOR_TANGENT_SPACE_ESTIM - KNS_range kns_range = m_points_ds_for_tse.query_k_nearest_neighbors( - p, num_pts_for_pca, false); + KNS_range kns_range = m_points_ds_for_tse.k_nearest_neighbors(p, num_pts_for_pca, false); const Points &points_for_pca = m_points_for_tse; #else - KNS_range kns_range = m_points_ds.query_k_nearest_neighbors(p, num_pts_for_pca, false); + KNS_range kns_range = m_points_ds.k_nearest_neighbors(p, num_pts_for_pca, false); const Points &points_for_pca = m_points; #endif diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h index fb669ef8..4f3cef4f 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h @@ -84,7 +84,7 @@ class Euclidean_strong_witness_complex : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) { nearest_landmark_table_.reserve(boost::size(witnesses)); for (auto w : witnesses) - nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w)); + nearest_landmark_table_.push_back(landmark_tree_.incremental_nearest_neighbors(w)); } /** \brief Returns the point corresponding to the given vertex. diff --git a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h index 6afe9a5d..ff8bb139 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h @@ -86,7 +86,7 @@ class Euclidean_witness_complex : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks) { nearest_landmark_table_.reserve(boost::size(witnesses)); for (auto w : witnesses) - nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w)); + nearest_landmark_table_.push_back(landmark_tree_.incremental_nearest_neighbors(w)); } /** \brief Returns the point corresponding to the given vertex. diff --git a/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp index 62fd1157..4f718203 100644 --- a/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp +++ b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp @@ -75,7 +75,7 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) { Kd_tree landmark_tree(landmarks); Nearest_landmark_table nearest_landmark_table; for (auto w: witnesses) - nearest_landmark_table.push_back(landmark_tree.query_incremental_nearest_neighbors(w)); + nearest_landmark_table.push_back(landmark_tree.incremental_nearest_neighbors(w)); // Weak witness complex: Euclidean version EuclideanWitnessComplex eucl_witness_complex(landmarks, diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index dbf2106a..f2bbafdc 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -123,7 +123,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND) find_program( SPHINX_PATH sphinx-build ) elseif(PYTHON_VERSION_MAJOR EQUAL 3) # No sphinx-build in Pyton3, just hack it - set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build") + set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build.py") else() message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.") endif(PYTHON_VERSION_MAJOR EQUAL 2) diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 7219bcfa..d6569f0c 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -160,7 +160,7 @@ <b>Author:</b> François Godi<br> <b>Introduced in:</b> GUDHI 2.0.0<br> <b>Copyright:</b> GPL v3<br> - <b>Requires:</b> \ref cgal ≥ 4.8.1 and \ref eigen3 + <b>Requires:</b> \ref cgal ≥ 4.8.1 </td> <td width="75%"> Bottleneck distance measures the similarity between two persistence diagrams. @@ -329,13 +329,29 @@ make doxygen * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> + * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> - * + * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> + * Spatial_searching/example_spatial_searching.cpp</a> + * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> + * Subsampling/example_choose_n_farthest_points.cpp</a> + * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> + * Subsampling/example_custom_kernel.cpp</a> + * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> + * Subsampling/example_pick_n_random_points.cpp</a> + * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> + * Subsampling/example_sparsify_point_set.cpp</a> + * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> + * Tangential_complex/example_basic.cpp</a> + * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> + * Tangential_complex/example_with_perturb.cpp</a> + * * \subsection tbb Threading Building Blocks * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel® TBB</a> lets you easily write parallel * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have diff --git a/src/common/utilities/off_file_from_shape_generator.cpp b/src/common/utilities/off_file_from_shape_generator.cpp index 0f310a13..afcd558c 100644 --- a/src/common/utilities/off_file_from_shape_generator.cpp +++ b/src/common/utilities/off_file_from_shape_generator.cpp @@ -77,7 +77,7 @@ int main(int argc, char **argv) { usage(argv[0]); } - enum class Data_shape { sphere, cube, curve, torus, klein, undefined } ; + enum class Data_shape { sphere, cube, curve, torus, klein, undefined}; Data_shape shape = Data_shape::undefined; if (memcmp(argv[2], "sphere", sizeof("sphere")) == 0) { diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index ab5ea9ef..afca9d60 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -15,6 +15,16 @@ function( add_gudhi_cython_lib THE_LIB ) endif(EXISTS ${THE_LIB}) endfunction( add_gudhi_cython_lib ) +# THE_TEST is the python test file name (without .py extension) containing tests functions +function( add_gudhi_py_test THE_TEST ) + # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python + # use py.test no cache provider, otherwise a .cache file is created in sources by py.test + add_test(NAME ${THE_TEST}_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py) +endfunction( add_gudhi_py_test ) + + if(CYTHON_FOUND) message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}") @@ -73,76 +83,20 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") endif (EIGEN3_FOUND) - # Copy recursively include, cython, example, doc and test repositories before packages finding - # Some tests and doc files are removed in case some packages are not found - file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - # Developper version for doc images - file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png") - file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg") - file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - # User version for doc images - file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png") - file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg") - file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - # Biblio - file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib") - file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - # Cubical complex perseus doc example - file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt") - file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - # Persistence graphical tools examples - file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - # If CGAL_VERSION >= 4.8.1, include subsampling - set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'") - set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'") - set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'") - else (NOT CGAL_VERSION VERSION_LESS 4.8.1) - # Remove subsampling unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst") - # Remove tangential complex and bottleneck unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py) - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst") + set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - # If CGAL_VERSION >= 4.7.0, include alpha - set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'") - else (NOT CGAL_VERSION VERSION_LESS 4.7.0) - # Remove alpha complex unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst") - endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") + set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'") + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX - "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n") - else (NOT CGAL_VERSION VERSION_LESS 4.6.0) - # Remove alpha complex unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst") - endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) + "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n") + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) if(CGAL_FOUND) # Add CGAL compilation args @@ -193,11 +147,6 @@ if(CYTHON_FOUND) set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") endif(UNIX) - # set sphinx-build in make files - configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY) - configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY) - configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) - # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY) # Generate gudhi.pyx - Gudhi cython file @@ -219,110 +168,147 @@ if(CYTHON_FOUND) PATTERN "*.pyd") # Test examples - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + # Bottleneck and Alpha 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" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_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}") + # Tangential 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" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_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_gudhi_py_test(test_tangential_complex) + + # Witness complex AND Subsampling 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" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_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" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_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}") + + # Subsampling + add_gudhi_py_test(test_subsampling) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + # Bottleneck + add_test(NAME bottleneck_basic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") + + add_gudhi_py_test(test_bottleneck_distance) endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + # Alpha 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}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") 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" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_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) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) + add_gudhi_py_test(test_alpha_complex) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + # Euclidean witness + add_gudhi_py_test(test_euclidean_witness_complex) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + + # Cubical add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME random_cubical_complex_persistence_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/random_cubical_complex_persistence_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" 10 10 10) - set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_gudhi_py_test(test_cubical_complex) + + # Rips add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) - set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_from_points_example.py) - set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) + + add_gudhi_py_test(test_rips_complex) + # Simplex tree add_test(NAME simplex_tree_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - 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}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) + add_gudhi_py_test(test_simplex_tree) + + # Witness add_test(NAME witness_complex_from_nearest_landmark_table_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py) - set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) + + add_gudhi_py_test(test_witness_complex) + + # Reader utils + add_gudhi_py_test(test_reader_utils) + + # Documentation generation is available through sphinx - requires all modules + if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") + # User warning - Sphinx is a static pages generator, and configured to work fine with user_version + # Images and biblio warnings because not found on developper version + if (GUDHI_CYTHON_PATH STREQUAL "src/cython") + set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss") + endif() + # sphinx target requires gudhi.so, because conf.py reads gudhi version from it + add_custom_target(sphinx + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx + DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM) + + add_test(NAME sphinx_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest) - # Unitary tests are available through py.test - add_test( - NAME gudhi_cython_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest) - set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - - # Documentation generation is available through sphinx - if(SPHINX_PATH) - if (UNIX) - add_custom_target(sphinx - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc - DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" - COMMAND make html doctest) - else (UNIX) - add_custom_target(sphinx - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc - COMMAND make.bat html doctest) - endif (UNIX) - endif(SPHINX_PATH) + endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) endif(CYTHON_FOUND) diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 47aa5311..45487158 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -36,9 +36,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>": Simplex_tree() - double filtration() double simplex_filtration(vector[int] simplex) - void set_filtration(double filtration) void initialize_filtration() int num_vertices() int num_simplices() @@ -115,14 +113,6 @@ cdef class SimplexTree: """ return self.thisptr.simplex_filtration(simplex) - def set_filtration(self, filtration): - """This function sets the main simplicial complex filtration value. - - :param filtration: The filtration value. - :type filtration: float. - """ - self.thisptr.set_filtration(<double> filtration) - def initialize_filtration(self): """This function initializes and sorts the simplicial complex filtration vector. diff --git a/src/cython/doc/Makefile.in b/src/cython/doc/Makefile.in deleted file mode 100644 index 526350b3..00000000 --- a/src/cython/doc/Makefile.in +++ /dev/null @@ -1,44 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = @SPHINX_PATH@ -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - -help: - @echo "Please use \`make <target>' where <target> is one of" - @echo " html to make standalone HTML files" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - rm -f examples.inc - rm -rf $(BUILDDIR)/* - -# GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean) - -html: - ./generate_examples.py - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst index a5f6420a..1680a712 100644 --- a/src/cython/doc/alpha_complex_sum.rst +++ b/src/cython/doc/alpha_complex_sum.rst @@ -5,7 +5,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | Alpha_complex is a simplicial complex constructed from the finite | -| img/alpha_complex_representation.png | cells of a Delaunay Triangulation. | +| ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | | :alt: Alpha complex representation | | | :figclass: align-center | The filtration value of each simplex is computed as the square of the | | | circumradius of the simplex if the circumsphere is empty (the simplex | diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index ff62390b..db7edd6f 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst @@ -75,7 +75,7 @@ In order to build the alpha complex, first, a Simplex tree is built from the cel (The filtration value is set to NaN, which stands for unknown value): .. figure:: - img/alpha_complex_doc.png + ../../doc/Alpha_complex/alpha_complex_doc.png :figclass: align-center :alt: Simplex tree structure construction example @@ -112,7 +112,7 @@ computes the filtration value of the triangle, and then propagates the filtratio here: .. figure:: - img/alpha_complex_doc_420.png + ../../doc/Alpha_complex/alpha_complex_doc_420.png :figclass: align-center :alt: Filtration value propagation example @@ -158,7 +158,8 @@ Then, it is asked to display information about the alpha complex: .. testcode:: import gudhi - alpha_complex = gudhi.AlphaComplex(off_file='alphacomplexdoc.off') + alpha_complex = gudhi.AlphaComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off') simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=59.0) result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ @@ -200,6 +201,6 @@ the program output is: CGAL citations ============== -.. bibliography:: how_to_cite_cgal.bib +.. bibliography:: ../../biblio/how_to_cite_cgal.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst index 5c475d0d..030fad9e 100644 --- a/src/cython/doc/bottleneck_distance_sum.rst +++ b/src/cython/doc/bottleneck_distance_sum.rst @@ -5,7 +5,7 @@ +-----------------------------------------------------------------+----------------------------------------------------------------------+ | .. figure:: | Bottleneck distance measures the similarity between two persistence | -| img/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | +| ../../doc/Bottleneck_distance/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | | :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | | | diagonal points) such that any couple of matched points are at | | Bottleneck distance is the length of | distance at most b. | diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst index 0066992f..7692dce2 100644 --- a/src/cython/doc/bottleneck_distance_user.rst +++ b/src/cython/doc/bottleneck_distance_user.rst @@ -25,7 +25,7 @@ This example computes the bottleneck distance from 2 persistence diagrams: message = "Bottleneck distance approximation=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0.1) print(message) - message = "Bottleneck distance exact value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0) + message = "Bottleneck distance value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2) print(message) The output is: @@ -33,4 +33,4 @@ The output is: .. testoutput:: Bottleneck distance approximation=0.81 - Bottleneck distance exact value=0.75 + Bottleneck distance value=0.75 diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst index 6cdfb7cc..f4fdf83b 100644 --- a/src/cython/doc/citation.rst +++ b/src/cython/doc/citation.rst @@ -12,4 +12,4 @@ Manual, as well as for publications directly related to the GUDHI library. GUDHI bibtex ************ -.. literalinclude:: how_to_cite_gudhi.bib +.. literalinclude:: ../../biblio/how_to_cite_gudhi.bib diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py index 072f7a94..19a880d4 100755 --- a/src/cython/doc/conf.py +++ b/src/cython/doc/conf.py @@ -21,7 +21,7 @@ import os #sys.path.insert(0, os.path.abspath('.')) # Path to Gudhi.so from source path -sys.path.insert(0, os.path.abspath('..')) +sys.path.insert(0, os.path.abspath('.')) # -- General configuration ------------------------------------------------ @@ -58,18 +58,20 @@ source_suffix = '.rst' # The master toctree document. master_doc = 'index' +import gudhi + # General information about the project. -project = u'GUDHI' -copyright = u'2016, GUDHI Editorial Board' +project = gudhi.__name__ +copyright = gudhi.__copyright__ # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. -version = '2.0' +version = gudhi.__version__ # The full version, including alpha/beta/rc tags. -release = '2.0.1-rc1' +#release = '2.0.1-rc1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. @@ -198,81 +200,3 @@ html_static_path = ['_static'] # Output file base name for HTML help builder. htmlhelp_basename = 'GUDHIdoc' - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - ('index', 'GUDHI.tex', u'GUDHI Documentation', - u'Vincent Rouvreau', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'gudhi', u'GUDHI Documentation', - [u'Vincent Rouvreau'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ('index', 'GUDHI', u'GUDHI Documentation', - u'Vincent Rouvreau', 'GUDHI', 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst index 3ddf6375..280ad0e0 100644 --- a/src/cython/doc/cubical_complex_sum.rst +++ b/src/cython/doc/cubical_complex_sum.rst @@ -2,14 +2,14 @@ :Author: Pawel Dlotko :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 ================================================================= =================================== =================================== -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| .. figure:: | The cubical complex is an example of a structured complex useful in | -| img/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image | -| :alt: Cubical complex representation | analysis. | -| :figclass: align-center | | -| | | -| Cubical complex representation | | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | -| | * :doc:`periodic_cubical_complex_ref` | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ +| .. figure:: | The cubical complex is an example of a structured complex useful in | +| ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image | +| :alt: Cubical complex representation | analysis. | +| :figclass: align-center | | +| | | +| Cubical complex representation | | ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ +| :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | +| | * :doc:`periodic_cubical_complex_ref` | ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 344b9554..2bfac62a 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -59,7 +59,7 @@ directions, allows to determine, dimension, neighborhood, boundary and coboundar :math:`C \in \mathcal{K}`. .. figure:: - img/Cubical_complex_representation.png + ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png :alt: Cubical complex. :figclass: align-center @@ -87,7 +87,7 @@ in the example below). Next, in lexicographical order, the filtration of top dim 20 4 7 6 5 in the example below). .. figure:: - img/exampleBitmap.png + ../../doc/Bitmap_cubical_complex/exampleBitmap.png :alt: Example of a input data. :figclass: align-center @@ -95,14 +95,15 @@ in the example below). Next, in lexicographical order, the filtration of top dim The input file for the following complex is: -.. literalinclude:: cubicalcomplexdoc.txt +.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt -.. centered:: cubicalcomplexdoc.txt +.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt .. testcode:: import gudhi - cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt') + cubical_complex = gudhi.CubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/cubicalcomplexdoc.txt') result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \ repr(cubical_complex.num_simplices()) + ' simplices.' print(result_str) @@ -127,16 +128,17 @@ complex with periodic boundary conditions. One can also use Perseus style input conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance: -.. literalinclude:: periodiccubicalcomplexdoc.txt +.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt -.. centered:: periodiccubicalcomplexdoc.txt +.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. .. testcode:: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='periodiccubicalcomplexdoc.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/periodiccubicalcomplexdoc.txt') result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \ repr(periodic_cc.num_simplices()) + ' simplices.' print(result_str) @@ -155,6 +157,6 @@ End user programs are available in cython/example/ folder. Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst index a89e0596..1e596e18 100644 --- a/src/cython/doc/examples.rst +++ b/src/cython/doc/examples.rst @@ -1,4 +1,21 @@ Examples ######## -.. include:: examples.inc +.. only:: builder_html + + * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_example.py>` + * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>` + * :download:`simplex_tree_example.py <../example/simplex_tree_example.py>` + * :download:`alpha_rips_persistence_bottleneck_distance.py <../example/alpha_rips_persistence_bottleneck_distance.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` + * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` + * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` + * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>` + * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>` + * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` + * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>` diff --git a/src/cython/doc/generate_examples.py b/src/cython/doc/generate_examples.py deleted file mode 100755 index d64d506c..00000000 --- a/src/cython/doc/generate_examples.py +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env python - -from os import listdir - -"""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): Vincent Rouvreau - - 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/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" -__license__ = "GPL v3" - -""" -generate_examples.py generates examples.inc to be included in examples.rst. -Refer to Makefile and make.bat to see if it is correctly launched. -""" - -output_file = open('examples.inc','w') - -output_file.write('.. only:: builder_html\n\n') - -for file in listdir('../example/'): - output_file.write(" * :download:`" + file + " <../example/" + file + ">`\n") - -output_file.close() diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst index f6d10567..3945d72a 100644 --- a/src/cython/doc/index.rst +++ b/src/cython/doc/index.rst @@ -1,8 +1,10 @@ GUDHI Python module documentation ################################# -.. image:: img/Gudhi_banner.png - :align: center +.. figure:: + ../../doc/common/Gudhi_banner.png + :alt: Gudhi banner + :figclass: align-center Introduction ************ @@ -81,6 +83,6 @@ Persistence graphical tools Bibliography ************ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index f98a5039..c182f176 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -68,31 +68,32 @@ The :doc:`Alpha complex </alpha_complex_user>`, C++ library which provides easy access to efficient and reliable geometric algorithms. -Having CGAL version 4.6.0 or higher installed is recommended. The procedure to -install this library according to your operating system is detailed +Having CGAL, the Computational Geometry Algorithms Library, version 4.7.0 or +higher installed is recommended. The procedure to install this library +according to your operating system is detailed `here <http://doc.cgal.org/latest/Manual/installation.html>`_. -The following examples require the Computational Geometry Algorithms Library: - -.. only:: builder_html - - * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` - * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` - -The following example requires CGAL version ≥ 4.7.0: +The following examples requires CGAL version ≥ 4.7.0: .. only:: builder_html * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>` -The following example requires CGAL version ≥ 4.8.0: +The following examples requires CGAL version ≥ 4.8.0: .. only:: builder_html * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` +The following examples requires CGAL version ≥ 4.8.1: + +.. only:: builder_html + + * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` + Eigen3 ====== diff --git a/src/cython/doc/make.bat.in b/src/cython/doc/make.bat.in deleted file mode 100644 index ff1a6d56..00000000 --- a/src/cython/doc/make.bat.in +++ /dev/null @@ -1,67 +0,0 @@ -@ECHO OFF
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
- set SPHINXBUILD=@SPHINX_PATH@
-)
-set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
-set I18NSPHINXOPTS=%SPHINXOPTS% .
-if NOT "%PAPER%" == "" (
- set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
- set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
-)
-
-if "%1" == "" goto help
-
-if "%1" == "help" (
- :help
- echo.Please use `make ^<target^>` where ^<target^> is one of
- echo. html to make standalone HTML files
- echo. doctest to run all doctests embedded in the documentation if enabled
- goto end
-)
-
-if "%1" == "clean" (
- del examples.inc
- for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
- del /q /s %BUILDDIR%\*
- goto end
-)
-
-
-%SPHINXBUILD% 2> nul
-if errorlevel 9009 (
- echo.
- echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
- echo.installed, then set the SPHINXBUILD environment variable to point
- echo.to the full path of the 'sphinx-build' executable. Alternatively you
- echo.may add the Sphinx directory to PATH.
- echo.
- echo.If you don't have Sphinx installed, grab it from
- echo.http://sphinx-doc.org/
- exit /b 1
-)
-
-:: GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)
-
-if "%1" == "html" (
- generate_examples.py
- %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The HTML pages are in %BUILDDIR%/html.
- goto end
-)
-
-if "%1" == "doctest" (
- %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
- if errorlevel 1 exit /b 1
- echo.
- echo.Testing of doctests in the sources finished, look at the ^
-results in %BUILDDIR%/doctest/output.txt.
- goto end
-)
-
-:end
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 13198162..9033331f 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -32,7 +32,8 @@ This function can display the persistence result as a barcode: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/3d_torus.txt') diag = periodic_cc.persistence() plt = gudhi.plot_persistence_barcode(diag) plt.show() @@ -41,8 +42,10 @@ This function can display the persistence result as a barcode: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/3d_torus.txt') diag = periodic_cc.persistence() + print("diag = ", diag) plt = gudhi.plot_persistence_barcode(diag) plt.show() @@ -55,7 +58,8 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) @@ -65,7 +69,8 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst index d1f79cb4..a26df1dc 100644 --- a/src/cython/doc/persistent_cohomology_sum.rst +++ b/src/cython/doc/persistent_cohomology_sum.rst @@ -4,7 +4,7 @@ +-----------------------------------------------------------------+-----------------------------------------------------------------------+ | .. figure:: | The theory of homology consists in attaching to a topological space | -| img/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | +| ../../doc/Persistent_cohomology/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | | :figclass: align-center | features like connected components, holes, cavities, etc. Persistent | | | homology studies the evolution -- birth, life and death -- of these | | Rips Persistent Cohomology on a 3D | features when the topological space is changing. Consequently, the | diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst index 72f1a7f7..bf90c163 100644 --- a/src/cython/doc/persistent_cohomology_user.rst +++ b/src/cython/doc/persistent_cohomology_user.rst @@ -109,6 +109,6 @@ We provide several example files: run these examples with -h for details on thei Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py index 9cd3149d..de33d506 100755 --- a/src/cython/doc/pyplots/barcode_persistence.py +++ b/src/cython/doc/pyplots/barcode_persistence.py @@ -1,6 +1,7 @@ import gudhi -periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') +periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/3d_torus.txt') diag = periodic_cc.persistence() plt = gudhi.plot_persistence_barcode(diag) plt.show() diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py index 30661965..c2fbf801 100755 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -1,6 +1,7 @@ import gudhi -rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) +rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) diff --git a/src/cython/doc/python3-sphinx-build.in b/src/cython/doc/python3-sphinx-build.py index c97965f5..44b94169 100755 --- a/src/cython/doc/python3-sphinx-build.in +++ b/src/cython/doc/python3-sphinx-build.py @@ -1,4 +1,4 @@ -#!@PYTHON_EXECUTABLE@ +#!/usr/bin/python3 """ Emulate sphinx-build for python3 diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst index 2b65fc19..5616bfa9 100644 --- a/src/cython/doc/rips_complex_sum.rst +++ b/src/cython/doc/rips_complex_sum.rst @@ -4,7 +4,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton | -| img/rips_complex_representation.png | graph. | +| ../../doc/Rips_complex/rips_complex_representation.png | graph. | | :figclass: align-center | | | | The filtration value of each edge is computed from a user-given | | Rips complex representation | distance function and is inserted until a user-given threshold | diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index f9760976..96ba9944 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -26,7 +26,7 @@ structure, and then expands the simplicial complex when required. Vertex name correspond to the index of the point in the given range (aka. the point cloud). .. figure:: - img/rips_complex_representation.png + ../../doc/Rips_complex/rips_complex_representation.png :align: center Rips-complex one skeleton graph representation @@ -101,7 +101,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(off_file='alphacomplexdoc.off', max_edge_length=12.0) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off', max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ @@ -205,7 +206,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(csv_file='full_square_distance_matrix.csv', max_edge_length=12.0) + rips_complex = gudhi.RipsComplex(csv_file=gudhi.__root_source_dir__ + \ + '/data/distance_matrix/full_square_distance_matrix.csv', max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst index 3174fb62..fb0e54c1 100644 --- a/src/cython/doc/simplex_tree_sum.rst +++ b/src/cython/doc/simplex_tree_sum.rst @@ -4,7 +4,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | The simplex tree is an efficient and flexible data structure for | -| img/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | +| ../../doc/Simplex_tree/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | | :alt: Simplex tree representation | | | :figclass: align-center | The data structure is described in | | | :cite:`boissonnatmariasimplextreealgorithmica` | diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst index 2b05bc10..72b4d7ba 100644 --- a/src/cython/doc/tangential_complex_sum.rst +++ b/src/cython/doc/tangential_complex_sum.rst @@ -5,10 +5,10 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to | -| img/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | +| ../../doc/Tangential_complex/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | | :figclass: align-center | dimensional Euclidean space. The input is a point sample coming from | | | an unknown manifold. The running time depends only linearly on the | -| **Tangential complex representation** | extrinsic dimension :math:`d` and exponentially on the intrinsic | +| Tangential complex representation | extrinsic dimension :math:`d` and exponentially on the intrinsic | | | dimension :math:`k`. | +----------------------------------------------------------------+------------------------------------------------------------------------+ | :doc:`tangential_complex_user` | :doc:`tangential_complex_ref` | diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst index 03f9fea6..efa6d7ce 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/cython/doc/tangential_complex_user.rst @@ -22,7 +22,7 @@ Let us start with the description of the Tangential complex of a simple example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points :math:`P` located on a curve embedded in 2D. -.. figure:: img/tc_example_01.png +.. figure:: ../../doc/Tangential_complex/tc_example_01.png :alt: The input :figclass: align-center @@ -31,7 +31,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g. using PCA). -.. figure:: img/tc_example_02.png +.. figure:: ../../doc/Tangential_complex/tc_example_02.png :alt: The estimated normals :figclass: align-center @@ -42,7 +42,7 @@ Let us add the Voronoi diagram of the points in orange. For each point :math:`p`, construct its star in the Delaunay triangulation of :math:`P` restricted to :math:`T_p`. -.. figure:: img/tc_example_03.png +.. figure:: ../../doc/Tangential_complex/tc_example_03.png :alt: The Voronoi diagram :figclass: align-center @@ -62,7 +62,7 @@ simplex is not in the star of all its vertices. Let us take the same example. -.. figure:: img/tc_example_07_before.png +.. figure:: ../../doc/Tangential_complex/tc_example_07_before.png :alt: Before :figclass: align-center @@ -70,7 +70,7 @@ Let us take the same example. Let us slightly move the tangent subspace :math:`T_q` -.. figure:: img/tc_example_07_after.png +.. figure:: ../../doc/Tangential_complex/tc_example_07_after.png :alt: After :figclass: align-center @@ -79,7 +79,7 @@ Let us slightly move the tangent subspace :math:`T_q` Now, the star of :math:`Q` contains :math:`QP`, but the star of :math:`P` does not contain :math:`QP`. We have an inconsistency. -.. figure:: img/tc_example_08.png +.. figure:: ../../doc/Tangential_complex/tc_example_08.png :alt: After :figclass: align-center @@ -122,7 +122,8 @@ This example builds the Tangential complex of point set read in an OFF file. .. testcode:: import gudhi - tc = gudhi.TangentialComplex(off_file='alphacomplexdoc.off') + tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off') result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \ ' simplices - ' + repr(tc.num_vertices()) + ' vertices.' print(result_str) @@ -190,6 +191,6 @@ The output is: Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst index b65522ba..a8a126a0 100644 --- a/src/cython/doc/witness_complex_sum.rst +++ b/src/cython/doc/witness_complex_sum.rst @@ -3,15 +3,17 @@ :Euclidean version requires: CGAL :math:`\geq` 4.6.0 Eigen3 ================================================================= =================================== =================================== -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| .. image:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | -| img/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | -| | | -| | The data structure is described in | -| | :cite:`boissonnatmariasimplextreealgorithmica`. | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | -| | * :doc:`strong_witness_complex_ref` | -| | * :doc:`euclidean_witness_complex_ref` | -| | * :doc:`euclidean_strong_witness_complex_ref` | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ ++-------------------------------------------------------------------+----------------------------------------------------------------------+ +| .. figure:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | +| ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | +| :alt: Witness complex representation | | +| :figclass: align-center | The data structure is described in | +| | :cite:`boissonnatmariasimplextreealgorithmica`. | +| | | +| Witness complex representation | | ++-------------------------------------------------------------------+----------------------------------------------------------------------+ +| :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | +| | * :doc:`strong_witness_complex_ref` | +| | * :doc:`euclidean_witness_complex_ref` | +| | * :doc:`euclidean_strong_witness_complex_ref` | ++-------------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst index aa9cbb2c..29413269 100644 --- a/src/cython/doc/witness_complex_user.rst +++ b/src/cython/doc/witness_complex_user.rst @@ -33,7 +33,7 @@ Both definitions can be relaxed by a real value :math:`\alpha`: which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and **strong relaxed witness complex** respectively. -.. figure:: img/swit.svg +.. figure:: ../../doc/Witness_complex/swit.svg :alt: Strongly witnessed simplex :figclass: align-center @@ -126,6 +126,6 @@ Here is an example of constructing a strong witness complex filtration and compu Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py index 3af20fcf..831d9da8 100755 --- a/src/cython/example/simplex_tree_example.py +++ b/src/cython/example/simplex_tree_example.py @@ -52,7 +52,6 @@ else: st.set_dimension(3) print("dimension=", st.dimension()) -st.set_filtration(4.0) st.initialize_filtration() print("filtration=", st.get_filtration()) print("filtration[1, 2]=", st.filtration([1, 2])) diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in index ed2d28cc..a8dd9f80 100644 --- a/src/cython/gudhi.pyx.in +++ b/src/cython/gudhi.pyx.in @@ -23,16 +23,19 @@ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 INRIA" __license__ = "GPL v3" +__version__ = "@GUDHI_VERSION@" +# This variable is used by doctest to find files +__root_source_dir__ = "@CMAKE_SOURCE_DIR@" -include "cython/off_reader.pyx" -include "cython/simplex_tree.pyx" -include "cython/rips_complex.pyx" -include "cython/cubical_complex.pyx" -include "cython/periodic_cubical_complex.pyx" -include "cython/persistence_graphical_tools.py" -include "cython/reader_utils.pyx" -include "cython/witness_complex.pyx" -include "cython/strong_witness_complex.pyx" +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/rips_complex.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/cubical_complex.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/periodic_cubical_complex.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/persistence_graphical_tools.py' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/reader_utils.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/witness_complex.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/strong_witness_complex.pyx' @GUDHI_CYTHON_ALPHA_COMPLEX@ @GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@ @GUDHI_CYTHON_SUBSAMPLING@ diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h index b87b6cca..8ec34f61 100644 --- a/src/cython/include/Reader_utils_interface.h +++ b/src/cython/include/Reader_utils_interface.h @@ -28,6 +28,8 @@ #include <iostream> #include <vector> #include <string> +#include <map> +#include <utility> // for pair<> namespace Gudhi { diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h index d06ee4bd..02985727 100644 --- a/src/cython/include/Rips_complex_interface.h +++ b/src/cython/include/Rips_complex_interface.h @@ -71,6 +71,10 @@ class Rips_complex_interface { } } + ~Rips_complex_interface() { + delete rips_complex_; + } + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) { rips_complex_->create_complex(*simplex_tree, dim_max); simplex_tree->initialize_filtration(); diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in index c1a1717a..fefa36bb 100644 --- a/src/cython/setup.py.in +++ b/src/cython/setup.py.in @@ -29,7 +29,7 @@ __license__ = "GPL v3" gudhi = Extension( "gudhi", - sources = ['gudhi.pyx',], + sources = ['@CMAKE_CURRENT_BINARY_DIR@/gudhi.pyx',], language = 'c++', extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@], extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@], diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index 3ae537e3..4d452d7d 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -53,7 +53,6 @@ def test_insertion(): assert st.find([2, 3]) == False # filtration test - st.set_filtration(5.0) st.initialize_filtration() assert st.filtration([0, 1, 2]) == 4.0 assert st.filtration([0, 2]) == 4.0 |