From d6c4c80e50d558034958f8fab0289d4cfb1a31b8 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 5 Aug 2015 15:03:29 +0000 Subject: Debug traces in DEBUG mode Alpha complex from delaunay triangulation in static dimension git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@725 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9dda5a16874ae009c24be39c5a9c9d4124a29063 --- src/Persistent_cohomology/example/CMakeLists.txt | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'src/Persistent_cohomology/example') diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 9487cce6..3276989d 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -28,8 +28,11 @@ if (NOT MSVC) target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if(CGAL_FOUND) - # uncomment to display debug traces - # add_definitions(-DDEBUG_TRACES) + if (CMAKE_BUILD_TYPE MATCHES Debug) + # For programs to be more verbose + add_definitions(-DDEBUG_TRACES) + endif() + add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) -- cgit v1.2.3 From 03b68a5206201bf5bbffb7e4f6a6718907f23b2a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 9 Nov 2015 09:18:55 +0000 Subject: Modification for Porquerolles Workshop Bar_code_persistence and alpha_complex_persistence git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@893 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 63d2d21d5ff7c9a94a67eafc326bf8a561bf8166 --- src/Alpha_complex/example/CMakeLists.txt | 14 ++++ src/GudhUI/CMakeLists.txt | 40 +++++++++++ src/GudhUI/alpha_complex_persistence.cpp | 78 ++++++++++++++++++++ src/GudhUI/model/Model.h | 2 +- src/GudhUI/utils/Bar_code_persistence.h | 84 ++++++++++++++++++++++ src/GudhUI/view/FirstCoordProjector.h | 5 +- src/Persistent_cohomology/example/CMakeLists.txt | 44 ++++++++++++ .../example/alpha_complex_persistence.cpp | 55 ++++++++++++++ .../example/alpha_shapes_persistence.cpp | 14 ++-- .../include/gudhi/Persistent_cohomology.h | 8 +++ src/Simplex_tree/include/gudhi/Simplex_tree.h | 2 +- .../include/gudhi/Delaunay_triangulation_off_io.h | 2 +- src/common/include/gudhi/Off_reader.h | 2 +- 13 files changed, 338 insertions(+), 12 deletions(-) create mode 100644 src/GudhUI/alpha_complex_persistence.cpp create mode 100644 src/GudhUI/utils/Bar_code_persistence.h create mode 100644 src/Persistent_cohomology/example/alpha_complex_persistence.cpp (limited to 'src/Persistent_cohomology/example') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 04fc34af..10b87f04 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -8,6 +8,20 @@ if(CGAL_FOUND) message(STATUS "CGAL version: ${CGAL_VERSION}.") include( ${CGAL_USE_FILE} ) + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. + # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 + # A workaround is to add "-std=c++11" again. + # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html + # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html + # but it implies to use cmake version 3.1 at least. + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index 71f4fd1a..5c2afdd0 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -78,6 +78,46 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND ) target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} ) target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ) +############################################################################### + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. + # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 + # A workaround is to add "-std=c++11" again. + # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html + # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html + # but it implies to use cmake version 3.1 at least. + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + if (CMAKE_BUILD_TYPE MATCHES Debug) + # For programs to be more verbose + add_definitions(-DDEBUG_TRACES) + endif() + + add_executable (acp alpha_complex_persistence.cpp) + target_link_libraries(acp ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${QT_LIBRARIES}) + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () +############################################################################### + else() message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.") endif() diff --git a/src/GudhUI/alpha_complex_persistence.cpp b/src/GudhUI/alpha_complex_persistence.cpp new file mode 100644 index 00000000..4f85459a --- /dev/null +++ b/src/GudhUI/alpha_complex_persistence.cpp @@ -0,0 +1,78 @@ +#include +#include + + +#include + +// to construct a Delaunay_triangulation from a OFF file +#include +#include +#include + +#include "utils/Bar_code_persistence.h" + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " filename.off " << // alpha_square_max_value[double] " << + "coeff_field_characteristic[integer > 0] min_persistence[double >= -1.0]" << std::endl; + std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0 2 0.02" << std::endl; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + usage(argv[0]); + } + + QApplication qtapp(argc, argv); + + std::string off_file_name(argv[1]); + // double alpha_square_max_value = atof(argv[2]); + double alpha_square_max_value = 1e20; + int coeff_field_characteristic = atoi(argv[2]); // argv[3] + double min_persistence = atof(argv[3]); // argv[4] + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; + Gudhi::alphacomplex::Alpha_complex alpha_complex_from_file(off_file_name, alpha_square_max_value); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() << + " - " << alpha_complex_from_file.num_simplices() << " simplices - " << + alpha_complex_from_file.num_vertices() << " vertices." << std::endl; + + // Sort the simplices in the order of the filtration + alpha_complex_from_file.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl; + // Compute the persistence diagram of the complex + Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alphacomplex::Alpha_complex, + Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file); + + std::cout << "coeff_field_characteristic " << coeff_field_characteristic << + " - min_persistence " << min_persistence << std::endl; + + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + std::vector> persistence_vector; + pcoh.get_persistence(persistence_vector); + + Bar_code_persistence bc_persistence; + + for (auto persistence : persistence_vector) { + bc_persistence.insert(persistence.first, persistence.second); + } + + bc_persistence.show(); + + return qtapp.exec(); +} diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h index d78cbad9..4f8d48ee 100644 --- a/src/GudhUI/model/Model.h +++ b/src/GudhUI/model/Model.h @@ -71,7 +71,7 @@ class CGAL_geometric_flag_complex_wrapper { void maximal_face(std::vector vertices) { if (!load_only_points_) { - std::cout << "size:" << vertices.size() << std::endl; + //std::cout << "size:" << vertices.size() << std::endl; for (int i = 0; i < vertices.size(); ++i) for (int j = i + 1; j < vertices.size(); ++j) complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j])); diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h new file mode 100644 index 00000000..a1a46ea8 --- /dev/null +++ b/src/GudhUI/utils/Bar_code_persistence.h @@ -0,0 +1,84 @@ +#include // isfinite + +#include + +#include +#include +#include +#include +#include + +#include +#include +#include // NaN, infinity +#include // for pair + +class Bar_code_persistence { + private: + typedef std::vector> Persistence; + Persistence persistence_vector; + double min_birth; + double max_death; + + public: + + Bar_code_persistence() + : min_birth(std::numeric_limits::quiet_NaN()), + max_death(std::numeric_limits::quiet_NaN()) { } + + void insert(double birth, double death) { + persistence_vector.push_back(std::make_pair(birth, death)); + if (std::isfinite(birth)) { + if ((birth < min_birth) || (std::isnan(min_birth))) + min_birth = birth; + if ((birth > max_death) || (std::isnan(max_death))) + max_death = birth; + } + if (std::isfinite(death)) + if ((death > max_death) || (std::isnan(max_death))) + max_death = death; + } + + void show() { + // Create a view, put a scene in it + QGraphicsView * view = new QGraphicsView(); + QGraphicsScene * scene = new QGraphicsScene(); + view->setScene(scene); + double ratio = 600.0 / (max_death - min_birth); + //std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl; + + double height = 0.0, birth = 0.0, death = 0.0; + int pers_num = 1; + for (auto& persistence : persistence_vector) { + height = 5.0 * pers_num; + //std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl; + if (std::isfinite(persistence.first)) + birth = ((persistence.first - min_birth) * ratio) + 50.0; + else + birth = 0.0; + + if (std::isfinite(persistence.second)) + death = ((persistence.second - min_birth) * ratio) + 50.0; + else + death = 700.0; + + scene->addLine(birth, height, death, height, QPen(Qt::blue, 2)); + pers_num++; + } + height += 10.0; + // scale line + scene->addLine(0, height, 700.0, height, QPen(Qt::black, 1)); + int modulo = 0; + for (double scale = 50.0; scale < 700.0; scale += 50.0) { + modulo++; + // scale small dash + scene->addLine(scale, height - 3.0, scale, height + 3.0, QPen(Qt::black, 1)); + // scale text + QString scale_value = QString::number(((scale - 50.0) / ratio) + min_birth); + QGraphicsTextItem* dimText = scene->addText(scale_value, QFont("Helvetica", 8)); + dimText->setPos(scale - (3.0 * scale_value.size()), height + 9.0 * (modulo % 2)); + } + // Show the view + view->show(); + } +}; diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h index 529d2d42..3ceda3f5 100644 --- a/src/GudhUI/view/FirstCoordProjector.h +++ b/src/GudhUI/view/FirstCoordProjector.h @@ -32,8 +32,11 @@ class FirstCoordProjector3D : public Projector3D { typedef Projector3D::Point_3 Point_3; Point_3 operator()(const Point& p) const { - assert(p.dimension() >= 3); + if (p.dimension() >= 3) return Point_3(p.x(), p.y(), p.z()); + else if (p.dimension() >= 2) + return Point_3(p.x(), p.y(), 0.0); + } }; diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index ea69352e..74c2e778 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -39,6 +39,50 @@ if(GMPXX_FOUND AND GMP_FOUND) target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) + + + + + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. + # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 + # A workaround is to add "-std=c++11" again. + # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html + # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html + # but it implies to use cmake version 3.1 at least. + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + if (CMAKE_BUILD_TYPE MATCHES Debug) + # For programs to be more verbose + add_definitions(-DDEBUG_TRACES) + endif() + + add_executable (alphacomplexpersistence alpha_complex_persistence.cpp) + target_link_libraries(alphacomplexpersistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () + + + endif() endif() diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp new file mode 100644 index 00000000..fbadf673 --- /dev/null +++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp @@ -0,0 +1,55 @@ +#include +#include + +// to construct a Delaunay_triangulation from a OFF file +#include +#include +#include + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value[double] " << + "coeff_field_characteristic[integer > 0] min_persistence[double >= -1.0]" << std::endl; + std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0 2 0.02" << std::endl; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if (argc != 5) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + usage(argv[0]); + } + + std::string off_file_name(argv[1]); + double alpha_square_max_value = atof(argv[2]); + int coeff_field_characteristic = atoi(argv[3]); + double min_persistence = atof(argv[4]); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; + Gudhi::alphacomplex::Alpha_complex alpha_complex_from_file(off_file_name, alpha_square_max_value); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() << + " - " << alpha_complex_from_file.num_simplices() << " simplices - " << + alpha_complex_from_file.num_vertices() << " vertices." << std::endl; + + // Sort the simplices in the order of the filtration + alpha_complex_from_file.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl; + // Compute the persistence diagram of the complex + Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alphacomplex::Alpha_complex, + Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp index 6d5eebcf..235ea141 100644 --- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp @@ -124,6 +124,12 @@ void usage(char * const progName) { } int main(int argc, char * const argv[]) { + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + int coeff_field_characteristic = 0; int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { @@ -138,12 +144,6 @@ int main(int argc, char * const argv[]) { usage(argv[0]); } - // program args management - if (argc != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - // Read points from file std::string filegraph = argv[1]; std::list lp; @@ -239,7 +239,7 @@ int main(int argc, char * const argv[]) { } } // Construction of the simplex_tree - Filtration_value filtr = std::sqrt(*the_alpha_value_iterator); + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index d096792f..f6773bac 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -713,6 +713,14 @@ class Persistent_cohomology { } } + void get_persistence(std::vector>& persistence) { + cmp_intervals_by_length cmp(cpx_); + std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp); + for (auto pair : persistent_pairs_) { + persistence.push_back(std::make_pair(cpx_->filtration(get<0>(pair)), cpx_->filtration(get<1>(pair)))); + } + } + void write_output_diagram(std::string diagram_name) { std::ofstream diagram_out(diagram_name.c_str()); cmp_intervals_by_length cmp(cpx_); diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index c7a0b5d5..1ca43ff9 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1096,7 +1096,7 @@ class Simplex_tree { os << filtration(sh) << " \n"; } } - + private: Vertex_handle null_vertex_; /** \brief Upper bound on the filtration values of the simplices.*/ diff --git a/src/common/include/gudhi/Delaunay_triangulation_off_io.h b/src/common/include/gudhi/Delaunay_triangulation_off_io.h index 0c5474c9..47066a94 100644 --- a/src/common/include/gudhi/Delaunay_triangulation_off_io.h +++ b/src/common/include/gudhi/Delaunay_triangulation_off_io.h @@ -278,7 +278,7 @@ class Delaunay_triangulation_off_writer { std::vector vertexVector; stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " "; for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) { - stream << points_to_vh[(*vit)->point()] << " "; + stream << points_to_vh[(*vit)->point()] - 1 << " "; } stream << std::endl; } diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h index bba5a63a..e45a7600 100644 --- a/src/common/include/gudhi/Off_reader.h +++ b/src/common/include/gudhi/Off_reader.h @@ -160,7 +160,7 @@ class Off_reader { iss >> num_face_vertices; std::vector face; face.assign(std::istream_iterator(iss), std::istream_iterator()); - if (face.size() != off_info_.dim) return false; + //if (face.size() != (off_info_.dim + 1)) return false; visitor.maximal_face(face); } return true; -- cgit v1.2.3 From c79ddda239336378d50255ef99ea6c34ceefbb47 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 27 Nov 2015 17:05:22 +0000 Subject: After doc review git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@931 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 578da0e6fff453560e666e8f00147f9e10cb6de6 --- CMakeLists.txt | 6 + src/Alpha_complex/doc/Intro_alpha_complex.h | 91 +++- .../doc/alpha_complex_doc_alpha_shape.ipe | 482 --------------------- .../doc/alpha_complex_doc_alpha_shape.png | Bin 62759 -> 0 bytes .../doc/alpha_complex_representation.ipe | 321 ++++++++++++++ .../example/Alpha_complex_from_off.cpp | 16 +- .../example/Alpha_complex_from_points.cpp | 36 +- src/Alpha_complex/example/CMakeLists.txt | 4 - .../example/alphaoffreader_for_doc.txt | 27 -- .../example/alphaoffreader_for_doc_32.txt | 22 + .../example/alphaoffreader_for_doc_60.txt | 27 ++ src/Alpha_complex/include/gudhi/Alpha_complex.h | 2 + src/CMakeLists.txt | 6 + src/Doxyfile | 3 +- src/GudhUI/CMakeLists.txt | 4 - src/Persistent_cohomology/example/CMakeLists.txt | 8 - src/common/doc/main_page.h | 2 +- src/common/example/CMakeLists.txt | 4 - 18 files changed, 486 insertions(+), 575 deletions(-) delete mode 100644 src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.ipe delete mode 100644 src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png create mode 100644 src/Alpha_complex/doc/alpha_complex_representation.ipe delete mode 100644 src/Alpha_complex/example/alphaoffreader_for_doc.txt create mode 100644 src/Alpha_complex/example/alphaoffreader_for_doc_32.txt create mode 100644 src/Alpha_complex/example/alphaoffreader_for_doc_60.txt (limited to 'src/Persistent_cohomology/example') diff --git a/CMakeLists.txt b/CMakeLists.txt index 197b6f95..d42f7af7 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -69,6 +69,12 @@ else() message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS}) message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) + if (DEBUG_TRACES) + # For programs to be more verbose + message(STATUS "DEBUG_TRACES are activated") + add_definitions(-DDEBUG_TRACES) + endif() + include_directories(src/common/include/) include_directories(src/Alpha_complex/include/) include_directories(src/Bottleneck/include/) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 1fb8fdee..685a4c2f 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -36,48 +36,58 @@ namespace alphacomplex { * * \section definition Definition * - * Alpha_complex is a Simplex_tree constructed from each finite cell of a Delaunay Triangulation. + * Alpha_complex is a simplicial complex + * constructed from each finite cell of a Delaunay Triangulation. * * The filtration value of each simplex is computed from the alpha square value of the simplex if it is Gabriel or * from the alpha value of the simplex coface that makes the simplex not Gabriel. * - * Please refer to \cite AlphaShapesDefinition for a more complete alpha complex definition. + * All simplices that have a filtration value strictly greater than a given alpha square value are not inserted into + * the simplex. * - * Alpha complex are interesting because it looks like an \ref alpha-shape "Alpha shape" as described in - * \cite AlphaShapesIntroduction (an alpha complex concept vulgarization). + * \image html "alpha_complex_representation.png" "Alpha simplicial complex representation" * - * \section example Example + * Alpha_complex is constructing a `Simplex_tree` using Delaunay Triangulation + * \cite cgal:hdj-t-15b from CGAL (the Computational Geometry + * Algorithms Library \cite cgal:eb-15b). * - * This example loads points from an OFF file, builds the Delaunay triangulation from the points, and finally - * initialize the alpha complex with it. + * The complex is a template class requiring a dD Geometry Kernel + * \cite cgal:s-gkd-15b from CGAL as template. + * + * \section pointsexample Example from points + * + * This example builds the Delaunay triangulation from the given points in a 2D static kernel, and initializes the + * alpha complex with it. * * Then, it is asked to display information about the alpha complex. * - * \include Alpha_complex_from_off.cpp + * \include Alpha_complex_from_points.cpp * * When launching: * - * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off 60.0 + * \code $> ./alphapoints 60.0 * \endcode * * the program output is: * - * \include alphaoffreader_for_doc.txt + * \include alphaoffreader_for_doc_60.txt * * \section algorithm Algorithm * - * Data structure + * \subsection datastructure Data structure * * In order to build the alpha complex, first, a Simplex tree is build from the cells of a Delaunay Triangulation. * (The filtration value is set to NaN, which stands for unknown value): * \image html "alpha_complex_doc.png" "Simplex tree structure construction example" * - * Filtration value computation algorithm - * + * \subsection filtrationcomputation Filtration value computation algorithm + * * \f{algorithm}{ * \caption{Filtration value computation algorithm}\label{alpha} * \begin{algorithmic} - * \For{i : dimension $\rightarrow$ 1} + * \For{i : dimension $\rightarrow$ 0} * \ForAll{$\sigma$ of dimension i} * \If {filtration($\sigma$) is NaN} * \State filtration($\sigma$) = $\alpha^2(\sigma)$ @@ -93,25 +103,58 @@ namespace alphacomplex { * \EndFor * \EndFor * \EndFor + * \State make\_filtration\_non\_decreasing() + * \State prune\_above\_filtration() * \end{algorithmic} * \f} * - * From the example above, it means the algorithm will look into each triangle ([1,2,3], [2,3,4], [1,3,5], ...), - * will compute the filtration value of the triangle, and then will propagate the filtration value as described + * \subsubsection dimension2 Dimension 2 + * + * From the example above, it means the algorithm looks into each triangle ([1,2,3], [2,3,4], [1,3,5], ...), + * computes the filtration value of the triangle, and then propagates the filtration value as described * here : * \image html "alpha_complex_doc_135.png" "Filtration value propagation example" - * Then, the algorithm will look into each edge ([1,2], [2,3], [1,3], ...), - * will compute the filtration value of the edge (in this case, propagation will have no effect). * - * Finally, the algorithm will look into each vertex ([1], [2], [3], [4], [5], [6] and [7]), - * will set the filtration value (0 in case of a vertex - propagation will have no effect). + * \subsubsection dimension1 Dimension 1 + * + * Then, the algorithm looks into each edge ([1,2], [2,3], [1,3], ...), + * computes the filtration value of the edge (in this case, propagation will have no effect). + * + * \subsubsection dimension0 Dimension 0 + * + * Finally, the algorithm looks into each vertex ([1], [2], [3], [4], [5], [6] and [7]) and + * sets the filtration value (0 in case of a vertex - propagation will have no effect). + * + * \subsubsection nondecreasing Non decreasing filtration values + * + * As Alpha square value computed from CGAL is an approximation, we have to make filtration non decreasing while + * increasing the dimension for our simplicial complex to be valid (cf. + * `Simplex_tree::make_filtration_non_decreasing()`). + * + * \subsubsection pruneabove Prune above given filtration value + * + * The simplex tree is pruned from the given maximum alpha square value (cf. `Simplex_tree::prune_above_filtration()`). + * In this example, the value is given by the user as argument of the program. * - * \section alpha-shape Alpha shape * - * In the example above, the alpha shape of \f$\alpha^2_{63} < \alpha^2 < \alpha^2_{62}\f$ is the alpha complex where the - * \f$\alpha^2_{63} <\f$ filtration value \f$< \alpha^2_{62}\f$ as described in \cite AlphaShapesIntroduction + * \section offexample Example from OFF file + * + * This example builds the Delaunay triangulation in a dynamic kernel, and initializes the alpha complex with it. + * + * + * Then, it is asked to display information about the alpha complex. + * + * \include Alpha_complex_from_off.cpp + * + * When launching: + * + * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off 32.0 + * \endcode + * + * the program output is: + * + * \include alphaoffreader_for_doc_32.txt * - * \image html "alpha_complex_doc_alpha_shape.png" "Alpha shape example" * \copyright GNU General Public License v3. * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ diff --git a/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.ipe b/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.ipe deleted file mode 100644 index 7563cf3d..00000000 --- a/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.ipe +++ /dev/null @@ -1,482 +0,0 @@ - - - - - - - -0 0 m --1 0.333 l --1 -0.333 l -h - - - - -0 0 m --1 0.333 l --1 -0.333 l -h - - - - -0.6 0 0 0.6 0 0 e -0.4 0 0 0.4 0 0 e - - - - -0.6 0 0 0.6 0 0 e - - - - - -0.5 0 0 0.5 0 0 e - - -0.6 0 0 0.6 0 0 e -0.4 0 0 0.4 0 0 e - - - - - --0.6 -0.6 m -0.6 -0.6 l -0.6 0.6 l --0.6 0.6 l -h --0.4 -0.4 m -0.4 -0.4 l -0.4 0.4 l --0.4 0.4 l -h - - - - --0.6 -0.6 m -0.6 -0.6 l -0.6 0.6 l --0.6 0.6 l -h - - - - - --0.5 -0.5 m -0.5 -0.5 l -0.5 0.5 l --0.5 0.5 l -h - - --0.6 -0.6 m -0.6 -0.6 l -0.6 0.6 l --0.6 0.6 l -h --0.4 -0.4 m -0.4 -0.4 l -0.4 0.4 l --0.4 0.4 l -h - - - - - - --0.43 -0.57 m -0.57 0.43 l -0.43 0.57 l --0.57 -0.43 l -h - - --0.43 0.57 m -0.57 -0.43 l -0.43 -0.57 l --0.57 0.43 l -h - - - - - -0 0 m --1 0.333 l --1 -0.333 l -h - - - - -0 0 m --1 0.333 l --0.8 0 l --1 -0.333 l -h - - - - -0 0 m --1 0.333 l --0.8 0 l --1 -0.333 l -h - - - - --1 0.333 m -0 0 l --1 -0.333 l - - - - -0 0 m --1 0.333 l --1 -0.333 l -h --1 0 m --2 0.333 l --2 -0.333 l -h - - - - -0 0 m --1 0.333 l --1 -0.333 l -h --1 0 m --2 0.333 l --2 -0.333 l -h - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Alpha shape -0 -1 -2 -3 -4 -5 -6 -0 -1 -2 -2 -1 -2 -2 -3 -3 -3 -3 -4 -4 -4 -4 -6 -6 -6 -6 -6 -6 -5 -6 -5 - -4 0 0 4 320 704 e - - -322.919 706.788 m -317.189 701.058 l -317.189 701.203 l - - -317.551 706.934 m -322.629 701.058 l - - -230 680 m -240 670 l - - -230 680 m -240 670 l - - -230 680 m -240 670 l - - -230 680 m -240 670 l - - -230 680 m -220 670 l - - -230 680 m -230 670 l - - -220 660 m -220 650 l - - -230 660 m -230 650 l - - -260 680 m -260 670 l - - -260 660 m -260 650 l - - -300 680 m -300 670 l - - -300 680 m -290 670 l - - -290 660 m -290 650 l - - -300 660 m -300 650 l - - -330 680 m -330 670 l - - -350 680 m -350 670 l - - -350 660 m -350 650 l - - -320 700 m -240 690 l - - -320 700 m -270 690 l - - -320 700 m -310 690 l - - -320 700 m -330 690 l - - -320 700 m -350 690 l - - -320 700 m -380 690 l - - -320 700 m -400 690 l - -Alpha complex structure - -58.1341 0 0 58.1341 218.925 692.601 e - - -58.1341 0 0 58.1341 218.925 692.601 e - - -58.1341 0 0 58.1341 218.925 692.601 e - - -58.1341 0 0 58.1341 218.925 692.601 e - - -58.1341 0 0 58.1341 218.925 692.601 e - - -58.1341 0 0 58.1341 218.925 692.601 e - - -58.1341 0 0 58.1341 218.925 692.601 e - - -58.1341 0 0 58.1341 218.925 692.601 e - - -58.1341 0 0 58.1341 218.925 692.601 e - - -60 710 m -40 660 l - - -40 660 m -130 690 l - - -130 690 m -60 710 l - - -40 660 m -80 580 l - - -80 580 m -130 580 l -130 580 l - - -130 580 m -110 520 l - - -110 520 m -50 530 l -50 530 l -50 530 l - - -50 530 m -80 580 l - - -130 580 m -130 690 l - - - -108.275 743.531 m -166.45 743.531 l - -$\alpha$ -filtration value $> \alpha$ are greyed - -280 660 m -300 680 l - - -280 660 m -300 640 l - - -370 660 m -350 680 l - - -370 660 m -350 640 l - - -290 670 m -360 670 l - - -290 650 m -360 650 l - -equivalent - - diff --git a/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png b/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png deleted file mode 100644 index 2d5f59a3..00000000 Binary files a/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png and /dev/null differ diff --git a/src/Alpha_complex/doc/alpha_complex_representation.ipe b/src/Alpha_complex/doc/alpha_complex_representation.ipe new file mode 100644 index 00000000..8687d694 --- /dev/null +++ b/src/Alpha_complex/doc/alpha_complex_representation.ipe @@ -0,0 +1,321 @@ + + + + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h + + + + +0.6 0 0 0.6 0 0 e +0.4 0 0 0.4 0 0 e + + + + +0.6 0 0 0.6 0 0 e + + + + + +0.5 0 0 0.5 0 0 e + + +0.6 0 0 0.6 0 0 e +0.4 0 0 0.4 0 0 e + + + + + +-0.6 -0.6 m +0.6 -0.6 l +0.6 0.6 l +-0.6 0.6 l +h +-0.4 -0.4 m +0.4 -0.4 l +0.4 0.4 l +-0.4 0.4 l +h + + + + +-0.6 -0.6 m +0.6 -0.6 l +0.6 0.6 l +-0.6 0.6 l +h + + + + + +-0.5 -0.5 m +0.5 -0.5 l +0.5 0.5 l +-0.5 0.5 l +h + + +-0.6 -0.6 m +0.6 -0.6 l +0.6 0.6 l +-0.6 0.6 l +h +-0.4 -0.4 m +0.4 -0.4 l +0.4 0.4 l +-0.4 0.4 l +h + + + + + + +-0.43 -0.57 m +0.57 0.43 l +0.43 0.57 l +-0.57 -0.43 l +h + + +-0.43 0.57 m +0.57 -0.43 l +0.43 -0.57 l +-0.57 0.43 l +h + + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h + + + + +0 0 m +-1 0.333 l +-0.8 0 l +-1 -0.333 l +h + + + + +0 0 m +-1 0.333 l +-0.8 0 l +-1 -0.333 l +h + + + + +-1 0.333 m +0 0 l +-1 -0.333 l + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h +-1 0 m +-2 0.333 l +-2 -0.333 l +h + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h +-1 0 m +-2 0.333 l +-2 -0.333 l +h + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +109.771 601.912 m +159.595 601.797 l +140.058 541.915 l +h + + +79.8776 552.169 m +109.756 601.699 l +139.812 542.209 l +h + + +69.8453 682.419 m +159.925 712.208 l +90.12 732.039 l +h + +Alpha complex +0 +1 +2 +3 +4 +5 +6 + +58.1341 0 0 58.1341 218.925 692.601 e + + +60 710 m +40 660 l + + +40 660 m +130 690 l + + +130 690 m +60 710 l + + +40 660 m +80 580 l + + +80 580 m +130 580 l +130 580 l + + +130 580 m +110 520 l + + +110 520 m +50 530 l +50 530 l +50 530 l + + +50 530 m +80 580 l + + +130 580 m +130 690 l + + + +108.275 743.531 m +166.45 743.531 l + +$\alpha$ + + + + + + +150.038 609.9 m +179.929 549.727 l + + + + + diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index cd6f5a4b..4f381892 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -1,8 +1,6 @@ #include #include -// to construct a Delaunay_triangulation from a OFF file -#include #include void usage(char * const progName) { @@ -35,14 +33,12 @@ int main(int argc, char **argv) { std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { - //if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) { - std::cout << " ( "; - for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; - } - std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] "; - std::cout << std::endl; - //} + std::cout << " ( "; + for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] "; + std::cout << std::endl; } return 0; } diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index e460f177..62f594d1 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -6,34 +6,50 @@ #include #include -// to construct a Delaunay_triangulation from a OFF file -#include "gudhi/Delaunay_triangulation_off_io.h" -#include "gudhi/Alpha_complex.h" +#include -typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; +typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel; typedef Kernel::Point_d Point; typedef std::vector Vector_of_points; +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " alpha_square_max_value" << std::endl; + std::cerr << " i.e.: " << progName << " 32.0" << std::endl; + exit(-1); // ----- >> +} + int main(int argc, char **argv) { + if (argc != 2) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + usage(argv[0]); + } + + double alpha_square_max_value = atof(argv[1]); + // ---------------------------------------------------------------------------- // Init of a list of points // ---------------------------------------------------------------------------- Vector_of_points points; - std::vector coords = { 0.0, 0.0, 0.0, 1.0 }; + std::vector coords = { 1.0, 1.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 7.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 4.0, 6.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 9.0, 6.0 }; points.push_back(Point(coords.begin(), coords.end())); - coords = { 0.0, 0.0, 1.0, 0.0 }; + coords = { 0.0, 14.0 }; points.push_back(Point(coords.begin(), coords.end())); - coords = { 0.0, 1.0, 0.0, 0.0 }; + coords = { 2.0, 19.0 }; points.push_back(Point(coords.begin(), coords.end())); - coords = { 1.0, 0.0, 0.0, 0.0 }; + coords = { 9.0, 17.0 }; points.push_back(Point(coords.begin(), coords.end())); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points // ---------------------------------------------------------------------------- - double max_alpha_square_value = 1e10; - Gudhi::alphacomplex::Alpha_complex alpha_complex_from_points(points, max_alpha_square_value); + Gudhi::alphacomplex::Alpha_complex alpha_complex_from_points(points, alpha_square_max_value); // ---------------------------------------------------------------------------- // Display information about the alpha complex diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 10b87f04..33ff6805 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -27,10 +27,6 @@ if(CGAL_FOUND) if (EIGEN3_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") include( ${EIGEN3_USE_FILE} ) - if (CMAKE_BUILD_TYPE MATCHES Debug) - # For programs to be more verbose - add_definitions(-DDEBUG_TRACES) - endif() add_executable ( alphaoffreader Alpha_complex_from_off.cpp ) target_link_libraries(alphaoffreader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc.txt b/src/Alpha_complex/example/alphaoffreader_for_doc.txt deleted file mode 100644 index 71f29a00..00000000 --- a/src/Alpha_complex/example/alphaoffreader_for_doc.txt +++ /dev/null @@ -1,27 +0,0 @@ -Alpha complex is of dimension 2 - 25 simplices - 7 vertices. -Iterator on alpha complex simplices in the filtration order, with [filtration value]: - ( 0 ) -> [0] - ( 1 ) -> [0] - ( 2 ) -> [0] - ( 3 ) -> [0] - ( 4 ) -> [0] - ( 5 ) -> [0] - ( 6 ) -> [0] - ( 3 2 ) -> [6.25] - ( 5 4 ) -> [7.25] - ( 2 0 ) -> [8.5] - ( 1 0 ) -> [9.25] - ( 3 1 ) -> [10] - ( 2 1 ) -> [11.25] - ( 3 2 1 ) -> [12.5] - ( 2 1 0 ) -> [12.9959] - ( 6 5 ) -> [13.25] - ( 4 2 ) -> [20] - ( 6 4 ) -> [22.7367] - ( 6 5 4 ) -> [22.7367] - ( 6 3 ) -> [30.25] - ( 6 2 ) -> [36.5] - ( 6 3 2 ) -> [36.5] - ( 6 4 2 ) -> [37.2449] - ( 4 0 ) -> [59.7107] - ( 4 2 0 ) -> [59.7107] diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt new file mode 100644 index 00000000..553431a9 --- /dev/null +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt @@ -0,0 +1,22 @@ +Alpha complex is of dimension 2 - 20 simplices - 7 vertices. +Iterator on alpha complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 5 4 ) -> [6.25] + ( 4 1 ) -> [20] + ( 4 2 ) -> [8.5] + ( 6 2 ) -> [9.25] + ( 6 5 ) -> [10] + ( 6 4 ) -> [11.25] + ( 6 5 4 ) -> [12.5] + ( 6 4 2 ) -> [12.9959] + ( 3 0 ) -> [13.25] + ( 4 1 ) -> [20] + ( 1 0 ) -> [22.7367] + ( 3 1 0 ) -> [22.7367] + ( 5 0 ) -> [30.25] diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt new file mode 100644 index 00000000..71f29a00 --- /dev/null +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt @@ -0,0 +1,27 @@ +Alpha complex is of dimension 2 - 25 simplices - 7 vertices. +Iterator on alpha complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] + ( 6 2 ) -> [36.5] + ( 6 3 2 ) -> [36.5] + ( 6 4 2 ) -> [37.2449] + ( 4 0 ) -> [59.7107] + ( 4 2 0 ) -> [59.7107] diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 6adfa2e6..2dae4028 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -27,6 +27,8 @@ #include #include #include +// to construct a Delaunay_triangulation from a OFF file +#include #include #include // isnan, fmax diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 9d1eac80..3a75527e 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -42,6 +42,12 @@ else() INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) + if (DEBUG_TRACES) + message(STATUS "DEBUG_TRACES are activated") + # For programs to be more verbose + add_definitions(-DDEBUG_TRACES) + endif() + #--------------------------------------------------------------------------------------- # Gudhi compilation part include_directories(include) diff --git a/src/Doxyfile b/src/Doxyfile index 81f55e29..9cd73444 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -673,6 +673,7 @@ LAYOUT_FILE = # also \cite for info how to create references. CITE_BIB_FILES = biblio/bibliography.bib \ + biblio/how_to_cite_cgal.bib \ biblio/how_to_cite_gudhi.bib #--------------------------------------------------------------------------- @@ -812,7 +813,7 @@ EXCLUDE_SYMBOLS = # that contain example code fragments that are included (see the \include # command). -EXAMPLE_PATH = biblio/ +EXAMPLE_PATH = biblio/ \ example/common/ \ example/Alpha_complex/ diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index 5c2afdd0..75adba08 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -102,10 +102,6 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND ) if (EIGEN3_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") include( ${EIGEN3_USE_FILE} ) - if (CMAKE_BUILD_TYPE MATCHES Debug) - # For programs to be more verbose - add_definitions(-DDEBUG_TRACES) - endif() add_executable (acp alpha_complex_persistence.cpp) target_link_libraries(acp ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${QT_LIBRARIES}) diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 8caf7d8b..eb4ee3e3 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -35,10 +35,6 @@ if(GMPXX_FOUND AND GMP_FOUND) target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if(CGAL_FOUND) - if (CMAKE_BUILD_TYPE MATCHES Debug) - # For programs to be more verbose - add_definitions(-DDEBUG_TRACES) - endif() add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) @@ -70,10 +66,6 @@ if(GMPXX_FOUND AND GMP_FOUND) if (EIGEN3_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") include( ${EIGEN3_USE_FILE} ) - if (CMAKE_BUILD_TYPE MATCHES Debug) - # For programs to be more verbose - add_definitions(-DDEBUG_TRACES) - endif() add_executable (alphacomplexpersistence alpha_complex_persistence.cpp) target_link_libraries(alphacomplexpersistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 3edcbd0b..3c42f72d 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -63,7 +63,7 @@ * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms. * * The following examples require the Computational Geometry Algorithms - * Library (CGAL) and will not be built if CGAL is not installed: + * Library (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: * \li GudhUI * \li Persistent_cohomology/alpha_shapes_persistence * \li Simplex_tree/simplex_tree_from_alpha_shapes_3 diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index 089f0c04..d29e31e7 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -26,10 +26,6 @@ if(CGAL_FOUND) if (EIGEN3_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") include( ${EIGEN3_USE_FILE} ) - if (CMAKE_BUILD_TYPE MATCHES Debug) - # For programs to be more verbose - add_definitions(-DDEBUG_TRACES) - endif() add_executable ( dtoffrw Delaunay_triangulation_off_rw.cpp ) target_link_libraries(dtoffrw ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) -- cgit v1.2.3 From 11b195d4e26d48cdc56883957cbad16e298e43ca Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 12 Jan 2016 16:07:10 +0000 Subject: Fix alpha complex remarks and bugs git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@957 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fa837fd1a4373c2322db16353d98767907f34c79 --- CMakeLists.txt | 4 +- biblio/how_to_cite_cgal.bib | 947 +++++++++++++++++++++ src/Alpha_complex/test/CMakeLists.txt | 2 - src/GudhUI/alpha_complex_persistence.cpp | 78 -- src/GudhUI/utils/Bar_code_persistence.h | 3 +- src/GudhUI/utils/Persistence_compute.h | 15 +- src/Persistent_cohomology/example/CMakeLists.txt | 100 ++- .../example/alpha_complex_persistence.cpp | 92 +- .../example/rips_persistence.cpp | 3 +- src/Simplex_tree/include/gudhi/Simplex_tree.h | 81 +- src/Simplex_tree/test/simplex_tree_unit_test.cpp | 56 +- src/common/include/gudhi/distance_functions.h | 4 +- src/common/include/gudhi/reader_utils.h | 4 +- 13 files changed, 1140 insertions(+), 249 deletions(-) create mode 100644 biblio/how_to_cite_cgal.bib delete mode 100644 src/GudhUI/alpha_complex_persistence.cpp (limited to 'src/Persistent_cohomology/example') diff --git a/CMakeLists.txt b/CMakeLists.txt index d0770dd7..54e86f72 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -10,7 +10,7 @@ endif() enable_testing() -set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") +set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}") # Generate GUDHI official version file @@ -22,7 +22,7 @@ if(MSVC) # Turn off some VC++ warnings SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -fsanitize=memory -fno-omit-frame-pointer -Wall -Wpedantic -Wsign-compare") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O1") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") endif() diff --git a/biblio/how_to_cite_cgal.bib b/biblio/how_to_cite_cgal.bib new file mode 100644 index 00000000..7336ee81 --- /dev/null +++ b/biblio/how_to_cite_cgal.bib @@ -0,0 +1,947 @@ +@book{ cgal:eb-15b +, title = "{CGAL} User and Reference Manual" +, author = "{The CGAL Project}" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, year = 2015 +, url = "http://doc.cgal.org/4.7/Manual/packages.html" +} +@incollection{cgal:h-af-15b +, author = "Michael Hemmer" +, title = "Algebraic Foundations" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAlgebraicFoundationsSummary" +, year = 2015 +} + +@incollection{cgal:hhkps-nt-15b +, author = "Michael Hemmer and Susan Hert and Sylvain Pion and Stefan Schirra" +, title = "Number Types" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgNumberTypesSummary" +, year = 2015 +} + +@incollection{cgal:h-ma-15b +, author = "Michael Hemmer and Sylvain Pion" +, title = "Modular Arithmetic" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgModularArithmeticSummary" +, year = 2015 +} + +@incollection{cgal:h-p-15b +, author = "Michael Hemmer" +, title = "Polynomial" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolynomialSummary" +, year = 2015 +} + +@incollection{cgal:bht-ak-15b +, author = "Eric Berberich and Michael Hemmer and Michael Kerber and Sylvain Lazard and Luis Pe{\~n}aranda and Monique Teillaud" +, title = "Algebraic Kernel" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAlgebraicKerneldSummary" +, year = 2015 +} + +@incollection{cgal:h-msms-15b +, author = "Michael Hoffmann" +, title = "Monotone and Sorted Matrix Search" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMatrixSearchSummary" +, year = 2015 +} + +@incollection{cgal:fgsw-lqps-15b +, author = "Kaspar Fischer and Bernd G{\"a}rtner and Sven Sch{\"o}nherr and Frans Wessendorp" +, title = "Linear and Quadratic Programming Solver" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgQPSolverSummary" +, year = 2015 +} + +@incollection{cgal:bfghhkps-lgk23-15b +, author = "Herv{\'e} Br{\"o}nnimann and Andreas Fabri and Geert-Jan Giezeman and Susan Hert and Michael Hoffmann and Lutz Kettner and Sylvain Pion and Stefan Schirra" +, title = "{2D} and {3D} Linear Geometry Kernel" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgKernel23Summary" +, year = 2015 +} + +@incollection{cgal:s-gkd-15b +, author = "Michael Seel" +, title = "{dD} Geometry Kernel" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgKernelDSummary" +, year = 2015 +} + +@incollection{cgal:cpt-cgk2-15b +, author = "Pedro Machado Manh{\~a}es de Castro and Sylvain Pion and Monique Teillaud" +, title = "{2D} Circular Geometry Kernel" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgCircularKernel2Summary" +, year = 2015 +} + +@incollection{cgal:cclt-sgk3-15b +, author = "Pedro Machado Manh{\~a}es de Castro and Fr{\'e}d{\'e}ric Cazals and S{\'e}bastien Loriot and Monique Teillaud" +, title = "{3D} Spherical Geometry Kernel" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSphericalKernel3Summary" +, year = 2015 +} + +@incollection{cgal:hs-chep2-15b +, author = "Susan Hert and Stefan Schirra" +, title = "{2D} Convex Hulls and Extreme Points" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgConvexHull2Summary" +, year = 2015 +} + +@incollection{cgal:hs-ch3-15b +, author = "Susan Hert and Stefan Schirra" +, title = "{3D} Convex Hulls" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgConvexHull3Summary" +, year = 2015 +} + +@incollection{cgal:hs-chdt3-15b +, author = "Susan Hert and Michael Seel" +, title = "{dD} Convex Hulls and Delaunay Triangulations" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgConvexHullDSummary" +, year = 2015 +} + +@incollection{cgal:gw-p2-15b +, author = "Geert-Jan Giezeman and Wieger Wesselink" +, title = "{2D} Polygons" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolygon2Summary" +, year = 2015 +} + +@incollection{cgal:fwzh-rbso2-15b +, author = "Efi Fogel and Ophir Setter and Ron Wein and Guy Zucker and Baruch Zukerman and Dan Halperin" +, title = "{2D} Regularized Boolean Set-Operations" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBooleanSetOperations2Summary" +, year = 2015 +} + +@incollection{cgal:s-bonp2-15b +, author = "Michael Seel" +, title = "{2D} Boolean Operations on Nef Polygons" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgNef2Summary" +, year = 2015 +} + +@incollection{cgal:hk-bonpes2-15b +, author = "Peter Hachenberger and Lutz Kettner" +, title = "{2D} Boolean Operations on Nef Polygons Embedded on the Sphere" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgNefS2Summary" +, year = 2015 +} + +@incollection{cgal:h-pp2-15b +, author = "Susan Hert" +, title = "{2D} Polygon Partitioning" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolygonPartitioning2Summary" +, year = 2015 +} + +@incollection{cgal:c-sspo2-15b +, author = "Fernando Cacciola" +, title = "{2D} Straight Skeleton and Polygon Offsetting" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgStraightSkeleton2Summary" +, year = 2015 +} + +@incollection{cgal:w-rms2-15b +, author = "Ron Wein and Alon Baram and Eyal Flato and Efi Fogel and Michael Hemmer and Sebastian Morr" +, title = "{2D} Minkowski Sums" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMinkowskiSum2Summary" +, year = 2015 +} + +@incollection{cgal:f-ps2-15b +, author = "Andreas Fabri" +, title = "{2D} Polyline Simplification" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolylineSimplification2Summary" +, year = 2015 +} + +@incollection{hhb-visibility-2-15b +, author = "Michael Hemmer and Kan Huang and Francisc Bungiu and Ning Xu" +, title = "{2D} Visibility Computation" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgVisibility_2Summary" +, year = 2015 +} + +@incollection{cgal:k-ps-15b +, author = "Lutz Kettner" +, title = "{3D} Polyhedral Surface" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolyhedronSummary" +, year = 2015 +} + +@incollection{cgal:k-hds-15b +, author = "Lutz Kettner" +, title = "Halfedge Data Structures" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgHDSSummary" +, year = 2015 +} + +@incollection{cgal:bsmf-sm-15b +, author = "Mario Botsch and Daniel Sieger and Philipp Moeller and Andreas Fabri" +, title = "Surface Mesh" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceMeshSummary" +, year = 2015 +} + +@incollection{cgal:d-cm-15b +, author = "Guillaume Damiand" +, title = "Combinatorial Maps" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgCombinatorialMapsSummary" +, year = 2015 +} + +@incollection{cgal:d-lcc-12-15b +, author = "Guillaume Damiand" +, title = "Linear Cell Complex" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgLinearCellComplexSummary" +, year = 2015 +} + +@incollection{cgal:hk-bonp3-15b +, author = "Peter Hachenberger and Lutz Kettner" +, title = "{3D} Boolean Operations on Nef Polyhedra" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgNef3Summary" +, year = 2015 +} + +@incollection{cgal:h-emspe-15b +, author = "Peter Hachenberger" +, title = "Convex Decomposition of Polyhedra" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgConvexDecomposition3Summary" +, year = 2015 +} + +@incollection{cgal:h-msp3-15b +, author = "Peter Hachenberger" +, title = "{3D} Minkowski Sum of Polyhedra" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMinkowskiSum3Summary" +, year = 2015 +} + +@incollection{cgal:wfzh-a2-15b +, author = "Ron Wein and Eric Berberich and Efi Fogel and Dan Halperin and Michael Hemmer and Oren Salzman and Baruch Zukerman" +, title = "{2D} Arrangements" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgArrangement2Summary" +, year = 2015 +} + +@incollection{cgal:wfz-ic2-15b +, author = "Baruch Zukerman and Ron Wein and Efi Fogel" +, title = "{2D} Intersection of Curves" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgIntersectionOfCurves2Summary" +, year = 2015 +} + +@incollection{cgal:p-sr2-15b +, author = "Eli Packer" +, title = "{2D} Snap Rounding" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSnapRounding2Summary" +, year = 2015 +} + +@incollection{cgal:w-e2-15b +, author = "Ron Wein" +, title = "{2D} Envelopes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgEnvelope2Summary" +, year = 2015 +} + +@incollection{cgal:mwz-e3-15b +, author = "Dan Halperin and Michal Meyerovitch and Ron Wein and Baruch Zukerman" +, title = "{3D} Envelopes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgEnvelope3Summary" +, year = 2015 +} + +@incollection{cgal:y-t2-15b +, author = "Mariette Yvinec" +, title = "{2D} Triangulation" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTriangulation2Summary" +, year = 2015 +} + +@incollection{cgal:py-tds2-15b +, author = "Sylvain Pion and Mariette Yvinec" +, title = "{2D} Triangulation Data Structure" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTDS2Summary" +, year = 2015 +} + +@incollection{cgal:k-pt2-13-15b +, author = "Nico Kruithof" +, title = "{2D} Periodic Triangulations" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPeriodic2Triangulation2Summary" +, year = 2015 +} + +@incollection{cgal:pt-t3-15b +, author = "Cl{\'e}ment Jamin and Sylvain Pion and Monique Teillaud" +, title = "{3D} Triangulations" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTriangulation3Summary" +, year = 2015 +} + +@incollection{cgal:pt-tds3-15b +, author = "Cl{\'e}ment Jamin and Sylvain Pion and Monique Teillaud" +, title = "{3D} Triangulation Data Structure" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTDS3Summary" +, year = 2015 +} + +@incollection{cgal:ct-pt3-15b +, author = "Manuel Caroli and Monique Teillaud" +, title = "{3D} Periodic Triangulations" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPeriodic3Triangulation3Summary" +, year = 2015 +} + +@incollection{cgal:hdj-t-15b +, author = "Samuel Hornus and Olivier Devillers and Cl{\'e}ment Jamin" +, title = "{dD} Triangulations" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTriangulationsSummary" +, year = 2015 +} + +@incollection{cgal:d-as2-15b +, author = "Tran Kai Frank Da" +, title = "{2D} Alpha Shapes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAlphaShape2Summary" +, year = 2015 +} + +@incollection{cgal:dy-as3-15b +, author = "Tran Kai Frank Da and S{\'e}bastien Loriot and Mariette Yvinec" +, title = "{3D} Alpha Shapes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAlphaShapes3Summary" +, year = 2015 +} + +@incollection{cgal:k-sdg2-15b +, author = "Menelaos Karavelas" +, title = "{2D} Segment Delaunay Graphs" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSegmentDelaunayGraph2Summary" +, year = 2015 +} + +@incollection{cgal:cdp-sdglinf2-15b +, author = "Panagiotis Cheilaris and Sandeep Kumar Dey and Evanthia Papadopoulou" +, title = "L Infinity Segment Delaunay Graphs" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSDGLinfSummary" +, year = 2015 +} + +@incollection{cgal:ky-ag2-15b +, author = "Menelaos Karavelas and Mariette Yvinec" +, title = "{2D} Apollonius Graphs (Delaunay Graphs of Disks)" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgApolloniusGraph2Summary" +, year = 2015 +} + +@incollection{cgal:k-vda2-15b +, author = "Menelaos Karavelas" +, title = "{2D} Voronoi Diagram Adaptor" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgVoronoiDiagramAdaptor2Summary" +, year = 2015 +} + +@incollection{cgal:r-ctm2-15b +, author = "Laurent Rineau" +, title = "{2D} Conforming Triangulations and Meshes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMesh2Summary" +, year = 2015 +} + +@incollection{cgal:ry-smg-15b +, author = "Laurent Rineau and Mariette Yvinec" +, title = "{3D} Surface Mesh Generation" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceMesher3Summary" +, year = 2015 +} + +@incollection{cgal:asg-srps-15b +, author = "Pierre Alliez and Laurent Saboret and Ga{\"e}l Guennebaud" +, title = "Surface Reconstruction from Point Sets" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceReconstructionFromPointSetsSummary" +, year = 2015 +} + +@incollection{cgal:ssr3-15b +, author = "Thijs van Lankveld" +, title = "Scale-Space Surface Reconstruction" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgScaleSpaceReconstruction3Summary" +, year = 2015 +} + +@incollection{cgal:dc-afsr-15b +, author = "Tran Kai Frank Da and David Cohen-Steiner" +, title = "Advancing Front Surface Reconstruction" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAdvancingFrontSurfaceReconstructionSummary" +, year = 2015 +} + +@incollection{cgal:k-ssm3-15b +, author = "Nico Kruithof" +, title = "{3D} Skin Surface Meshing" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSkinSurface3Summary" +, year = 2015 +} + +@incollection{cgal:rty-m3-15b +, author = "Pierre Alliez and Cl{\'e}ment Jamin and Laurent Rineau and St{\'e}phane Tayeb and Jane Tournois and Mariette Yvinec" +, title = "{3D} Mesh Generation" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMesh_3Summary" +, year = 2015 +} + +@incollection{cgal:lty-pmp-15b +, author = "S{\'e}bastien Loriot and Jane Tournois and Ilker O. Yaz" +, title = "Polygon Mesh Processing" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolygonMeshProcessingSummary" +, year = 2015 +} + +@incollection{cgal:s-ssm2-15b +, author = "Le-Jeng Andy Shiue" +, title = "{3D} Surface Subdivision Methods" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceSubdivisionMethods3Summary" +, year = 2015 +} + +@incollection{cgal:y-smsimpl-15b +, author = "Ilker O. Yaz and S{\'e}bastien Loriot" +, title = "Triangulated Surface Mesh Segmentation" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceSegmentationSummary" +, year = 2015 +} + +@incollection{cgal:c-tsms-12-15b +, author = "Fernando Cacciola" +, title = "Triangulated Surface Mesh Simplification" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceMeshSimplificationSummary" +, year = 2015 +} + +@incollection{cgal:lsxy-tsmd-15b +, author = "S{\'e}bastien Loriot and Olga Sorkine-Hornung and Yin Xu and Ilker O. Yaz" +, title = "Triangulated Surface Mesh Deformation" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceModelingSummary" +, year = 2015 +} + +@incollection{cgal:sal-pptsm2-15b +, author = "Laurent Saboret and Pierre Alliez and Bruno L{\'e}vy" +, title = "Planar Parameterization of Triangulated Surface Meshes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceParameterizationSummary" +, year = 2015 +} + +@incollection{cgal:klcdv-tsmsp-15b +, author = "Stephen Kiazyk and S{\'e}bastien Loriot and {\'E}ric Colin de Verdi{\`e}re" +, title = "Triangulated Surface Mesh Shortest Paths" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceMeshShortestPathSummary" +, year = 2015 +} + +@incollection{cgal:glt-tsms-15b +, author = "Xiang Gao and S{\'e}bastien Loriot and Andrea Tagliasacchi" +, title = "Triangulated Surface Mesh Skeletonization" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMeanCurvatureSkeleton3Summary" +, year = 2015 +} + +@incollection{cgal:cp-arutsm-15b +, author = "Marc Pouget and Fr{\'e}d{\'e}ric Cazals" +, title = "Approximation of Ridges and Umbilics on Triangulated Surface Meshes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgRidges_3Summary" +, year = 2015 +} + +@incollection{cgal:pc-eldp-15b +, author = "Marc Pouget and Fr{\'e}d{\'e}ric Cazals" +, title = "Estimation of Local Differential Properties of Point-Sampled Surfaces" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgJet_fitting_3Summary" +, year = 2015 +} + +@incollection{cgal:ass-psp-15b +, author = "Pierre Alliez and Cl{\'e}ment Jamin and Quentin M{\'e}rigot and Jocelyn Meyron and Laurent Saboret and Nader Salman and Shihao Wu" +, title = "Point Set Processing" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPointSetProcessingSummary" +, year = 2015 +} + +@incollection{cgal:ovja-pssd-15b +, author = "Sven Oesau and Yannick Verdie and Cl{\'e}ment Jamin and Pierre Alliez" +, title = "Point Set Shape Detection" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPointSetShapeDetection3Summary" +, year = 2015 +} + +@incollection{cgal:m-ps-15b +, author = "Abdelkrim Mebarki" +, title = "{2D} Placement of Streamlines" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPlacementOfStreamlines2Summary" +, year = 2015 +} + +@incollection{cgal:b-ss2-15b +, author = "Matthias B{\"a}sken" +, title = "{2D} Range and Neighbor Search" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPointSet2Summary" +, year = 2015 +} + +@incollection{cgal:f-isl-15b +, author = "Andreas Fabri" +, title = "Interval Skip List" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgIntervalSkipListSummary" +, year = 2015 +} + +@incollection{cgal:tf-ssd-15b +, author = "Hans Tangelder and Andreas Fabri" +, title = "{dD} Spatial Searching" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSpatialSearchingDSummary" +, year = 2015 +} + +@incollection{cgal:n-rstd-15b +, author = "Gabriele Neyer" +, title = "{dD} Range and Segment Trees" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgRangeSegmentTreesDSummary" +, year = 2015 +} + +@incollection{cgal:kmz-isiobd-15b +, author = "Lutz Kettner and Andreas Meyer and Afra Zomorodian" +, title = "Intersecting Sequences of {dD} Iso-oriented Boxes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBoxIntersectionDSummary" +, year = 2015 +} + +@incollection{cgal:atw-aabb-15b +, author = "Pierre Alliez and St{\'e}phane Tayeb and Camille Wormser" +, title = "{3D} Fast Intersection and Distance Computation" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAABB_treeSummary" +, year = 2015 +} + +@incollection{cgal:dd-ss-15b +, author = "Christophe Delage and Olivier Devillers" +, title = "Spatial Sorting" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSpatialSortingSummary" +, year = 2015 +} + +@incollection{cgal:fghhs-bv-15b +, author = "Kaspar Fischer and Bernd G{\"a}rtner and Thomas Herrmann and Michael Hoffmann and Sven Sch{\"o}nherr" +, title = "Bounding Volumes" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBoundingVolumesSummary" +, year = 2015 +} + +@incollection{cgal:hp-ia-15b +, author = "Michael Hoffmann and Eli Packer" +, title = "Inscribed Areas" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgInscribedAreasSummary" +, year = 2015 +} + +@incollection{cgal:fghhs-od-15b +, author = "Kaspar Fischer and Bernd G{\"a}rtner and Thomas Herrmann and Michael Hoffmann and Sven Sch{\"o}nherr" +, title = "Optimal Distances" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgOptimalDistancesSummary" +, year = 2015 +} + +@incollection{cgal:ap-pcad-15b +, author = "Pierre Alliez and Sylvain Pion and Ankit Gupta" +, title = "Principal Component Analysis" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPrincipalComponentAnalysisDSummary" +, year = 2015 +} + +@incollection{cgal:f-i-15b +, author = "Julia Fl{\"o}totto" +, title = "{2D} and Surface Function Interpolation" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgInterpolation2Summary" +, year = 2015 +} + +@incollection{cgal:abha-gbc-15b +, author = "Dmitry Anisimov and David Bommes and Kai Hormann and Pierre Alliez" +, title = "{2D} Generalized Barycentric Coordinates" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBarycentric_coordinates_2Summary" +, year = 2015 +} + +@incollection{cgal:r-kds-15b +, author = "Daniel Russel" +, title = "Kinetic Data Structures" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgKdsSummary" +, year = 2015 +} + +@incollection{cgal:r-kdsf-15b +, author = "Daniel Russel" +, title = "Kinetic Framework" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgKdsFrameworkSummary" +, year = 2015 +} + +@incollection{cgal:hkpw-se-15b +, author = "Michael Hoffmann and Lutz Kettner and Sylvain Pion and Ron Wein" +, title = "STL Extensions for {CGAL}" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgStlExtensionSummary" +, year = 2015 +} + +@incollection{cgal:cfw-cbgl-15b +, author = "Andreas Fabri and Fernando Cacciola and Philipp Moeller and Ron Wein" +, title = "{CGAL} and the {Boost} Graph Library" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBGLSummary" +, year = 2015 +} + +@incollection{cgal:fs-cbpm-15b +, author = "Andreas Fabri and Laurent Saboret" +, title = "{CGAL} and {Boost} Property Maps" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgProperty_mapSummary" +, year = 2015 +} + +@incollection{cgal:dksy-hc-15b +, author = "Olivier Devillers and Lutz Kettner and Sylvain Pion and Michael Seel and Mariette Yvinec" +, title = "Handles and Circulators" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgHandlesAndCirculatorsSummary" +, year = 2015 +} + +@incollection{cgal:dhhk-gog-15b +, author = "Pedro M. M. de Castro and Olivier Devillers and Susan Hert and Michael Hoffmann and Lutz Kettner and Sven Sch{\"o}nherr and Alexandru Tifrea" +, title = "Geometric Object Generators" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgGeneratorsSummary" +, year = 2015 +} + +@incollection{cgal:kps-pthum-15b +, author = "Lutz Kettner and Sylvain Pion and Michael Seel" +, title = "Profiling tools, Hash Map, Union-find, Modifiers" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgProfilingToolsSummary" +, year = 2015 +} + +@incollection{cgal:fgk-ios-12-15b +, author = "Andreas Fabri and Geert-Jan Giezeman and Lutz Kettner" +, title = "IO Streams" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgIOstreamsSummary" +, year = 2015 +} + +@incollection{cgal:fp-gv-15b +, author = "Andreas Fabri and Sylvain Pion" +, title = "Geomview" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgGeomviewSummary" +, year = 2015 +} + +@incollection{cgal:fr-cqgvf-15b +, author = "Andreas Fabri and Laurent Rineau" +, title = "{CGAL} and the {Qt} Graphics View Framework" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgGraphicsViewSummary" +, year = 2015 +} + +@incollection{cgal:lp-gi-15b +, author = "Olivier Devillers and S{\'e}bastien Loriot and Sylvain Pion" +, title = "{CGAL} Ipelets" +, publisher = "{CGAL Editorial Board}" +, edition = "{4.7}" +, booktitle = "{CGAL} User and Reference Manual" +, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgCGALIpeletsSummary" +, year = 2015 +} diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index d7c13da0..fa24e1b1 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -18,8 +18,6 @@ if(CGAL_FOUND) add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp ) target_link_libraries(AlphaComplexUT ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - add_executable ( cerr cerr.cpp ) - # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) diff --git a/src/GudhUI/alpha_complex_persistence.cpp b/src/GudhUI/alpha_complex_persistence.cpp deleted file mode 100644 index 4f85459a..00000000 --- a/src/GudhUI/alpha_complex_persistence.cpp +++ /dev/null @@ -1,78 +0,0 @@ -#include -#include - - -#include - -// to construct a Delaunay_triangulation from a OFF file -#include -#include -#include - -#include "utils/Bar_code_persistence.h" - -void usage(char * const progName) { - std::cerr << "Usage: " << progName << " filename.off " << // alpha_square_max_value[double] " << - "coeff_field_characteristic[integer > 0] min_persistence[double >= -1.0]" << std::endl; - std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0 2 0.02" << std::endl; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if (argc != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; - usage(argv[0]); - } - - QApplication qtapp(argc, argv); - - std::string off_file_name(argv[1]); - // double alpha_square_max_value = atof(argv[2]); - double alpha_square_max_value = 1e20; - int coeff_field_characteristic = atoi(argv[2]); // argv[3] - double min_persistence = atof(argv[3]); // argv[4] - - // ---------------------------------------------------------------------------- - // Init of an alpha complex from an OFF file - // ---------------------------------------------------------------------------- - typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; - Gudhi::alphacomplex::Alpha_complex alpha_complex_from_file(off_file_name, alpha_square_max_value); - - // ---------------------------------------------------------------------------- - // Display information about the alpha complex - // ---------------------------------------------------------------------------- - std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() << - " - " << alpha_complex_from_file.num_simplices() << " simplices - " << - alpha_complex_from_file.num_vertices() << " vertices." << std::endl; - - // Sort the simplices in the order of the filtration - alpha_complex_from_file.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl; - // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alphacomplex::Alpha_complex, - Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file); - - std::cout << "coeff_field_characteristic " << coeff_field_characteristic << - " - min_persistence " << min_persistence << std::endl; - - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - std::vector> persistence_vector; - pcoh.get_persistence(persistence_vector); - - Bar_code_persistence bc_persistence; - - for (auto persistence : persistence_vector) { - bc_persistence.insert(persistence.first, persistence.second); - } - - bc_persistence.show(); - - return qtapp.exec(); -} diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h index a1a46ea8..a4cd8156 100644 --- a/src/GudhUI/utils/Bar_code_persistence.h +++ b/src/GudhUI/utils/Bar_code_persistence.h @@ -39,7 +39,7 @@ class Bar_code_persistence { max_death = death; } - void show() { + void show(const std::string& window_title) { // Create a view, put a scene in it QGraphicsView * view = new QGraphicsView(); QGraphicsScene * scene = new QGraphicsScene(); @@ -78,6 +78,7 @@ class Bar_code_persistence { QGraphicsTextItem* dimText = scene->addText(scale_value, QFont("Helvetica", 8)); dimText->setPos(scale - (3.0 * scale_value.size()), height + 9.0 * (modulo % 2)); } + view->setWindowTitle(window_title.c_str()); // Show the view view->show(); } diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h index 0b9961d3..1f04cc6b 100644 --- a/src/GudhUI/utils/Persistence_compute.h +++ b/src/GudhUI/utils/Persistence_compute.h @@ -46,10 +46,6 @@ struct Persistence_params { * Show persistence into output stream */ template class Persistence_compute { - private: - SkBlComplex& complex_; - std::ostream& stream_; - public: typedef typename SkBlComplex::Vertex_handle Vertex_handle; typedef typename SkBlComplex::Edge_handle Edge_handle; @@ -61,9 +57,7 @@ template class Persistence_compute { * double threshold * int p for coefficient Z_p */ - Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) : - // double threshold = 0.5,unsigned dim_max = 8): - complex_(complex), stream_(stream) { + Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) { // for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an // initial vector typedef std::vector Point_t; @@ -87,10 +81,11 @@ template class Persistence_compute { pcoh.init_coefficients(params.p); // put params.min_pers pcoh.compute_persistent_cohomology(params.min_pers); - stream_ << "persistence: \n"; - stream_ << "p dimension birth death: \n"; + stream << "persistence: \n"; + stream << "p dimension birth death: \n"; - pcoh.output_diagram(stream_); + pcoh.output_diagram(stream); + } }; diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index eb4ee3e3..9e96adc0 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -22,63 +22,61 @@ add_executable(persistence_from_file persistence_from_file.cpp) target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0) add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) - -if(GMPXX_FOUND AND GMP_FOUND) - message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") - message("GMP_LIBRARIES = ${GMP_LIBRARIES}") - - add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) - target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) - add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100) - - add_executable ( performance_rips_persistence performance_rips_persistence.cpp ) - target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) - - if(CGAL_FOUND) - add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) - target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) - add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) - #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) - - - - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - message(STATUS "CGAL version: ${CGAL_VERSION}.") - - include( ${CGAL_USE_FILE} ) - # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. - # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 - # A workaround is to add "-std=c++11" again. - # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html - # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html - # but it implies to use cmake version 3.1 at least. - if(NOT MSVC) - include(CheckCXXCompilerFlag) - CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) - if(COMPILER_SUPPORTS_CXX11) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") +if(GMPXX_FOUND AND GMP_FOUND) + message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") + message("GMP_LIBRARIES = ${GMP_LIBRARIES}") + + add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) + target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100) + + add_executable ( performance_rips_persistence performance_rips_persistence.cpp ) + target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + + if(CGAL_FOUND) + add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) + target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) + add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) + #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) + + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. + # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 + # A workaround is to add "-std=c++11" again. + # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html + # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html + # but it implies to use cmake version 3.1 at least. + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() endif() - endif() - # - End of workaround + # - End of workaround - find_package(Eigen3 3.1.0) - if (EIGEN3_FOUND) - message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") - include( ${EIGEN3_USE_FILE} ) + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) - add_executable (alphacomplexpersistence alpha_complex_persistence.cpp) - target_link_libraries(alphacomplexpersistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) + target_link_libraries(alpha_complex_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() else() - message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") - endif() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () else() - message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") - endif () - - - - endif() + # message(WARNING "CGAL not found.") + endif() +else() + # message(WARNING "GMP not found.") endif() diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp index fbadf673..0dabdeac 100644 --- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp @@ -1,34 +1,35 @@ #include #include +#include + // to construct a Delaunay_triangulation from a OFF file #include #include #include -void usage(char * const progName) { - std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value[double] " << - "coeff_field_characteristic[integer > 0] min_persistence[double >= -1.0]" << std::endl; - std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0 2 0.02" << std::endl; - exit(-1); // ----- >> -} +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & output_file_diag + , Filtration_value & alpha_square_max_value + , int & coeff_field_characteristic + , Filtration_value & min_persistence); int main(int argc, char **argv) { - if (argc != 5) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; - usage(argv[0]); - } + std::string off_file_points; + std::string output_file_diag; + Filtration_value alpha_square_max_value; + int coeff_field_characteristic; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic, min_persistence); - std::string off_file_name(argv[1]); - double alpha_square_max_value = atof(argv[2]); - int coeff_field_characteristic = atoi(argv[3]); - double min_persistence = atof(argv[4]); // ---------------------------------------------------------------------------- // Init of an alpha complex from an OFF file // ---------------------------------------------------------------------------- typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; - Gudhi::alphacomplex::Alpha_complex alpha_complex_from_file(off_file_name, alpha_square_max_value); + Gudhi::alphacomplex::Alpha_complex alpha_complex_from_file(off_file_points, alpha_square_max_value); // ---------------------------------------------------------------------------- // Display information about the alpha complex @@ -49,7 +50,66 @@ int main(int argc, char **argv) { pcoh.compute_persistent_cohomology(min_persistence); - pcoh.output_diagram(); + // Output the diagram in filediag + if (output_file_diag.empty()) { + pcoh.output_diagram(); + } else { + std::cout << "Result in file: " << output_file_diag << std::endl; + std::ofstream out(output_file_diag); + pcoh.output_diagram(out); + out.close(); + } return 0; } + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , std::string & output_file_diag + , Filtration_value & alpha_square_max_value + , int & coeff_field_characteristic + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&output_file_diag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-alpha-square-value,r", po::value(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), + "Maximal alpha square value for the Alpha complex construction.") + ("field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of an Alpha complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp index 9b1ef42f..fa0449a8 100644 --- a/src/Persistent_cohomology/example/rips_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_persistence.cpp @@ -30,6 +30,7 @@ #include #include +#include // infinity using namespace Gudhi; using namespace Gudhi::persistent_cohomology; @@ -114,7 +115,7 @@ void program_options(int argc, char * argv[] ("help,h", "produce help message") ("output-file,o", po::value(&filediag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-edge-length,r", po::value(&threshold)->default_value(0), + ("max-edge-length,r", po::value(&threshold)->default_value(std::numeric_limits::infinity()), "Maximal length of an edge for the Rips complex construction.") ("cpx-dimension,d", po::value(&dim_max)->default_value(1), "Maximal dimension of the Rips complex we want to compute.") diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 4b04e75a..d4f9aeae 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1160,43 +1160,28 @@ std::cout << "prune_above_filtration - filtration=" << filtration << std::endl; threshold_ = filtration; // Initialize filtration_vect_ if required if (filtration_vect_.empty()) { -std::cout << "prune_above_filtration - initialize_filtration" << std::endl; initialize_filtration(); } - -std::cout << "prune_above_filtration - after initialize_filtration "; -for(auto sh : filtration_vect_) { -for (auto vertex : simplex_vertex_range(sh)) { -std::cout << (int) vertex << ", "; -} -std::cout << " - filtration=" << sh->second.filtration() << " - " << &(sh->second) << std::endl; -} - + std::vector> simplex_list_to_removed; // Loop in reverse mode until threshold is reached - auto f_simplex = filtration_vect_.rbegin(); - for (; (f_simplex != filtration_vect_.rend()) && ((*f_simplex)->second.filtration() > threshold_); f_simplex++) { - -std::cout << "prune_above_filtration - remove "; -for (auto vertex : simplex_vertex_range(*f_simplex)) { -std::cout << (int) vertex << ", "; -} -std::cout << " - " << &((*f_simplex)->second) << std::endl; - - remove_maximal_simplex(*f_simplex); + // Do not erase while looping, because removing is shifting data in a flat_map + for (auto f_simplex = filtration_vect_.rbegin(); + (f_simplex != filtration_vect_.rend()) && ((*f_simplex)->second.filtration() > threshold_); + f_simplex++) { + std::vector simplex_to_remove; + for (auto vertex : simplex_vertex_range(*f_simplex)) + simplex_to_remove.insert(simplex_to_remove.begin(), vertex); + simplex_list_to_removed.push_back(simplex_to_remove); } -std::cout << "prune_above_filtration - remove STOPPED ON "; -for (auto vertex : simplex_vertex_range(*f_simplex)) { -std::cout << (int) vertex << ", "; -} -std::cout << " - filtration=" << (*f_simplex)->second.filtration() << " - " << &(*f_simplex->second) << std::endl; - if (f_simplex != filtration_vect_.rbegin()) { - // Do not forget to update filtration_vect_ - resize is enough - std::size_t new_size = filtration_vect_.size() - (f_simplex - filtration_vect_.rbegin()); -std::cout << "prune_above_filtration - resize" << new_size << std::endl; - filtration_vect_.resize(new_size); + for (auto simplex_to_remove : simplex_list_to_removed) { + Simplex_handle sh = find_simplex(simplex_to_remove); + if (sh != null_simplex()) + remove_maximal_simplex(sh); } - + // Re-initialize filtration_vect_ if dta were removed, because removing is shifting data in a flat_map + if (simplex_list_to_removed.size() > 0) + initialize_filtration(); } } } @@ -1205,6 +1190,7 @@ std::cout << "prune_above_filtration - resize" << new_size << std::endl; * @param[in] sh Simplex handle on the maximal simplex to remove. * \pre Please check the simplex has no coface before removing it. * \warning In debug mode, the exception std::invalid_argument is thrown if sh has children. + * \warning Be aware that removing is shifting data in a flat_map (initialize_filtration to be done). */ void remove_maximal_simplex(Simplex_handle sh) { // Guarantee the simplex has no children @@ -1213,49 +1199,18 @@ std::cout << "prune_above_filtration - resize" << new_size << std::endl; // Simplex is a leaf, it means the child is the Siblings owning the leaf Siblings* child = sh->second.children(); + if ((child->size() > 1) || (child == root())) { // Not alone, just remove it from members // Special case when child is the root of the simplex tree, just remove it from members -std::cout << "remove_maximal_simplex - members removal" << std::endl; child->erase(sh->first); } else { // Sibling is emptied : must be deleted, and its parent must point on his own Sibling -std::cout << "remove_maximal_simplex - members is empty" << std::endl; child->oncles()->members().at(child->parent()).assign_children(child->oncles()); delete child; } } -/***************************************************************************************************************/ - public: - /** \brief Prints the simplex_tree hierarchically. - * Since it prints the vertices recursively, one can watch its tree shape. - */ - void print_tree() { - for (auto sh = root_.members().begin(); sh != root_.members().end(); ++sh) { - std::cout << sh->first << " "; - if (has_children(sh)) { - std::cout << "("; - rec_print(sh->second.children()); - std::cout << ")"; - } - std::cout << std::endl; - } - } - - /** \brief Recursively prints the simplex_tree, using depth first search. */ - private: - void rec_print(Siblings * sib) { - for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) { - std::cout << " " << sh->first << " "; - if (has_children(sh)) { - std::cout << "("; - rec_print(sh->second.children()); - std::cout << ")"; - } - } - } -/*****************************************************************************************************************/ private: Vertex_handle null_vertex_; /** \brief Upper bound on the filtration values of the simplices.*/ diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index f6bd5411..0d73d347 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -351,7 +351,7 @@ BOOST_AUTO_TEST_CASE(simplex_tree_insertion) { // 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 << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + std::cout << "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) << "] "; for (auto vertex : st.simplex_vertex_range(f_simplex)) { @@ -549,7 +549,7 @@ BOOST_AUTO_TEST_CASE(NSimplexAndSubfaces_tree_insertion) { // 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 << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + std::cout << "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) << "] "; for (auto vertex : st.simplex_vertex_range(f_simplex)) { @@ -805,7 +805,7 @@ struct MyOptions : Simplex_tree_options_full_featured { }; typedef Simplex_tree miniST; -/*BOOST_AUTO_TEST_CASE(remove_maximal_simplex) { +BOOST_AUTO_TEST_CASE(remove_maximal_simplex) { std::cout << "********************************************************************" << std::endl; std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl; @@ -887,7 +887,7 @@ typedef Simplex_tree miniST; st.remove_maximal_simplex(st.find({7})); BOOST_CHECK(st == st_wo_seven); -}*/ +} BOOST_AUTO_TEST_CASE(prune_above_filtration) { std::cout << "********************************************************************" << std::endl; @@ -939,10 +939,10 @@ BOOST_AUTO_TEST_CASE(prune_above_filtration) { st.prune_above_filtration(5.0); BOOST_CHECK(st == st_complete); - // Display the Simplex_tree - Can not be done in the middle of 2 inserts + // 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 << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + std::cout << "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) << "] "; for (auto vertex : st.simplex_vertex_range(f_simplex)) { @@ -955,35 +955,45 @@ BOOST_AUTO_TEST_CASE(prune_above_filtration) { // Set the st_pruned filtration for operator== st_pruned.set_filtration(2.5); st.prune_above_filtration(2.5); - /*BOOST_CHECK(st == st_pruned); + BOOST_CHECK(st == st_pruned); + + // Display the Simplex_tree + std::cout << "The complex pruned at 2.5 contains " << st.num_simplices() << " simplices" << std::endl; + std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << "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) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << (int) vertex << " "; + } + std::cout << std::endl; + } st_pruned.set_filtration(2.0); st.prune_above_filtration(2.0); BOOST_CHECK(st == st_pruned); -*/ -/* std::cout << "The complex contains " << st.num_simplices() << " simplices --------------------------" << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; - st.print_tree(); - std::cout << "The pruned complex contains " << st_pruned.num_simplices() << " simplices --------------------------" << std::endl; - std::cout << " - dimension " << st_pruned.dimension() << " - filtration " << st_pruned.filtration() << std::endl; - st_pruned.print_tree(); - typeST st_empty; // FIXME st_empty.set_dimension(3); st.prune_above_filtration(0.0); - */ - /*BOOST_CHECK(st == st_empty); + + // Display the Simplex_tree + std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices" << std::endl; + std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << "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) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << (int) vertex << " "; + } + std::cout << std::endl; + } + + BOOST_CHECK(st == st_empty); // Test case to the limit st.prune_above_filtration(-1.0); st_empty.set_filtration(-1.0); BOOST_CHECK(st == st_empty); -*/ } - -/*BOOST_AUTO_TEST_CASE(sanitizer) { - int a[2] = {1, 0}; - int b=a[2]; -}*/ diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index e5c79ded..cd518581 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -23,6 +23,8 @@ #ifndef DISTANCE_FUNCTIONS_H_ #define DISTANCE_FUNCTIONS_H_ +#include // for std::sqrt + /* Compute the Euclidean distance between two Points given * by a range of coordinates. The points are assumed to have * the same dimension. */ @@ -35,7 +37,7 @@ double euclidean_distance(Point &p1, Point &p2) { double tmp = *it1 - *it2; dist += tmp*tmp; } - return sqrt(dist); + return std::sqrt(dist); } #endif // DISTANCE_FUNCTIONS_H_ diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index e05714c7..da2c2c36 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -58,7 +58,9 @@ inline void read_points(std::string file_name, std::vector< std::vector< double while (iss >> x) { point.push_back(x); } - points.push_back(point); + // Check for empty lines + if (!point.empty()) + points.push_back(point); } in_file.close(); } -- cgit v1.2.3 From 57eb57ed2092beaceb978e31aebb500450b9599b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 2 Feb 2016 09:07:16 +0000 Subject: rename alpha_shapes_persistence test with alpha_complex_3d_persistence git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@991 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 455ee94450098bbcc000fb2ab2c4d39a326dea2c --- src/Persistent_cohomology/example/CMakeLists.txt | 39 ++- .../example/alpha_complex_3d_persistence.cpp | 294 +++++++++++++++++++++ .../example/alpha_shapes_persistence.cpp | 294 --------------------- 3 files changed, 313 insertions(+), 314 deletions(-) create mode 100644 src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp delete mode 100644 src/Persistent_cohomology/example/alpha_shapes_persistence.cpp (limited to 'src/Persistent_cohomology/example') diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 5fec8ad4..779a9e89 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -40,30 +40,29 @@ if(GMPXX_FOUND AND GMP_FOUND) target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if(CGAL_FOUND) - add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) - target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) - add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) - #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) + include( ${CGAL_USE_FILE} ) + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. + # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 + # A workaround is to add "-std=c++11" again. + # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html + # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html + # but it implies to use cmake version 3.1 at least. + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround + + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) + add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) if (NOT CGAL_VERSION VERSION_LESS 4.7.0) message(STATUS "CGAL version: ${CGAL_VERSION}.") - include( ${CGAL_USE_FILE} ) - # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. - # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 - # A workaround is to add "-std=c++11" again. - # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html - # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html - # but it implies to use cmake version 3.1 at least. - if(NOT MSVC) - include(CheckCXXCompilerFlag) - CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) - if(COMPILER_SUPPORTS_CXX11) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") - endif() - endif() - # - End of workaround - find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..ac208957 --- /dev/null +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -0,0 +1,294 @@ +/* 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) 2014 INRIA Saclay (France) + * + * 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 . + */ + +#include +#include +#include +#include + +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +// Alpha_shape_3 templates type definitions +typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; +typedef CGAL::Alpha_shape_vertex_base_3 Vb; +typedef CGAL::Alpha_shape_cell_base_3 Fb; +typedef CGAL::Triangulation_data_structure_3 Tds; +typedef CGAL::Delaunay_triangulation_3 Triangulation_3; +typedef CGAL::Alpha_shape_3 Alpha_shape_3; + +// From file type definition +typedef Kernel::Point_3 Point_3; + +// filtration with alpha values needed type definition +typedef Alpha_shape_3::FT Alpha_value_type; +typedef CGAL::Object Object; +typedef CGAL::Dispatch_output_iterator< +CGAL::cpp11::tuple, +CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > > Dispatch; +typedef Alpha_shape_3::Cell_handle Cell_handle; +typedef Alpha_shape_3::Facet Facet; +typedef Alpha_shape_3::Edge Edge_3; +typedef std::list Vertex_list; + +// gudhi type definition +typedef Simplex_tree ST; +typedef ST::Vertex_handle Simplex_tree_vertex; +typedef std::map Alpha_shape_simplex_tree_map; +typedef std::pair Alpha_shape_simplex_tree_pair; +typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; + +Vertex_list from(const Cell_handle& ch) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { +#ifdef DEBUG_TRACES + std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(ch->vertex(i)); + } + return the_list; +} + +Vertex_list from(const Facet& fct) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if (fct.second != i) { +#ifdef DEBUG_TRACES + std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(fct.first->vertex(i)); + } + } + return the_list; +} + +Vertex_list from(const Edge_3& edg) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if ((edg.second == i) || (edg.third == i)) { +#ifdef DEBUG_TRACES + std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(edg.first->vertex(i)); + } + } + return the_list; +} + +Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) { + Vertex_list the_list; +#ifdef DEBUG_TRACES + std::cout << "from vertex=" << vh->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(vh); + return the_list; +} + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << + " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = 0; + int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); + if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { + std::cerr << "Error: " << argv[2] << " is not correct\n"; + usage(argv[0]); + } + + Filtration_value min_persistence = 0.0; + returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); + if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { + std::cerr << "Error: " << argv[3] << " is not correct\n"; + usage(argv[0]); + } + + // Read points from file + std::string filegraph = argv[1]; + std::list lp; + std::ifstream is(filegraph.c_str()); + int n; + is >> n; +#ifdef DEBUG_TRACES + std::cout << "Reading " << n << " points " << std::endl; +#endif // DEBUG_TRACES + Point_3 p; + for (; n > 0; n--) { + is >> p; + lp.push_back(p); + } + + // 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); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_filtration(filtration_max); + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + 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 + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + Persistent_cohomology< ST, Field_Zp > pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp deleted file mode 100644 index ac208957..00000000 --- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp +++ /dev/null @@ -1,294 +0,0 @@ -/* 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) 2014 INRIA Saclay (France) - * - * 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 . - */ - -#include -#include -#include -#include - -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -using namespace Gudhi; -using namespace Gudhi::persistent_cohomology; - -// Alpha_shape_3 templates type definitions -typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; -typedef CGAL::Alpha_shape_vertex_base_3 Vb; -typedef CGAL::Alpha_shape_cell_base_3 Fb; -typedef CGAL::Triangulation_data_structure_3 Tds; -typedef CGAL::Delaunay_triangulation_3 Triangulation_3; -typedef CGAL::Alpha_shape_3 Alpha_shape_3; - -// From file type definition -typedef Kernel::Point_3 Point_3; - -// filtration with alpha values needed type definition -typedef Alpha_shape_3::FT Alpha_value_type; -typedef CGAL::Object Object; -typedef CGAL::Dispatch_output_iterator< -CGAL::cpp11::tuple, -CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > > Dispatch; -typedef Alpha_shape_3::Cell_handle Cell_handle; -typedef Alpha_shape_3::Facet Facet; -typedef Alpha_shape_3::Edge Edge_3; -typedef std::list Vertex_list; - -// gudhi type definition -typedef Simplex_tree ST; -typedef ST::Vertex_handle Simplex_tree_vertex; -typedef std::map Alpha_shape_simplex_tree_map; -typedef std::pair Alpha_shape_simplex_tree_pair; -typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; - -Vertex_list from(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -Vertex_list from(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -Vertex_list from(const Edge_3& edg) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if ((edg.second == i) || (edg.third == i)) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - } - return the_list; -} - -Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - -void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; - exit(-1); -} - -int main(int argc, char * const argv[]) { - // program args management - if (argc != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = 0; - int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); - if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { - std::cerr << "Error: " << argv[2] << " is not correct\n"; - usage(argv[0]); - } - - Filtration_value min_persistence = 0.0; - returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } - - // Read points from file - std::string filegraph = argv[1]; - std::list lp; - std::ifstream is(filegraph.c_str()); - int n; - is >> n; -#ifdef DEBUG_TRACES - std::cout << "Reading " << n << " points " << std::endl; -#endif // DEBUG_TRACES - Point_3 p; - for (; n > 0; n--) { - is >> p; - lp.push_back(p); - } - - // 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); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - int dim_max = 0; - Filtration_value filtration_max = 0.0; - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from(*cell); - count_cells++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from(*edge); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } else if (const Alpha_shape_3::Vertex_handle * vertex = - CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex_tree; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex_tree.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - - std::cout << "Information of the Simplex Tree: " << std::endl; - 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 - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - Persistent_cohomology< ST, Field_Zp > pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - return 0; -} -- cgit v1.2.3 From cbf1f4c98c9e6d7ba3b7c552e43c7c98ed349954 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 2 Feb 2016 10:03:48 +0000 Subject: Make example for doc shorter. Include strategy reviewal git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@992 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 23d3e71d7d0fb4d649f73e53959626c5cbb0acd8 --- src/Alpha_complex/example/Alpha_complex_from_off.cpp | 9 +++++---- .../example/Alpha_complex_from_points.cpp | 18 ++---------------- src/Alpha_complex/include/gudhi/Alpha_complex.h | 1 - .../example/alpha_complex_persistence.cpp | 17 ++++++++++------- 4 files changed, 17 insertions(+), 28 deletions(-) (limited to 'src/Persistent_cohomology/example') diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index 4f381892..780f904b 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -1,12 +1,13 @@ +#include +#include + #include #include -#include - void usage(char * const progName) { std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value" << std::endl; std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0" << std::endl; - exit(-1); // ----- >> + exit(-1); // ----- >> } int main(int argc, char **argv) { @@ -23,7 +24,7 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; Gudhi::alphacomplex::Alpha_complex alpha_complex_from_file(off_file_name, alpha_square_max_value); - + // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index 00e988a6..dab161c9 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -1,31 +1,17 @@ -#include -#include #include +#include #include #include #include -#include - typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel; typedef Kernel::Point_d Point; typedef std::vector Vector_of_points; -void usage(char * const progName) { - std::cerr << "Usage: " << progName << " alpha_square_max_value" << std::endl; - std::cerr << " i.e.: " << progName << " 32.0" << std::endl; - exit(-1); // ----- >> -} - int main(int argc, char **argv) { - if (argc != 2) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; - usage(argv[0]); - } + double alpha_square_max_value = 32.0; - double alpha_square_max_value = atof(argv[1]); - // ---------------------------------------------------------------------------- // Init of a list of points // ---------------------------------------------------------------------------- diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 1ab6766c..962ed8dc 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -34,7 +34,6 @@ #include // isnan, fmax #include -#include #include #include diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp index 0dabdeac..d2f9a4a2 100644 --- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp @@ -1,13 +1,15 @@ -#include -#include - #include +#include // to construct a Delaunay_triangulation from a OFF file #include #include #include +#include +#include +#include // for numeric_limits + void program_options(int argc, char * argv[] , std::string & off_file_points , std::string & output_file_diag @@ -21,10 +23,10 @@ int main(int argc, char **argv) { Filtration_value alpha_square_max_value; int coeff_field_characteristic; Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic, min_persistence); - + program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, + coeff_field_characteristic, min_persistence); + // ---------------------------------------------------------------------------- // Init of an alpha complex from an OFF file // ---------------------------------------------------------------------------- @@ -80,7 +82,8 @@ void program_options(int argc, char * argv[] ("help,h", "produce help message") ("output-file,o", po::value(&output_file_diag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-alpha-square-value,r", po::value(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), + ("max-alpha-square-value,r", + po::value(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), "Maximal alpha square value for the Alpha complex construction.") ("field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), "Characteristic p of the coefficient field Z/pZ for computing homology.") -- cgit v1.2.3 From 298c080b45250f2b8f16a0c31ace9bb6fc666c93 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 16 Mar 2016 08:33:04 +0000 Subject: CppCheck and CppLint fixes for alpha complexes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@1047 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a9b42ad2f8751384b5227fa3da8f380cda9b3696 --- src/Alpha_complex/doc/Intro_alpha_complex.h | 4 ++-- .../example/Alpha_complex_from_off.cpp | 2 +- src/Alpha_complex/include/gudhi/Alpha_complex.h | 21 ++++++++++----------- src/GudhUI/model/Model.h | 2 +- src/GudhUI/utils/Bar_code_persistence.h | 11 ++++++++--- src/GudhUI/utils/Persistence_compute.h | 1 - src/GudhUI/view/FirstCoordProjector.h | 1 - .../example/alpha_complex_3d_persistence.cpp | 15 ++++----------- .../example/Delaunay_triangulation_off_rw.cpp | 14 +++++++------- .../include/gudhi/Delaunay_triangulation_off_io.h | 10 +++------- src/common/include/gudhi/Off_reader.h | 2 +- 11 files changed, 37 insertions(+), 46 deletions(-) (limited to 'src/Persistent_cohomology/example') diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index deecf93f..f55d7029 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -161,8 +161,8 @@ namespace alphacomplex { */ /** @} */ // end defgroup alpha_complex -} // namespace alphacomplex +} // namespace alphacomplex -} // namespace Gudhi +} // namespace Gudhi #endif // INTRO_ALPHA_COMPLEX_H_ diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index 80445a22..18a1a20d 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -27,7 +27,7 @@ int main(int argc, char **argv) { std::streambuf* streambufffer; std::ofstream ouput_file_stream; - + if (argc == 4) { ouput_file_stream.open(std::string(argv[3])); streambufffer = ouput_file_stream.rdbuf(); diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index a69afb51..eab66384 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -20,8 +20,8 @@ * along with this program. If not, see . */ -#ifndef ALPHA_COMPLEX_H_ -#define ALPHA_COMPLEX_H_ +#ifndef DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_ +#define DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_ // to construct a simplex_tree from Delaunay_triangulation #include @@ -97,7 +97,6 @@ class Alpha_complex : public Simplex_tree<> { // Double map type to switch from CGAL vertex iterator to simplex tree vertex handle and vice versa. typedef typename std::map< CGAL_vertex_iterator, Vertex_handle > Map_vertex_iterator_to_handle; - //typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Map_vertex_handle_to_iterator; typedef typename std::vector< CGAL_vertex_iterator > Vector_vertex_iterator; private: @@ -141,7 +140,7 @@ class Alpha_complex : public Simplex_tree<> { Alpha_complex(Delaunay_triangulation* triangulation_ptr, Filtration_value max_alpha_square = std::numeric_limits::infinity()) : triangulation_(triangulation_ptr) { - init(max_alpha_square); + init(max_alpha_square); } /** \brief Alpha_complex constructor from a list of points. @@ -160,17 +159,17 @@ class Alpha_complex : public Simplex_tree<> { : triangulation_(nullptr) { auto first = std::begin(points); auto last = std::end(points); - + GUDHI_CHECK((first == last), - std::invalid_argument ("Alpha_complex::Alpha_complex(InputPointRange) - Empty input point range")); - + std::invalid_argument("Alpha_complex::Alpha_complex(InputPointRange) - Empty input point range")); + if (first != last) { // point_dimension function initialization Point_Dimension point_dimension = kernel_.point_dimension_d_object(); // Delaunay triangulation is point dimension minus one. triangulation_ = new Delaunay_triangulation(point_dimension(*first) - 1); - + size_type inserted = triangulation_->insert(first, last); if (inserted != (last -first)) { std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << (last -first) << "\n"; @@ -227,7 +226,7 @@ class Alpha_complex : public Simplex_tree<> { } set_dimension(triangulation_->maximal_dimension()); - // set_filtration to +inf for prune_above_filtration to be done (if necessary) + // set_filtration to +inf for prune_above_filtration to be done (if necessary) set_filtration(std::numeric_limits::infinity()); // -------------------------------------------------------------------------------------------- @@ -247,7 +246,7 @@ class Alpha_complex : public Simplex_tree<> { } } // -------------------------------------------------------------------------------------------- - + // -------------------------------------------------------------------------------------------- // Simplex_tree construction from loop on triangulation finite full cells list for (auto cit = triangulation_->finite_full_cells_begin(); cit != triangulation_->finite_full_cells_end(); ++cit) { @@ -393,4 +392,4 @@ class Alpha_complex : public Simplex_tree<> { } // namespace Gudhi -#endif // ALPHA_COMPLEX_H_ +#endif // DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_ diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h index 99a82eba..1c39c0d7 100644 --- a/src/GudhUI/model/Model.h +++ b/src/GudhUI/model/Model.h @@ -71,7 +71,7 @@ class CGAL_geometric_flag_complex_wrapper { void maximal_face(std::vector vertices) { if (!load_only_points_) { - //std::cout << "size:" << vertices.size() << std::endl; + // std::cout << "size:" << vertices.size() << std::endl; for (int i = 0; i < vertices.size(); ++i) for (int j = i + 1; j < vertices.size(); ++j) complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j])); diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h index a4cd8156..b527d684 100644 --- a/src/GudhUI/utils/Bar_code_persistence.h +++ b/src/GudhUI/utils/Bar_code_persistence.h @@ -12,6 +12,10 @@ #include #include // NaN, infinity #include // for pair +#include + +#ifndef UTILS_BAR_CODE_PERSISTENCE_H_ +#define UTILS_BAR_CODE_PERSISTENCE_H_ class Bar_code_persistence { private: @@ -21,7 +25,6 @@ class Bar_code_persistence { double max_death; public: - Bar_code_persistence() : min_birth(std::numeric_limits::quiet_NaN()), max_death(std::numeric_limits::quiet_NaN()) { } @@ -45,13 +48,13 @@ class Bar_code_persistence { QGraphicsScene * scene = new QGraphicsScene(); view->setScene(scene); double ratio = 600.0 / (max_death - min_birth); - //std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl; + // std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl; double height = 0.0, birth = 0.0, death = 0.0; int pers_num = 1; for (auto& persistence : persistence_vector) { height = 5.0 * pers_num; - //std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl; + // std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl; if (std::isfinite(persistence.first)) birth = ((persistence.first - min_birth) * ratio) + 50.0; else @@ -83,3 +86,5 @@ class Bar_code_persistence { view->show(); } }; + +#endif // UTILS_BAR_CODE_PERSISTENCE_H_ diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h index 1f04cc6b..97165490 100644 --- a/src/GudhUI/utils/Persistence_compute.h +++ b/src/GudhUI/utils/Persistence_compute.h @@ -85,7 +85,6 @@ template class Persistence_compute { stream << "p dimension birth death: \n"; pcoh.output_diagram(stream); - } }; diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h index 3ceda3f5..a4027b7f 100644 --- a/src/GudhUI/view/FirstCoordProjector.h +++ b/src/GudhUI/view/FirstCoordProjector.h @@ -36,7 +36,6 @@ class FirstCoordProjector3D : public Projector3D { return Point_3(p.x(), p.y(), p.z()); else if (p.dimension() >= 2) return Point_3(p.x(), p.y(), 0.0); - } }; diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index ac208957..f81951ce 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -39,9 +39,6 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::persistent_cohomology; - // Alpha_shape_3 templates type definitions typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; typedef CGAL::Alpha_shape_vertex_base_3 Vb; @@ -66,11 +63,12 @@ typedef Alpha_shape_3::Edge Edge_3; typedef std::list Vertex_list; // gudhi type definition -typedef Simplex_tree ST; +typedef Gudhi::Simplex_tree ST; typedef ST::Vertex_handle Simplex_tree_vertex; typedef std::map Alpha_shape_simplex_tree_map; typedef std::pair Alpha_shape_simplex_tree_pair; typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; +typedef Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp > PCOH; Vertex_list from(const Cell_handle& ch) { Vertex_list the_list; @@ -131,12 +129,7 @@ int main(int argc, char * const argv[]) { usage(argv[0]); } - int coeff_field_characteristic = 0; - int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); - if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { - std::cerr << "Error: " << argv[2] << " is not correct\n"; - usage(argv[0]); - } + int coeff_field_characteristic = atoi(argv[2]); Filtration_value min_persistence = 0.0; returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); @@ -282,7 +275,7 @@ int main(int argc, char * const argv[]) { std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; // Compute the persistence diagram of the complex - Persistent_cohomology< ST, Field_Zp > pcoh(simplex_tree); + PCOH pcoh(simplex_tree); // initializes the coefficient field for homology pcoh.init_coefficients(coeff_field_characteristic); diff --git a/src/common/example/Delaunay_triangulation_off_rw.cpp b/src/common/example/Delaunay_triangulation_off_rw.cpp index 75e4fafb..4c7a9aaf 100644 --- a/src/common/example/Delaunay_triangulation_off_rw.cpp +++ b/src/common/example/Delaunay_triangulation_off_rw.cpp @@ -10,12 +10,12 @@ // Use dynamic_dimension_tag for the user to be able to set dimension typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K; typedef CGAL::Delaunay_triangulation T; -// The triangulation uses the default instantiation of the +// The triangulation uses the default instantiation of the // TriangulationDataStructure template parameter void usage(char * const progName) { std::cerr << "Usage: " << progName << " inputFile.off outputFile.off" << std::endl; - exit(-1); // ----- >> + exit(-1); } int main(int argc, char **argv) { @@ -30,9 +30,9 @@ int main(int argc, char **argv) { // Check the read operation was correct if (!off_reader.is_valid()) { std::cerr << "Unable to read file " << offInputFile << std::endl; - exit(-1); // ----- >> + exit(-1); } - + // Retrieve the triangulation T* triangulation = off_reader.get_complex(); // Operations on triangulation @@ -47,8 +47,8 @@ int main(int argc, char **argv) { // Check the write operation was correct if (!off_writer.is_valid()) { std::cerr << "Unable to write file " << offOutputFile << std::endl; - exit(-1); // ----- >> + exit(-1); } - + return 0; -} \ No newline at end of file +} diff --git a/src/common/include/gudhi/Delaunay_triangulation_off_io.h b/src/common/include/gudhi/Delaunay_triangulation_off_io.h index 529774f0..e623cf7b 100644 --- a/src/common/include/gudhi/Delaunay_triangulation_off_io.h +++ b/src/common/include/gudhi/Delaunay_triangulation_off_io.h @@ -44,8 +44,8 @@ class Delaunay_triangulation_off_visitor_reader { Complex* complex_; typedef typename Complex::Point Point; std::vector point_cloud; - public: + public: // TODO(VR) : Pass a Complex as a parameter is required, even if not used. Otherwise, compilation is KO. /** \brief Delaunay_triangulation_off_visitor_reader constructor @@ -153,7 +153,6 @@ class Delaunay_triangulation_off_visitor_reader { template class Delaunay_triangulation_off_reader { public: - /** \brief Reads the OFF file and constructs the Delaunay triangulation from the points * that are in the OFF file. * @@ -180,7 +179,6 @@ class Delaunay_triangulation_off_reader { std::cerr << "Delaunay_triangulation_off_reader::Delaunay_triangulation_off_reader could not open file " << name_file << "\n"; } - } /** \brief Returns if the OFF file read operation was successful or not. @@ -201,7 +199,6 @@ class Delaunay_triangulation_off_reader { if (valid_) return complex_; return nullptr; - } private: @@ -285,7 +282,6 @@ class Delaunay_triangulation_off_writer { } for (auto cit = complex_ptr->finite_full_cells_begin(); cit != complex_ptr->finite_full_cells_end(); ++cit) { - std::vector vertexVector; stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " "; for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) { stream << points_to_vh[(*vit)->point()] - 1 << " "; @@ -299,7 +295,7 @@ class Delaunay_triangulation_off_writer { name_file << "\n"; } } - + /** \brief Returns if the OFF write operation was successful or not. * * @return OFF file write status. @@ -313,6 +309,6 @@ class Delaunay_triangulation_off_writer { bool valid_; }; -} // namespace Gudhi +} // namespace Gudhi #endif // DELAUNAY_TRIANGULATION_OFF_IO_H_ diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h index e45a7600..2420ae72 100644 --- a/src/common/include/gudhi/Off_reader.h +++ b/src/common/include/gudhi/Off_reader.h @@ -160,7 +160,7 @@ class Off_reader { iss >> num_face_vertices; std::vector face; face.assign(std::istream_iterator(iss), std::istream_iterator()); - //if (face.size() != (off_info_.dim + 1)) return false; + // if (face.size() != (off_info_.dim + 1)) return false; visitor.maximal_face(face); } return true; -- cgit v1.2.3 From 6996f2a16a1fdaa0d0faee1c559855fbea25b6c1 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 16 Mar 2016 08:49:20 +0000 Subject: Compil issue git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@1048 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4fcfc1498408eb98a12ed5d48e620dc38d4c442d --- src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/Persistent_cohomology/example') diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index f81951ce..01497c7c 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -132,7 +132,7 @@ int main(int argc, char * const argv[]) { int coeff_field_characteristic = atoi(argv[2]); Filtration_value min_persistence = 0.0; - returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); + int returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { std::cerr << "Error: " << argv[3] << " is not correct\n"; usage(argv[0]); -- cgit v1.2.3 From d29bdae1281bb2b9b9778365c5dc3d44cffa4de4 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 31 Mar 2016 13:03:58 +0000 Subject: Fix TBB issue in CMake Add TBB in Doxygen git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Doxygen_for_GUDHI_1.3.0@1086 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e3d3251431193d21ebf9344c230d12df624cd905 --- CMakeLists.txt | 4 + src/Bitmap_cubical_complex/example/CMakeLists.txt | 15 +++- .../include/gudhi/Bitmap_cubical_complex.h | 3 +- src/Bitmap_cubical_complex/test/CMakeLists.txt | 3 + src/CMakeLists.txt | 4 + src/Doxyfile | 8 +- src/GudhUI/CMakeLists.txt | 3 + src/Persistent_cohomology/example/CMakeLists.txt | 26 ++++++- src/Persistent_cohomology/test/CMakeLists.txt | 8 +- src/Simplex_tree/example/CMakeLists.txt | 9 +++ src/Simplex_tree/include/gudhi/Simplex_tree.h | 7 +- src/Simplex_tree/test/CMakeLists.txt | 3 + src/common/doc/main_page.h | 89 ++++++++++++++++++++-- 13 files changed, 163 insertions(+), 19 deletions(-) (limited to 'src/Persistent_cohomology/example') diff --git a/CMakeLists.txt b/CMakeLists.txt index abb66ec2..9cb8b86b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -58,6 +58,10 @@ else() # Find TBB package for parallel sort - not mandatory, just optional. set(TBB_FIND_QUIETLY ON) find_package(TBB) + if (TBB_FOUND) + message("TBB found in ${TBB_LIBRARY_DIRS}") + add_definitions(-DGUDHI_USE_TBB) + endif() # Required programs for unitary tests purpose FIND_PROGRAM( GCOVR_PATH gcovr ) diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index 8f9cfa80..ad86b763 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -2,16 +2,25 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIBitmap) add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp ) -target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) +target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Bitmap_cubical_complex ${TBB_RELEASE_LIBRARY}) +endif() add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt) add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp ) -target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) +target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Random_bitmap_cubical_complex ${TBB_RELEASE_LIBRARY}) +endif() add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100) add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp ) -target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY}) +target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_RELEASE_LIBRARY}) +endif() add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt) add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt) diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h index 54ae47d0..a6ba60d3 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h @@ -546,7 +546,8 @@ void Bitmap_cubical_complex::initialize_simplex_associated_to_key() { this->simplex_associated_to_key = std::vector(this->data.size()); std::iota(std::begin(simplex_associated_to_key), std::end(simplex_associated_to_key), 0); #ifdef GUDHI_USE_TBB - tbb::parallel_sort(simplex_associated_to_key, is_before_in_filtration(this)); + tbb::parallel_sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(), + is_before_in_filtration(this)); #else std::sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(), is_before_in_filtration(this)); #endif diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt index 97c374e6..96a41c62 100644 --- a/src/Bitmap_cubical_complex/test/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt @@ -16,6 +16,9 @@ endif() add_executable ( BitmapCCUT Bitmap_test.cpp ) target_link_libraries(BitmapCCUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(BitmapCCUT ${TBB_RELEASE_LIBRARY}) +endif() # Unitary tests add_test(NAME BitmapCCUT diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 40b7dd58..d4abe96d 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -53,6 +53,10 @@ else() # Find TBB package for parallel sort - not mandatory, just optional. set(TBB_FIND_QUIETLY ON) find_package(TBB) + if (TBB_FOUND) + message("TBB found in ${TBB_LIBRARY_DIRS}") + add_definitions(-DGUDHI_USE_TBB) + endif() # BOOST ISSUE result_of vs C++11 add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) diff --git a/src/Doxyfile b/src/Doxyfile index f7fba3e6..63e7145c 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -780,7 +780,8 @@ RECURSIVE = YES # run. EXCLUDE = data/ \ - GudhUI/ + example/ \ + GudhUI/ # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded @@ -813,14 +814,15 @@ EXCLUDE_SYMBOLS = # that contain example code fragments that are included (see the \include # command). -EXAMPLE_PATH = biblio/ +EXAMPLE_PATH = biblio/ \ + example/ # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and # *.h) to filter out the source-files in the directories. If left blank all # files are included. -EXAMPLE_PATTERNS = +EXAMPLE_PATTERNS = # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude commands diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index 1ee43d91..fd7397ea 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -57,6 +57,9 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND ) target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} ) target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ) +if (TBB_FOUND) + target_link_libraries( GudhUI ${TBB_RELEASE_LIBRARY}) +endif() else() message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.") diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 95506631..9702a5f9 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -7,24 +7,37 @@ add_definitions( -DBOOST_ALL_DYN_LINK ) add_executable(plain_homology plain_homology.cpp) target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(plain_homology ${TBB_RELEASE_LIBRARY}) +endif() add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(persistence_from_simple_simplex_tree ${TBB_RELEASE_LIBRARY}) +endif() add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0) add_executable(rips_persistence rips_persistence.cpp) target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - +if (TBB_FOUND) + target_link_libraries(rips_persistence ${TBB_RELEASE_LIBRARY}) +endif() add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100) add_executable(parallel_rips_persistence parallel_rips_persistence.cpp) target_link_libraries(parallel_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - +if (TBB_FOUND) + target_link_libraries(parallel_rips_persistence ${TBB_RELEASE_LIBRARY}) +endif() add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100) add_executable(persistence_from_file persistence_from_file.cpp) target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(persistence_from_file ${TBB_RELEASE_LIBRARY}) +endif() add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0) add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) @@ -34,10 +47,16 @@ if(GMPXX_FOUND AND GMP_FOUND) add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + if (TBB_FOUND) + target_link_libraries(rips_multifield_persistence ${TBB_RELEASE_LIBRARY}) + endif() add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100) add_executable ( performance_rips_persistence performance_rips_persistence.cpp ) target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + if (TBB_FOUND) + target_link_libraries(performance_rips_persistence ${TBB_RELEASE_LIBRARY}) + endif() if(CGAL_FOUND) if (CMAKE_BUILD_TYPE MATCHES Debug) @@ -46,6 +65,9 @@ if(GMPXX_FOUND AND GMP_FOUND) endif() add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(alpha_shapes_persistence ${TBB_RELEASE_LIBRARY}) + endif() add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) endif() diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index d16be5be..459cc000 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -12,6 +12,9 @@ endif() add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp ) target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(PersistentCohomologyUT ${TBB_RELEASE_LIBRARY}) +endif() # Unitary tests add_test(NAME PersistentCohomologyUT @@ -22,7 +25,10 @@ add_test(NAME PersistentCohomologyUT if(GMPXX_FOUND AND GMP_FOUND) add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp ) - target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) +target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) +if (TBB_FOUND) + target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_RELEASE_LIBRARY}) +endif() # Unitary tests add_test(NAME PersistentCohomologyMultiFieldUT diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index 200161a6..89a4e053 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -2,10 +2,16 @@ cmake_minimum_required(VERSION 2.6) project(GUDHISimplexTreeFromFile) add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp ) +if (TBB_FOUND) + target_link_libraries(simplex_tree_from_cliques_of_graph ${TBB_RELEASE_LIBRARY}) +endif() add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2) add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3) add_executable ( simple_simplex_tree simple_simplex_tree.cpp ) +if (TBB_FOUND) + target_link_libraries(simple_simplex_tree ${TBB_RELEASE_LIBRARY}) +endif() add_test(simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/simple_simplex_tree) add_executable ( mini_simplex_tree mini_simplex_tree.cpp ) @@ -16,5 +22,8 @@ add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree) if(GMP_FOUND AND CGAL_FOUND) add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp ) target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(simplex_tree_from_alpha_shapes_3 ${TBB_RELEASE_LIBRARY}) + endif() add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000) endif() diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index ba09db63..dea475ac 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -797,10 +797,11 @@ class Simplex_tree { * possible. */ #ifdef GUDHI_USE_TBB - tbb::parallel_sort(filtration_vect_, is_before_in_filtration(this)); + std::cout << "TBB is ON !!!" << std::endl; + tbb::parallel_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this)); #else - std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(), - is_before_in_filtration(this)); + std::cout << "TBB is OFF..." << std::endl; + std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this)); #endif } diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index 1f2f7d33..609d8669 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -12,6 +12,9 @@ endif() add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp ) target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(SimplexTreeUT ${TBB_RELEASE_LIBRARY}) +endif() # Do not forget to copy test files in current binary dir file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 6f3d8603..1e088552 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -148,21 +148,72 @@ * * The following example requires the GNU Multiple Precision Arithmetic * Library (GMP) and will not be built if GMP is not installed: - * \li Persistent_cohomology/rips_multifield_persistence + * \li + * Persistent_cohomology/alpha_shapes_persistence.cpp + * \li + * Persistent_cohomology/performance_rips_persistence.cpp + * \li + * Persistent_cohomology/rips_multifield_persistence.cpp + * \li + * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp * * Having GMP version 4.2 or higher installed is recommended. * * \subsection cgal CGAL: * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms. * + * Having CGAL version 4.4 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 (CGAL) and will not be built if CGAL is not installed: - * \li GudhUI - * \li Persistent_cohomology/alpha_shapes_persistence - * \li Simplex_tree/simplex_tree_from_alpha_shapes_3 + * \li + * Persistent_cohomology/alpha_shapes_persistence.cpp + * \li + * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp * - * Having CGAL version 4.4 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 example requires CGAL version ≥ 4.6: + * \li + * Witness_complex/witness_complex_sphere.cpp + * + * \subsection tbb Threading Building Blocks: + * Intel® TBB lets you easily write parallel + * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have + * future-proof scalability. + * + * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. + * + * The following examples are using Intel® TBB if installed: + * \li + * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp + * \li + * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp + * \li + * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp + * \li + * Persistent_cohomology/alpha_shapes_persistence.cpp + * \li + * Simplex_tree/simple_simplex_tree.cpp + * \li + * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp + * \li + * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp + * \li + * Persistent_cohomology/alpha_shapes_persistence.cpp + * \li + * Persistent_cohomology/parallel_rips_persistence.cpp + * \li + * Persistent_cohomology/performance_rips_persistence.cpp + * \li + * Persistent_cohomology/persistence_from_file.cpp + * \li + * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp + * \li + * Persistent_cohomology/plain_homology.cpp + * \li + * Persistent_cohomology/rips_multifield_persistence.cpp + * \li + * Persistent_cohomology/rips_persistence.cpp * * \subsection demos Demos and examples * To build the demos and libraries, run the following commands in a terminal: @@ -206,3 +257,29 @@ make \endverbatim * \verbinclude biblio/how_to_cite_gudhi.bib */ +// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments +/*! @file Examples + * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp + * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp + * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp + * @example Contraction/Garland_heckbert.cpp + * @example Contraction/Rips_contraction.cpp + * @example Persistent_cohomology/alpha_shapes_persistence.cpp + * @example Persistent_cohomology/parallel_rips_persistence.cpp + * @example Persistent_cohomology/performance_rips_persistence.cpp + * @example Persistent_cohomology/persistence_from_file.cpp + * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp + * @example Persistent_cohomology/plain_homology.cpp + * @example Persistent_cohomology/rips_multifield_persistence.cpp + * @example Persistent_cohomology/rips_persistence.cpp + * @example Simplex_tree/mini_simplex_tree.cpp + * @example Simplex_tree/simple_simplex_tree.cpp + * @example Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp + * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp + * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp + * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp + * @example Skeleton_blocker/Skeleton_blocker_link.cpp + * @example Witness_complex/witness_complex_from_file.cpp + * @example Witness_complex/witness_complex_sphere.cpp + */ + -- cgit v1.2.3 From fb22bc9ca84f5b3c55a598bf0c903a73c117e783 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 6 Apr 2016 11:08:33 +0000 Subject: Replace Delaunay_triangulation_off_io.h and Delaunay_triangulation_off_rw.cpp with Points_off_io.h and CGAL_points_off_reader.cpp Adapt UT and examples for this Adapt Alpha complex for it Alpha complex is now inserting points in a faster way (after a spatial_sort). Remove Alpha complex construction from a pointer on Delaunay triangulation (no more needed). Adapt documentation to all these modifications Forbid copy/move constructor/assignment operator on Alpha complex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@1098 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 08a673b66451b5cb03fbdf482d696d93b35d220f --- src/Alpha_complex/doc/Intro_alpha_complex.h | 6 +- src/Alpha_complex/doc/alpha_complex_doc.ipe | 136 ++++-- src/Alpha_complex/doc/alpha_complex_doc.png | Bin 25150 -> 25554 bytes src/Alpha_complex/doc/alpha_complex_doc_420.ipe | 514 +++++++++++++++++++++ src/Alpha_complex/doc/alpha_complex_doc_420.png | Bin 0 -> 80794 bytes src/Alpha_complex/doc/alpha_complex_doc_421.ipe | 514 --------------------- src/Alpha_complex/doc/alpha_complex_doc_421.png | Bin 100798 -> 0 bytes .../doc/alpha_complex_representation.ipe | 16 +- .../doc/alpha_complex_representation.png | Bin 14628 -> 14606 bytes .../example/Alpha_complex_from_off.cpp | 8 +- .../example/Alpha_complex_from_points.cpp | 15 +- .../example/alphaoffreader_for_doc_32.txt | 26 +- .../example/alphaoffreader_for_doc_60.txt | 36 +- src/Alpha_complex/include/gudhi/Alpha_complex.h | 109 +++-- src/Alpha_complex/test/Alpha_complex_unit_test.cpp | 2 - .../example/alpha_complex_persistence.cpp | 3 +- src/common/example/CGAL_points_off_reader.cpp | 43 ++ src/common/example/CMakeLists.txt | 12 +- .../example/Delaunay_triangulation_off_rw.cpp | 54 --- src/common/example/cgaloffreader_result.txt | 7 + .../example/dtoffrw_alphashapedoc_result.off | 15 - .../example/dtoffrw_alphashapedoc_result.txt | 2 - .../include/gudhi/Delaunay_triangulation_off_io.h | 348 -------------- src/common/include/gudhi/Points_off_io.h | 178 +++++++ src/common/test/CMakeLists.txt | 14 +- src/common/test/dtoffrw_alphashapedoc_result.off | 22 +- src/common/test/dtoffrw_unit_test.cpp | 90 ---- src/common/test/points_off_reader_unit_test.cpp | 78 ++++ 28 files changed, 1044 insertions(+), 1204 deletions(-) create mode 100644 src/Alpha_complex/doc/alpha_complex_doc_420.ipe create mode 100644 src/Alpha_complex/doc/alpha_complex_doc_420.png delete mode 100644 src/Alpha_complex/doc/alpha_complex_doc_421.ipe delete mode 100644 src/Alpha_complex/doc/alpha_complex_doc_421.png create mode 100644 src/common/example/CGAL_points_off_reader.cpp delete mode 100644 src/common/example/Delaunay_triangulation_off_rw.cpp create mode 100644 src/common/example/cgaloffreader_result.txt delete mode 100644 src/common/example/dtoffrw_alphashapedoc_result.off delete mode 100644 src/common/example/dtoffrw_alphashapedoc_result.txt delete mode 100644 src/common/include/gudhi/Delaunay_triangulation_off_io.h create mode 100644 src/common/include/gudhi/Points_off_io.h delete mode 100644 src/common/test/dtoffrw_unit_test.cpp create mode 100644 src/common/test/points_off_reader_unit_test.cpp (limited to 'src/Persistent_cohomology/example') diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 0dea2b16..9d0dcefa 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -112,14 +112,14 @@ namespace alphacomplex { * * \subsubsection dimension2 Dimension 2 * - * From the example above, it means the algorithm looks into each triangle ([4,2,1], [2,4,6], [4,5,6], ...), + * From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...), * computes the filtration value of the triangle, and then propagates the filtration value as described * here : - * \image html "alpha_complex_doc_421.png" "Filtration value propagation example" + * \image html "alpha_complex_doc_420.png" "Filtration value propagation example" * * \subsubsection dimension1 Dimension 1 * - * Then, the algorithm looks into each edge ([1,2], [4,2], [4,1], ...), + * Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...), * computes the filtration value of the edge (in this case, propagation will have no effect). * * \subsubsection dimension0 Dimension 0 diff --git a/src/Alpha_complex/doc/alpha_complex_doc.ipe b/src/Alpha_complex/doc/alpha_complex_doc.ipe index 99bd05af..baf0d26a 100644 --- a/src/Alpha_complex/doc/alpha_complex_doc.ipe +++ b/src/Alpha_complex/doc/alpha_complex_doc.ipe @@ -1,7 +1,7 @@ - + @@ -253,13 +253,13 @@ h 320 580 l Delaunay triangulation -2 -6 -4 -5 -1 -3 -0 +0 +1 +2 +3 +4 +5 +6 280 660 m 300 710 l @@ -314,7 +314,7 @@ h -3 +2 300 688 m 300 676 l @@ -322,15 +322,14 @@ h 312 688 l h - +2 + 300 688 m 300 676 l 312 676 l 312 688 l h -4 -3 300 688 m 300 676 l @@ -338,6 +337,8 @@ h 312 688 l h +4 +1 300 688 m 300 676 l @@ -345,39 +346,15 @@ h 312 688 l h -4 -1 - -300 688 m -300 676 l -312 676 l -312 688 l -h - - -300 688 m -300 676 l -312 676 l -312 688 l -h - -5 - + 300 688 m 300 676 l 312 676 l 312 688 l h -5 +4 3 - -300 688 m -300 676 l -312 676 l -312 688 l -h - 300 688 m 300 676 l @@ -385,7 +362,6 @@ h 312 688 l h -4 2 300 688 m @@ -401,7 +377,7 @@ h 312 688 l h -4 +3 6 300 688 m @@ -418,14 +394,14 @@ h 312 688 l h - + 300 688 m 300 676 l 312 676 l 312 688 l h -6 +6 6 300 688 m @@ -442,22 +418,22 @@ h 312 688 l h - + 300 688 m 300 676 l 312 676 l 312 688 l h -6 - +6 + 300 688 m 300 676 l 312 676 l 312 688 l h -6 +6 292 716 m 292 728 l @@ -514,11 +490,11 @@ h 4 5 6 - + 436 708 m 436 716 l - + 364 708 m 364 716 l @@ -535,11 +511,11 @@ h 308 716 l 308 716 l - + 264 688 m 268 696 l - + 292 688 m 292 696 l @@ -555,5 +531,65 @@ h 448 612 m 448 620 l +3 + +300 688 m +300 676 l +312 676 l +312 688 l +h + + +300 688 m +300 676 l +312 676 l +312 688 l +h + +6 + +364 688 m +364 696 l + + +300 688 m +300 676 l +312 676 l +312 688 l +h + +6 + +300 688 m +300 676 l +312 676 l +312 688 l +h + +6 + +436 708 m +436 716 l + + +300 688 m +300 676 l +312 676 l +312 688 l +h + +6 + +300 688 m +300 676 l +312 676 l +312 688 l +h + +6 + +436 708 m +436 716 l + diff --git a/src/Alpha_complex/doc/alpha_complex_doc.png b/src/Alpha_complex/doc/alpha_complex_doc.png index cfe3ede6..0b6201da 100644 Binary files a/src/Alpha_complex/doc/alpha_complex_doc.png and b/src/Alpha_complex/doc/alpha_complex_doc.png differ diff --git a/src/Alpha_complex/doc/alpha_complex_doc_420.ipe b/src/Alpha_complex/doc/alpha_complex_doc_420.ipe new file mode 100644 index 00000000..5d1d29d4 --- /dev/null +++ b/src/Alpha_complex/doc/alpha_complex_doc_420.ipe @@ -0,0 +1,514 @@ + + + + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h + + + + +0.6 0 0 0.6 0 0 e +0.4 0 0 0.4 0 0 e + + + + +0.6 0 0 0.6 0 0 e + + + + + +0.5 0 0 0.5 0 0 e + + +0.6 0 0 0.6 0 0 e +0.4 0 0 0.4 0 0 e + + + + + +-0.6 -0.6 m +0.6 -0.6 l +0.6 0.6 l +-0.6 0.6 l +h +-0.4 -0.4 m +0.4 -0.4 l +0.4 0.4 l +-0.4 0.4 l +h + + + + +-0.6 -0.6 m +0.6 -0.6 l +0.6 0.6 l +-0.6 0.6 l +h + + + + + +-0.5 -0.5 m +0.5 -0.5 l +0.5 0.5 l +-0.5 0.5 l +h + + +-0.6 -0.6 m +0.6 -0.6 l +0.6 0.6 l +-0.6 0.6 l +h +-0.4 -0.4 m +0.4 -0.4 l +0.4 0.4 l +-0.4 0.4 l +h + + + + + + +-0.43 -0.57 m +0.57 0.43 l +0.43 0.57 l +-0.57 -0.43 l +h + + +-0.43 0.57 m +0.57 -0.43 l +0.43 -0.57 l +-0.57 0.43 l +h + + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h + + + + +0 0 m +-1 0.333 l +-0.8 0 l +-1 -0.333 l +h + + + + +0 0 m +-1 0.333 l +-0.8 0 l +-1 -0.333 l +h + + + + +-1 0.333 m +0 0 l +-1 -0.333 l + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h +-1 0 m +-2 0.333 l +-2 -0.333 l +h + + + + +0 0 m +-1 0.333 l +-1 -0.333 l +h +-1 0 m +-2 0.333 l +-2 -0.333 l +h + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +320 580 m +350 520 l +290 530 l +320 580 l +320 580 l + + +320 580 m +280 660 l +290 530 l +320 580 l +320 580 l + + +320 580 m +370 580 l +350 520 l +320 580 l + +Cell [4,2,0] +0 +1 +2 +3 +4 +5 +6 + +280 660 m +300 710 l +370 690 l +280 660 l + + +320 580 m +370 690 l +370 580 l +320 580 l + + +280 660 m +370 690 l +320 580 l +280 660 l + + +77.2727 0 0 77.2727 243.636 591.818 e + + +243.428 591.569 m +186.061 643.28 l + +$\alpha_{420}$ + +320 580 m +350 520 l +290 530 l +320 580 l +320 580 l + + +320 580 m +280 660 l +290 530 l +320 580 l +320 580 l + + +320 580 m +370 580 l +350 520 l +320 580 l + +[2,0] is Gabriel $\rightarrow$ $\alpha_{20}$ is not$\\$ +modified (NaN) + +0 +2 +3 +4 +5 +6 + +280 660 m +300 710 l +370 690 l +280 660 l + + +320 580 m +370 690 l +370 580 l +320 580 l + + +280 660 m +370 690 l +320 580 l +280 660 l + +$\alpha_{20}$ + +290 530 m +320 580 l + + +29.1548 0 0 29.1548 305 555 e + + +304.883 555.015 m +334.509 555.015 l + + +320 580 m +350 520 l +290 530 l +320 580 l +320 580 l + + +320 580 m +280 660 l +290 530 l +320 580 l +320 580 l + + +320 580 m +370 580 l +350 520 l +320 580 l + +[0,4] is not Gabriel $\rightarrow$ $\alpha_{40} = \alpha_{420}$ +0 +3 +5 +6 + +280 660 m +300 710 l +370 690 l +280 660 l + + +320 580 m +370 690 l +370 580 l +320 580 l + + +280 660 m +370 690 l +320 580 l +280 660 l + +$\alpha_{40}$ + +290 530 m +280 660 l + + +320 580 m +350 520 l +290 530 l +320 580 l +320 580 l + + +320 580 m +280 660 l +290 530 l +320 580 l +320 580 l + + +320 580 m +370 580 l +350 520 l +320 580 l + +0 +1 +2 +3 +5 +6 + +280 660 m +300 710 l +370 690 l +280 660 l + + +320 580 m +370 690 l +370 580 l +320 580 l + + +280 660 m +370 690 l +320 580 l +280 660 l + +$\alpha_{42}$ +4 + +406.093 497.775 m +446.094 418.092 l + + +44.5799 0 0 44.5799 425.934 457.774 e + + +425.854 457.774 m +470.795 457.774 l + +[2,4] is Gabriel $\rightarrow$ $\alpha_{42}$ is not modified (NaN) + + +205.028 596.091 m +110.946 544.02 l + + +280.768 588.99 m +280.768 547.57 l + + +341.123 594.316 m +413.904 554.079 l + +For all faces of [4,2,0] +N.B. : is Gabriel on a single point has no sense. +Dimension =2 - $\sigma$ = [4,2,0] + +247.333 430.892 m +311.764 430.892 l + + + + + + + + + + + + + + +1 + + + + + +4 + + +1 + + +2 + +65.192 0 0 65.192 285 595 e + + + + + + + + + + + + + diff --git a/src/Alpha_complex/doc/alpha_complex_doc_420.png b/src/Alpha_complex/doc/alpha_complex_doc_420.png new file mode 100644 index 00000000..ef7187f7 Binary files /dev/null and b/src/Alpha_complex/doc/alpha_complex_doc_420.png differ diff --git a/src/Alpha_complex/doc/alpha_complex_doc_421.ipe b/src/Alpha_complex/doc/alpha_complex_doc_421.ipe deleted file mode 100644 index 727816c5..00000000 --- a/src/Alpha_complex/doc/alpha_complex_doc_421.ipe +++ /dev/null @@ -1,514 +0,0 @@ - - - - - - - -0 0 m --1 0.333 l --1 -0.333 l -h - - - - -0 0 m --1 0.333 l --1 -0.333 l -h - - - - -0.6 0 0 0.6 0 0 e -0.4 0 0 0.4 0 0 e - - - - -0.6 0 0 0.6 0 0 e - - - - - -0.5 0 0 0.5 0 0 e - - -0.6 0 0 0.6 0 0 e -0.4 0 0 0.4 0 0 e - - - - - --0.6 -0.6 m -0.6 -0.6 l -0.6 0.6 l --0.6 0.6 l -h --0.4 -0.4 m -0.4 -0.4 l -0.4 0.4 l --0.4 0.4 l -h - - - - --0.6 -0.6 m -0.6 -0.6 l -0.6 0.6 l --0.6 0.6 l -h - - - - - --0.5 -0.5 m -0.5 -0.5 l -0.5 0.5 l --0.5 0.5 l -h - - --0.6 -0.6 m -0.6 -0.6 l -0.6 0.6 l --0.6 0.6 l -h --0.4 -0.4 m -0.4 -0.4 l -0.4 0.4 l --0.4 0.4 l -h - - - - - - --0.43 -0.57 m -0.57 0.43 l -0.43 0.57 l --0.57 -0.43 l -h - - --0.43 0.57 m -0.57 -0.43 l -0.43 -0.57 l --0.57 0.43 l -h - - - - - -0 0 m --1 0.333 l --1 -0.333 l -h - - - - -0 0 m --1 0.333 l --0.8 0 l --1 -0.333 l -h - - - - -0 0 m --1 0.333 l --0.8 0 l --1 -0.333 l -h - - - - --1 0.333 m -0 0 l --1 -0.333 l - - - - -0 0 m --1 0.333 l --1 -0.333 l -h --1 0 m --2 0.333 l --2 -0.333 l -h - - - - -0 0 m --1 0.333 l --1 -0.333 l -h --1 0 m --2 0.333 l --2 -0.333 l -h - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -320 580 m -350 520 l -290 530 l -320 580 l -320 580 l - - -320 580 m -280 660 l -290 530 l -320 580 l -320 580 l - - -320 580 m -370 580 l -350 520 l -320 580 l - -Cell [4,2,1] -2 -6 -4 -5 -1 -3 -0 - -280 660 m -300 710 l -370 690 l -280 660 l - - -320 580 m -370 690 l -370 580 l -320 580 l - - -280 660 m -370 690 l -320 580 l -280 660 l - - -77.2727 0 0 77.2727 243.636 591.818 e - - -243.428 591.569 m -186.061 643.28 l - -$\alpha_{421}$ - -320 580 m -350 520 l -290 530 l -320 580 l -320 580 l - - -320 580 m -280 660 l -290 530 l -320 580 l -320 580 l - - -320 580 m -370 580 l -350 520 l -320 580 l - -[4,2] is Gabriel $\rightarrow$ $\alpha_{42}$ is not$\\$ -modified (NaN) - -2 -4 -5 -1 -3 -0 - -280 660 m -300 710 l -370 690 l -280 660 l - - -320 580 m -370 690 l -370 580 l -320 580 l - - -280 660 m -370 690 l -320 580 l -280 660 l - -$\alpha_{42}$ - -290 530 m -320 580 l - - -29.1548 0 0 29.1548 305 555 e - - -304.883 555.015 m -334.509 555.015 l - - -320 580 m -350 520 l -290 530 l -320 580 l -320 580 l - - -320 580 m -280 660 l -290 530 l -320 580 l -320 580 l - - -320 580 m -370 580 l -350 520 l -320 580 l - -[2,1] is not Gabriel $\rightarrow$ $\alpha_{21} = \alpha_{421}$ -2 -5 -3 -0 - -280 660 m -300 710 l -370 690 l -280 660 l - - -320 580 m -370 690 l -370 580 l -320 580 l - - -280 660 m -370 690 l -320 580 l -280 660 l - -$\alpha_{12}$ - -290 530 m -280 660 l - - -320 580 m -350 520 l -290 530 l -320 580 l -320 580 l - - -320 580 m -280 660 l -290 530 l -320 580 l -320 580 l - - -320 580 m -370 580 l -350 520 l -320 580 l - -2 -6 -4 -5 -3 -0 - -280 660 m -300 710 l -370 690 l -280 660 l - - -320 580 m -370 690 l -370 580 l -320 580 l - - -280 660 m -370 690 l -320 580 l -280 660 l - -$\alpha_{41}$ -1 - -406.093 497.775 m -446.094 418.092 l - - -44.5799 0 0 44.5799 425.934 457.774 e - - -425.854 457.774 m -470.795 457.774 l - -[4,1] is Gabriel $\rightarrow$ $\alpha_{41}$ is not modified (NaN) - - -205.028 596.091 m -110.946 544.02 l - - -280.768 588.99 m -280.768 547.57 l - - -341.123 594.316 m -413.904 554.079 l - -For all faces of [4,2,1] -N.B. : is Gabriel on a single point has no sense. -Dimension =2 - $\sigma$ = [4,2,1] - -247.333 430.892 m -311.764 430.892 l - - - - - - - - - - - - - - -6 - - - - - -1 - - -6 - - -4 - -65.192 0 0 65.192 285 595 e - - - - - - - - - - - - - diff --git a/src/Alpha_complex/doc/alpha_complex_doc_421.png b/src/Alpha_complex/doc/alpha_complex_doc_421.png deleted file mode 100644 index 1cce4402..00000000 Binary files a/src/Alpha_complex/doc/alpha_complex_doc_421.png and /dev/null differ diff --git a/src/Alpha_complex/doc/alpha_complex_representation.ipe b/src/Alpha_complex/doc/alpha_complex_representation.ipe index fead1661..e8096b93 100644 --- a/src/Alpha_complex/doc/alpha_complex_representation.ipe +++ b/src/Alpha_complex/doc/alpha_complex_representation.ipe @@ -1,7 +1,7 @@ - + @@ -251,13 +251,13 @@ h h Alpha complex -2 -6 -4 -5 -1 -3 -0 +0 +1 +2 +3 +4 +5 +6 58.1341 0 0 58.1341 218.925 692.601 e diff --git a/src/Alpha_complex/doc/alpha_complex_representation.png b/src/Alpha_complex/doc/alpha_complex_representation.png index 9833bff3..7b81cd69 100644 Binary files a/src/Alpha_complex/doc/alpha_complex_representation.png and b/src/Alpha_complex/doc/alpha_complex_representation.png differ diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index 18a1a20d..963ef5ca 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -4,17 +4,15 @@ #include #include -void usage(char * const progName) { +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value [ouput_file.txt]\n"; std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n"; exit(-1); // ----- >> } int main(int argc, char **argv) { - if ((argc != 3) && (argc != 4)) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } + if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1)); std::string off_file_name(argv[1]); double alpha_square_max_value = atof(argv[2]); diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index 815e40d7..cd17af1e 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -4,13 +4,26 @@ #include #include #include +#include // for numeric limits typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel; typedef Kernel::Point_d Point; typedef std::vector Vector_of_points; +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " [alpha_square_max_value]\n"; + std::cerr << " i.e.: " << progName << " 60.0\n"; + exit(-1); // ----- >> +} + int main(int argc, char **argv) { - double alpha_square_max_value = 60.0; + if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1)); + + // Delaunay complex if alpha_square_max_value is not given by the user. + double alpha_square_max_value = std::numeric_limits::infinity(); + if (argc == 2) + alpha_square_max_value = atof(argv[1]); // ---------------------------------------------------------------------------- // Init of a list of points diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt index 5869fdff..13183e86 100644 --- a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt @@ -7,16 +7,16 @@ Iterator on alpha complex simplices in the filtration order, with [filtration va ( 4 ) -> [0] ( 5 ) -> [0] ( 6 ) -> [0] - ( 5 4 ) -> [6.25] - ( 3 1 ) -> [7.25] - ( 4 2 ) -> [8.5] - ( 6 2 ) -> [9.25] - ( 6 5 ) -> [10] - ( 6 4 ) -> [11.25] - ( 6 5 4 ) -> [12.5] - ( 6 4 2 ) -> [12.9959] - ( 3 0 ) -> [13.25] - ( 4 1 ) -> [20] - ( 1 0 ) -> [22.7367] - ( 3 1 0 ) -> [22.7367] - ( 5 0 ) -> [30.25] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt index 1d17a58a..71f29a00 100644 --- a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt @@ -7,21 +7,21 @@ Iterator on alpha complex simplices in the filtration order, with [filtration va ( 4 ) -> [0] ( 5 ) -> [0] ( 6 ) -> [0] - ( 5 4 ) -> [6.25] - ( 3 1 ) -> [7.25] - ( 4 2 ) -> [8.5] - ( 6 2 ) -> [9.25] - ( 6 5 ) -> [10] - ( 6 4 ) -> [11.25] - ( 6 5 4 ) -> [12.5] - ( 6 4 2 ) -> [12.9959] - ( 3 0 ) -> [13.25] - ( 4 1 ) -> [20] - ( 1 0 ) -> [22.7367] - ( 3 1 0 ) -> [22.7367] - ( 5 0 ) -> [30.25] - ( 4 0 ) -> [36.5] - ( 5 4 0 ) -> [36.5] - ( 4 1 0 ) -> [37.2449] - ( 2 1 ) -> [59.7107] - ( 4 2 1 ) -> [59.7107] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] + ( 6 2 ) -> [36.5] + ( 6 3 2 ) -> [36.5] + ( 6 4 2 ) -> [37.2449] + ( 4 0 ) -> [59.7107] + ( 4 2 0 ) -> [59.7107] diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 2b27a459..21eb5f48 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -27,14 +27,16 @@ #include #include #include -// to construct a Delaunay_triangulation from a OFF file -#include +// to construct Alpha_complex from a OFF file of points +#include #include #include // isnan, fmax +//#include #include #include +#include #include #include @@ -43,6 +45,7 @@ #include #include // std::pair #include +#include // for std::iota namespace Gudhi { @@ -57,7 +60,7 @@ namespace alphacomplex { * \details * The data structure can be constructed from a CGAL Delaunay triangulation (for more informations on CGAL Delaunay * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) or from - * an OFF file (cf. Delaunay_triangulation_off_reader). + * an OFF file (cf. Points_off_reader). * * Please refer to \ref alpha_complex for examples. * @@ -74,13 +77,19 @@ namespace alphacomplex { template> class Alpha_complex : public Simplex_tree<> { public: + // Add an int in TDS to save point index in the structure + typedef CGAL::Triangulation_data_structure, + CGAL::Triangulation_full_cell > TDS; /** \brief A Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ - typedef typename CGAL::Delaunay_triangulation Delaunay_triangulation; + typedef CGAL::Delaunay_triangulation Delaunay_triangulation; + /** \brief A point in Euclidean space.*/ typedef typename Kernel::Point_d Point_d; /** \brief Geometric traits class that provides the geometric types and predicates needed by Delaunay * triangulations.*/ typedef Kernel Geom_traits; + private: // From Simplex_tree // Type required to insert into a simplex_tree (with or without subfaces). @@ -104,7 +113,7 @@ class Alpha_complex : public Simplex_tree<> { // Double map type to switch from CGAL vertex iterator to simplex tree vertex handle and vice versa. typedef typename std::map< CGAL_vertex_iterator, Vertex_handle > Map_vertex_iterator_to_handle; - typedef typename std::vector< CGAL_vertex_iterator > Vector_vertex_iterator; + typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Vector_vertex_iterator; private: /** \brief Map to switch from CGAL vertex iterator to simplex tree vertex handle.*/ @@ -128,28 +137,13 @@ class Alpha_complex : public Simplex_tree<> { Alpha_complex(const std::string& off_file_name, Filtration_value max_alpha_square = std::numeric_limits::infinity()) : triangulation_(nullptr) { - Gudhi::Delaunay_triangulation_off_reader off_reader(off_file_name); + Gudhi::Points_off_reader off_reader(off_file_name); if (!off_reader.is_valid()) { std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n"; exit(-1); // ----- >> } - triangulation_ = off_reader.get_complex(); - init(max_alpha_square); - } - /** \brief Alpha_complex constructor from a Delaunay triangulation. - * - * @param[in] triangulation_ptr Pointer on a - * CGAL::Delaunay_triangulation \cite cgal:hdj-t-15b. - * Alpha_complex takes ownership of the Delaunay_triangulation object, which must have been allocated using operator - * new. - * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. - */ - Alpha_complex(Delaunay_triangulation* triangulation_ptr, - Filtration_value max_alpha_square = std::numeric_limits::infinity()) - : triangulation_(triangulation_ptr) { - init(max_alpha_square); + init_from_range(off_reader.get_point_cloud(), max_alpha_square); } /** \brief Alpha_complex constructor from a list of points. @@ -164,23 +158,7 @@ class Alpha_complex : public Simplex_tree<> { Alpha_complex(const InputPointRange& points, Filtration_value max_alpha_square = std::numeric_limits::infinity()) : triangulation_(nullptr) { - auto first = std::begin(points); - auto last = std::end(points); - - if (first != last) { - // point_dimension function initialization - Point_Dimension point_dimension = kernel_.point_dimension_d_object(); - - // Delaunay triangulation is point dimension. - triangulation_ = new Delaunay_triangulation(point_dimension(*first)); - - size_type inserted = triangulation_->insert(first, last); - if (inserted != (last -first)) { - std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << (last -first) << "\n"; - exit(-1); // ----- >> - } - init(max_alpha_square); - } + init_from_range(points, max_alpha_square); } /** \brief Alpha_complex destructor. @@ -191,6 +169,12 @@ class Alpha_complex : public Simplex_tree<> { delete triangulation_; } + // Forbid copy/move constructor/assignment operator + Alpha_complex(const Alpha_complex& other) = delete; + Alpha_complex& operator= (const Alpha_complex& other) = delete; + Alpha_complex (Alpha_complex&& other) = delete; + Alpha_complex& operator= (Alpha_complex&& other) = delete; + /** \brief get_point returns the point corresponding to the vertex given as parameter. * * @param[in] vertex Vertex handle of the point to retrieve. @@ -202,6 +186,44 @@ class Alpha_complex : public Simplex_tree<> { } private: + template + void init_from_range(const InputPointRange& points, Filtration_value max_alpha_square) { + auto first = std::begin(points); + auto last = std::end(points); + if (first != last) { + // point_dimension function initialization + Point_Dimension point_dimension = kernel_.point_dimension_d_object(); + + // Delaunay triangulation is point dimension. + triangulation_ = new Delaunay_triangulation(point_dimension(*first)); + + std::vector points(first, last); + + // Creates a vector {0, 1, ..., N-1} + std::vector indices(boost::counting_iterator(0), + boost::counting_iterator(points.size())); + + // Sort indices considering CGAL spatial sort + typedef CGAL::Spatial_sort_traits_adapter_d Search_traits_d; + spatial_sort(indices.begin(),indices.end(),Search_traits_d(&(points[0]))); + + typename Delaunay_triangulation::Full_cell_handle hint; + for (auto index : indices) { + typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(points[index], hint); + // Save index value as data to retrieve it after insertion + pos->data() = index; + hint = pos->full_cell(); + } + + if (triangulation_->number_of_vertices() != (last -first)) { + std::cerr << "Alpha_complex - insertion failed " << triangulation_->number_of_vertices() << " != " << + (last -first) << "\n"; + exit(-1); // ----- >> + } + init(max_alpha_square); + } + } + /** \brief Initialize the Alpha_complex from the Delaunay triangulation. * * @param[in] max_alpha_square maximum for alpha square value. @@ -233,18 +255,15 @@ class Alpha_complex : public Simplex_tree<> { // -------------------------------------------------------------------------------------------- // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa - // Start to insert at handle = 0 - default integer value - Vertex_handle vertex_handle = Vertex_handle(); // Loop on triangulation vertices list for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) { if (!triangulation_->is_infinite(*vit)) { #ifdef DEBUG_TRACES - std::cout << "Vertex insertion - " << vertex_handle << " -> " << vit->point() << std::endl; + std::cout << "Vertex insertion - " << vit->data() << " -> " << vit->point() << std::endl; #endif // DEBUG_TRACES - vertex_iterator_to_handle_.emplace(vit, vertex_handle); - vertex_handle_to_iterator_.push_back(vit); - vertex_handle++; + vertex_iterator_to_handle_.emplace(vit, vit->data()); + vertex_handle_to_iterator_.emplace(vit->data(), vit); } } // -------------------------------------------------------------------------------------------- diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp index 315582d1..80b39924 100644 --- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -32,8 +32,6 @@ #include #include -// to construct a Delaunay_triangulation from a OFF file -#include #include // Use dynamic_dimension_tag for the user to be able to set dimension diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp index d2f9a4a2..8f9f077c 100644 --- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp @@ -1,8 +1,7 @@ #include #include -// to construct a Delaunay_triangulation from a OFF file -#include + #include #include diff --git a/src/common/example/CGAL_points_off_reader.cpp b/src/common/example/CGAL_points_off_reader.cpp new file mode 100644 index 00000000..076afd5b --- /dev/null +++ b/src/common/example/CGAL_points_off_reader.cpp @@ -0,0 +1,43 @@ +#include + +// For CGAL points type in dimension d +// cf. http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Point__d.html +#include + +#include +#include + +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; +typedef typename Kernel::Point_d Point_d; + +void usage(int argc, char * const progName) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + std::cerr << "Usage: " << progName << " inputFile.off" << std::endl; + exit(-1); +} + +int main(int argc, char **argv) { + if (argc != 2) usage(argc, (argv[0] - 1)); + + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + exit(-1); + } + + // Retrieve the triangulation + std::vector point_cloud = off_reader.get_point_cloud(); + + int n = 0; + for (auto point : point_cloud) { + std::cout << "Point[" << n << "] = "; + for (int i = 0; i < point.dimension(); i++) + std::cout << point[i] << " "; + std::cout << "\n"; + ++n; + } + return 0; +} diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index 91e78ea2..2914756e 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -9,15 +9,9 @@ if(CGAL_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") include( ${EIGEN3_USE_FILE} ) - add_executable ( dtoffrw Delaunay_triangulation_off_rw.cpp ) - target_link_libraries(dtoffrw ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - add_test(dtoffrw ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off ${CMAKE_CURRENT_BINARY_DIR}/result.off) - - if (DIFF_PATH) - # Do not forget to copy test results files in current binary dir - file(COPY "dtoffrw_alphashapedoc_result.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(dtoffrw_result_off_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw_alphashapedoc_result.off ${CMAKE_CURRENT_BINARY_DIR}/result.off) - endif() + add_executable ( cgaloffreader CGAL_points_off_reader.cpp ) + target_link_libraries(cgaloffreader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(cgaloffreader ${CMAKE_CURRENT_BINARY_DIR}/cgaloffreader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off) else() message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") diff --git a/src/common/example/Delaunay_triangulation_off_rw.cpp b/src/common/example/Delaunay_triangulation_off_rw.cpp deleted file mode 100644 index 4c7a9aaf..00000000 --- a/src/common/example/Delaunay_triangulation_off_rw.cpp +++ /dev/null @@ -1,54 +0,0 @@ -// to construct a Delaunay_triangulation from a OFF file -#include - -#include -#include - -#include -#include - -// Use dynamic_dimension_tag for the user to be able to set dimension -typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K; -typedef CGAL::Delaunay_triangulation T; -// The triangulation uses the default instantiation of the -// TriangulationDataStructure template parameter - -void usage(char * const progName) { - std::cerr << "Usage: " << progName << " inputFile.off outputFile.off" << std::endl; - exit(-1); -} - -int main(int argc, char **argv) { - if (argc != 3) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; - usage(argv[0]); - } - - std::string offInputFile(argv[1]); - // Read the OFF file (input file name given as parameter) and triangulates points - Gudhi::Delaunay_triangulation_off_reader off_reader(offInputFile); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; - exit(-1); - } - - // Retrieve the triangulation - T* triangulation = off_reader.get_complex(); - // Operations on triangulation - std::cout << "Number of vertices= " << triangulation->number_of_vertices() << std::endl; - std::cout << "Number of finite full cells= " << triangulation->number_of_finite_full_cells() << std::endl; - - std::string outFileName(argv[2]); - std::string offOutputFile(outFileName); - // Write the OFF file (output file name given as parameter) with the points and triangulated cells as faces - Gudhi::Delaunay_triangulation_off_writer off_writer(offOutputFile, triangulation); - - // Check the write operation was correct - if (!off_writer.is_valid()) { - std::cerr << "Unable to write file " << offOutputFile << std::endl; - exit(-1); - } - - return 0; -} diff --git a/src/common/example/cgaloffreader_result.txt b/src/common/example/cgaloffreader_result.txt new file mode 100644 index 00000000..1deb8dbd --- /dev/null +++ b/src/common/example/cgaloffreader_result.txt @@ -0,0 +1,7 @@ +Point[0] = 1 1 +Point[1] = 7 0 +Point[2] = 4 6 +Point[3] = 9 6 +Point[4] = 0 14 +Point[5] = 2 19 +Point[6] = 9 17 diff --git a/src/common/example/dtoffrw_alphashapedoc_result.off b/src/common/example/dtoffrw_alphashapedoc_result.off deleted file mode 100644 index d1839a43..00000000 --- a/src/common/example/dtoffrw_alphashapedoc_result.off +++ /dev/null @@ -1,15 +0,0 @@ -nOFF -2 7 6 0 -9 17 -0 14 -1 1 -2 19 -4 6 -9 6 -7 0 -3 5 0 4 -3 0 1 4 -3 3 1 0 -3 4 1 2 -3 5 4 6 -3 6 4 2 diff --git a/src/common/example/dtoffrw_alphashapedoc_result.txt b/src/common/example/dtoffrw_alphashapedoc_result.txt deleted file mode 100644 index 8e659740..00000000 --- a/src/common/example/dtoffrw_alphashapedoc_result.txt +++ /dev/null @@ -1,2 +0,0 @@ -Number of vertices= 7 -Number of finite full cells= 6 diff --git a/src/common/include/gudhi/Delaunay_triangulation_off_io.h b/src/common/include/gudhi/Delaunay_triangulation_off_io.h deleted file mode 100644 index 50be9a59..00000000 --- a/src/common/include/gudhi/Delaunay_triangulation_off_io.h +++ /dev/null @@ -1,348 +0,0 @@ -/* 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) 2015 INRIA Saclay (France) - * - * 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 . - */ -#ifndef DELAUNAY_TRIANGULATION_OFF_IO_H_ -#define DELAUNAY_TRIANGULATION_OFF_IO_H_ - -#include -#include -#include -#include - -#include - -#include - -#include "gudhi/Off_reader.h" - -namespace Gudhi { - -/** - * \class Delaunay_triangulation_off_visitor_reader Delaunay_triangulation_off_io.h gudhi/Delaunay_triangulation_off_io.h - * \brief OFF file visitor implementation according to Off_reader in order to construct a CGAL Delaunay triangulation. - * - * For more informations on CGAL Delaunay triangulation, please refer to the corresponding chapter in page - * http://doc.cgal.org/latest/Triangulation/ - */ -template -class Delaunay_triangulation_off_visitor_reader { - private: - Complex* complex_; - typedef typename Complex::Point_d Point_d; - typedef typename Complex::size_type size_type; - std::vector point_cloud; - - public: - // TODO(VR) : Pass a Complex as a parameter is required, even if not used. Otherwise, compilation is KO. - - /** \brief Delaunay_triangulation_off_visitor_reader constructor - * - * @param[in] complex_ptr_ pointer on a Delaunay triangulation. - */ - Delaunay_triangulation_off_visitor_reader(Complex* complex_ptr_) - : complex_(nullptr) { } - - /** \brief Off_reader visitor init implementation. - * - * The init parameters are set from OFF file header. - * Dimension value is required in order to construct Delaunay triangulation. - * - * @param[in] dim space dimension of vertices. - * @param[in] num_vertices number of vertices in the OFF file (not used). - * @param[in] num_faces number of faces in the OFF file (not used). - * @param[in] num_edges number of edges in the OFF file (not used). - */ - void init(int dim, int num_vertices, int num_faces, int num_edges) { -#ifdef DEBUG_TRACES - std::cout << "Delaunay_triangulation_off_visitor_reader::init - dim=" << dim << " - num_vertices=" << - num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl; -#endif // DEBUG_TRACES - if (num_faces > 0) { - std::cerr << "Delaunay_triangulation_off_visitor_reader::init faces are not taken into account from OFF " << - "file for Delaunay triangulation - faces are computed.\n"; - } - if (num_edges > 0) { - std::cerr << "Delaunay_triangulation_off_visitor_reader::init edges are not taken into account from OFF " << - "file for Delaunay triangulation - edges are computed.\n"; - } - // Complex construction with dimension from file - complex_ = new Complex(dim); - } - - /** \brief Off_reader visitor point implementation. - * - * The point function is called on each vertex line from OFF file. - * This function inserts the vertex in the Delaunay triangulation. - * - * @param[in] point vector of vertex coordinates. - */ - void point(const std::vector& point) { -#ifdef DEBUG_TRACES - std::cout << "Delaunay_triangulation_off_visitor_reader::point "; - for (auto coordinate : point) { - std::cout << coordinate << " | "; - } - std::cout << std::endl; -#endif // DEBUG_TRACES - // Fill the point cloud - point_cloud.push_back(Point_d(point.size(), point.begin(), point.end())); - } - - // Off_reader visitor maximal_face implementation - not used - void maximal_face(const std::vector& face) { - // For Delaunay Triangulation, only points are read - } - - // Off_reader visitor done implementation - void done() { - // It is advised to insert all the points at a time in a Delaunay Triangulation because points are sorted at the - // beginning of the insertion - size_type inserted = complex_->insert(point_cloud.begin(), point_cloud.end()); - if (inserted != (point_cloud.end() -point_cloud.begin())) { - std::cerr << "Delaunay_triangulation_off_visitor_reader::done - insertion failed " << inserted << " != " << - (point_cloud.end() -point_cloud.begin()) << "\n"; - } - } - - /** \brief Returns the constructed Delaunay triangulation. - * - * @return A pointer on the Delaunay triangulation. Default value is nullptr. - */ - Complex* get_complex() const { - return complex_; - } - - private: - template - size_type insert_with_index(const PointRangeIterator& first, const PointRangeIterator& last) { - size_type vertices_before_insertion = complex_->number_of_vertices(); - std::vector points(first, last); - - std::vector indices; - indices.reserve(points.size()); - - // Creates a vector {0, 1, ..., N-1} - std::copy(boost::counting_iterator(0), boost::counting_iterator(points.size()), - std::back_inserter(indices)); - - // Sort indices considering CGAL spatial sort - typedef CGAL::Spatial_sort_traits_adapter_d Search_traits_d; - spatial_sort(indices.begin(),indices.end(),Search_traits_d(&(points[0]))); - - typename Delaunay_triangulation::Full_cell_handle hint; - for (typename std::vector::const_iterator it = indices.begin(), end = indices.end(); - it != end; ++it) { - typename Delaunay_triangulation::Vertex_handle pos = complex_->insert(points[*it], hint); - // Save index value as data to retrieve it after insertion - pos->data() = *it; - hint = pos->full_cell(); - } - - return (complex_->number_of_vertices() - vertices_before_insertion); - } - -}; - -/** - * \class Delaunay_triangulation_off_reader Delaunay_triangulation_off_io.h gudhi/Delaunay_triangulation_off_io.h - * \brief OFF file reader implementation in order to construct a Delaunay triangulation. - * - * This class is using the Delaunay_triangulation_off_visitor_reader to visit the OFF file according to Off_reader. - * - * For more informations on CGAL Delaunay triangulation, please refer to the corresponding chapter in page - * http://doc.cgal.org/latest/Triangulation/ - * - * \section Example - * - * This example loads points from an OFF file and builds the Delaunay triangulation. - * Then, it is asked to display the number of vertices and finites full cells from the Delaunay triangulation. - * - * \include Delaunay_triangulation_off_rw.cpp - * - * When launching: - * - * \code $> ./dtoffrw ../../data/points/alphacomplexdoc.off triangulated.off - * \endcode - * - * the program output is: - * - * \include dtoffrw_alphashapedoc_result.txt - */ -template -class Delaunay_triangulation_off_reader { - public: - /** \brief Reads the OFF file and constructs the Delaunay triangulation from the points - * that are in the OFF file. - * - * @param[in] name_file OFF file to read. - * - * \post Check with is_valid() function to see if read operation was successful. - */ - Delaunay_triangulation_off_reader(const std::string & name_file) - : valid_(false) { - std::ifstream stream(name_file); - if (stream.is_open()) { - Delaunay_triangulation_off_visitor_reader off_visitor(complex_); - Off_reader off_reader(stream); - valid_ = off_reader.read(off_visitor); - if (valid_) { - complex_ = off_visitor.get_complex(); - if (complex_ == nullptr) { - std::cerr << "Delaunay_triangulation_off_reader::Delaunay_triangulation_off_reader off_visitor returns " << - "an empty pointer\n"; - valid_ = false; - } - } - } else { - std::cerr << "Delaunay_triangulation_off_reader::Delaunay_triangulation_off_reader could not open file " << - name_file << "\n"; - } - } - - /** \brief Returns if the OFF file read operation was successful or not. - * - * @return OFF file read status. - */ - bool is_valid() const { - return valid_; - } - - /** \brief Returns the constructed Delaunay triangulation. - * - * @return A pointer on the Delaunay triangulation. Default value is nullptr. - */ - Complex* get_complex() const { - if (valid_) - return complex_; - return nullptr; - } - - private: - /** \brief OFF file read status.*/ - bool valid_; - /** \brief A pointer on the Delaunay triangulation.*/ - Complex* complex_; -}; - -/** - * \class Delaunay_triangulation_off_writer Delaunay_triangulation_off_io.h gudhi/Delaunay_triangulation_off_io.h - * \brief OFF file writer from a Delaunay triangulation. - * - * This class constructs the OFF file header according to http://www.geomview.org/docs/html/OFF.html - * - * The header is followed by the list of points coordinates (Delaunay triangulation vertices) - * - * And finally is followed by the list of faces (Delaunay triangulation finite full cells) - * - * For more informations on CGAL Delaunay triangulation, please refer to the corresponding chapter in page - * http://doc.cgal.org/latest/Triangulation/ - * - * \section Example - * - * This example loads points from an OFF file and builds the Delaunay triangulation. - * Then, the Delaunay triangulation is saved in a new file including the triangulation as a list of faces. - * - * \include Delaunay_triangulation_off_rw.cpp - * - * When launching: - * - * \code $> ./dtoffrw ../../data/points/alphashapedoc.off triangulated.off - * \endcode - * - * The result will be an OFF file of dimension 2 with the 7 points from alphashapedoc.off followed by the 6 - * triangulations of dimension 3 (the first value on each faces): - * \include dtoffrw_alphashapedoc_result.off - */ -template -class Delaunay_triangulation_off_writer { - public: - typedef typename Complex::Point Point; - - /** \brief Writes the OFF file from the Delaunay triangulation. - * - * @param[in] name_file OFF file to write. - * @param[in] complex_ptr pointer on a Delaunay triangulation. - * - * \post Check with is_valid() function to see if write operation was successful. - */ - Delaunay_triangulation_off_writer(const std::string & name_file, Complex* complex_ptr) - : valid_(false) { - std::ofstream stream(name_file); - if (stream.is_open()) { - if (complex_ptr->current_dimension() == 3) { - // OFF header - stream << "OFF" << std::endl; - // no endl on next line - don't know why... - stream << complex_ptr->number_of_vertices() << " " << complex_ptr->number_of_finite_full_cells() << " 0"; - } else { - // nOFF header - stream << "nOFF" << std::endl; - // no endl on next line - don't know why... - stream << complex_ptr->current_dimension() << " " << complex_ptr->number_of_vertices() << " " << - complex_ptr->number_of_finite_full_cells() << " 0"; - } - - // bimap to retrieve vertex handles from points and vice versa - std::map< Point, int > points_to_vh; - // Start to insert at default handle value - int vertex_handle = int(); - - // Points list - for (auto vit = complex_ptr->vertices_begin(); vit != complex_ptr->vertices_end(); ++vit) { - for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) { - stream << *Coord << " "; - } - stream << std::endl; - points_to_vh[vit->point()] = vertex_handle; - vertex_handle++; - } - - for (auto cit = complex_ptr->finite_full_cells_begin(); cit != complex_ptr->finite_full_cells_end(); ++cit) { - stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " "; - for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) { - stream << points_to_vh[(*vit)->point()] - 1 << " "; - } - stream << std::endl; - } - stream.close(); - valid_ = true; - } else { - std::cerr << "Delaunay_triangulation_off_writer::Delaunay_triangulation_off_writer could not open file " << - name_file << "\n"; - } - } - - /** \brief Returns if the OFF write operation was successful or not. - * - * @return OFF file write status. - */ - bool is_valid() const { - return valid_; - } - - private: - /* \brief OFF file write status. */ - bool valid_; -}; - -} // namespace Gudhi - -#endif // DELAUNAY_TRIANGULATION_OFF_IO_H_ diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h new file mode 100644 index 00000000..d9f9a74b --- /dev/null +++ b/src/common/include/gudhi/Points_off_io.h @@ -0,0 +1,178 @@ +/* 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) 2015 INRIA Saclay (France) + * + * 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 . + */ +#ifndef POINTS_OFF_IO_H_ +#define POINTS_OFF_IO_H_ + +#include +#include +#include +#include + +#include + +namespace Gudhi { + +/** + * \brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file. + */ +template +class Points_off_visitor_reader { + private: + std::vector point_cloud; + + public: + /** \brief Off_reader visitor init implementation. + * + * The init parameters are set from OFF file header. + * Dimension value is required in order to construct Alpha complex. + * + * @param[in] dim space dimension of vertices. + * @param[in] num_vertices number of vertices in the OFF file (not used). + * @param[in] num_faces number of faces in the OFF file (not used). + * @param[in] num_edges number of edges in the OFF file (not used). + */ + void init(int dim, int num_vertices, int num_faces, int num_edges) { +#ifdef DEBUG_TRACES + std::cout << "Points_off_visitor_reader::init - dim=" << dim << " - num_vertices=" << + num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl; +#endif // DEBUG_TRACES + if (num_faces > 0) { + std::cerr << "Points_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n"; + } + if (num_edges > 0) { + std::cerr << "Points_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n"; + } + } + + /** \brief Off_reader visitor point implementation. + * + * The point function is called on each vertex line from OFF file. + * This function inserts the vertex in the Alpha complex. + * + * @param[in] point vector of vertex coordinates. + */ + void point(const std::vector& point) { +#ifdef DEBUG_TRACES + std::cout << "Points_off_visitor_reader::point "; + for (auto coordinate : point) { + std::cout << coordinate << " | "; + } + std::cout << std::endl; +#endif // DEBUG_TRACES + // Fill the point cloud + point_cloud.push_back(Point_d(point.size(), point.begin(), point.end())); + } + + // Off_reader visitor maximal_face implementation - Only points are read + void maximal_face(const std::vector& face) { } + + // Off_reader visitor done implementation - Only points are read + void done() { } + + /** \brief Point cloud getter. + * + * @return point_cloud. + */ + const std::vector& get_point_cloud() { + return point_cloud; + } + +}; + +/** + * \brief OFF file reader implementation in order to read points from an OFF file. + * + * This class is using the Points_off_visitor_reader to visit the OFF file according to Off_reader. + * + * Point_d must have a constructor with the following form: + * + * \code template Point_d::Point_d(int d, InputIterator first, InputIterator last) \endcode + * + * where d is the point dimension. + * + * \section Example + * + * This example loads points from an OFF file and builds a vector of CGAL points in dimension d. + * Then, it is asked to display the points. + * + * \include CGAL_points_off_reader.cpp + * + * When launching: + * + * \code $> ./cgaloffreader ../../data/points/alphacomplexdoc.off + * \endcode + * + * the program output is: + * + * \include cgaloffreader_result.txt + */ +template +class Points_off_reader { + public: + /** \brief Reads the OFF file and constructs the Alpha complex from the points + * that are in the OFF file. + * + * @param[in] name_file OFF file to read. + * + * \post Check with is_valid() function to see if read operation was successful. + */ + Points_off_reader(const std::string& name_file) + : valid_(false) { + std::ifstream stream(name_file); + if (stream.is_open()) { + Off_reader off_reader(stream); + Points_off_visitor_reader off_visitor; + valid_ = off_reader.read(off_visitor); + if (valid_) { + point_cloud = off_visitor.get_point_cloud(); + } + } else { + std::cerr << "Points_off_reader::Points_off_reader could not open file " << name_file << "\n"; + } + } + + /** \brief Returns if the OFF file read operation was successful or not. + * + * @return OFF file read status. + */ + bool is_valid() const { + return valid_; + } + + /** \brief Point cloud getter. + * + * @return point_cloud. + */ + const std::vector& get_point_cloud() { + return point_cloud; + } + + private: + /** \brief point_cloud.*/ + std::vector point_cloud; + /** \brief OFF file read status.*/ + bool valid_; +}; + +} // namespace Gudhi + +#endif // POINTS_OFF_IO_H_ diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt index 12eecda8..6205f0e4 100644 --- a/src/common/test/CMakeLists.txt +++ b/src/common/test/CMakeLists.txt @@ -18,22 +18,16 @@ if(CGAL_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") include( ${EIGEN3_USE_FILE} ) - add_executable ( dtoffrw_UT dtoffrw_unit_test.cpp ) - target_link_libraries(dtoffrw_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + add_executable ( poffreader_UT points_off_reader_unit_test.cpp ) + target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) # Unitary tests - add_test(dtoffrw_UT ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw_UT + add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/dtoffrw_UT.xml --log_level=test_suite --report_level=no) - - if (DIFF_PATH) - # Do not forget to copy test result files in current binary dir - file(COPY "dtoffrw_alphashapedoc_result.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(dtoffrw_diff_files_UT ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/UT.off ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw_alphashapedoc_result.off) - endif() + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no) else() message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") diff --git a/src/common/test/dtoffrw_alphashapedoc_result.off b/src/common/test/dtoffrw_alphashapedoc_result.off index d1839a43..1deb8dbd 100644 --- a/src/common/test/dtoffrw_alphashapedoc_result.off +++ b/src/common/test/dtoffrw_alphashapedoc_result.off @@ -1,15 +1,7 @@ -nOFF -2 7 6 0 -9 17 -0 14 -1 1 -2 19 -4 6 -9 6 -7 0 -3 5 0 4 -3 0 1 4 -3 3 1 0 -3 4 1 2 -3 5 4 6 -3 6 4 2 +Point[0] = 1 1 +Point[1] = 7 0 +Point[2] = 4 6 +Point[3] = 9 6 +Point[4] = 0 14 +Point[5] = 2 19 +Point[6] = 9 17 diff --git a/src/common/test/dtoffrw_unit_test.cpp b/src/common/test/dtoffrw_unit_test.cpp deleted file mode 100644 index f682df1a..00000000 --- a/src/common/test/dtoffrw_unit_test.cpp +++ /dev/null @@ -1,90 +0,0 @@ -/* 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) 2015 INRIA Saclay (France) - * - * 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 . - */ - -// to construct a Delaunay_triangulation from a OFF file -#include "gudhi/Delaunay_triangulation_off_io.h" - -#include -#include - -#include - -#include -#include - -#define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "delaunay_triangulation_off_read_write" -#include - -// Use dynamic_dimension_tag for the user to be able to set dimension -typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K; -typedef CGAL::Delaunay_triangulation T; - -BOOST_AUTO_TEST_CASE( Delaunay_triangulation_doc_test ) -{ - // Read the OFF file (input file name given as parameter) and triangulates points - Gudhi::Delaunay_triangulation_off_reader off_reader("alphacomplexdoc.off"); - // Check the read operation was correct - BOOST_CHECK(off_reader.is_valid()); - - // Retrieve the triangulation - T* triangulation = off_reader.get_complex(); - BOOST_CHECK(triangulation != nullptr); - // Operations on triangulation - BOOST_CHECK(triangulation->number_of_vertices() == 7); - BOOST_CHECK(triangulation->number_of_finite_full_cells() == 6); - - // Write the OFF file (output file name given as parameter) with the points and triangulated cells as faces - Gudhi::Delaunay_triangulation_off_writer off_writer("UT.off", triangulation); - - // Check the write operation was correct - BOOST_CHECK(off_writer.is_valid()); - - delete triangulation; -} - -BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_read_test ) -{ - Gudhi::Delaunay_triangulation_off_reader off_reader("some_impossible_weird_file_name.off"); - // Check the read operation was correct - BOOST_CHECK(!off_reader.is_valid()); - T* triangulation = off_reader.get_complex(); - BOOST_CHECK(triangulation == nullptr); -} - -BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_write_test ) -{ - // Read the OFF file (input file name given as parameter) and triangulates points - Gudhi::Delaunay_triangulation_off_reader off_reader("alphacomplexdoc.off"); - - // Retrieve the triangulation - T* triangulation = off_reader.get_complex(); - - // Write the OFF file (output file name given as parameter) with the points and triangulated cells as faces - Gudhi::Delaunay_triangulation_off_writer off_writer("/some_impossible_weird_directory_name/another_weird_directory_name/some_impossible_weird_file_name.off", triangulation); - - // Check the write operation was correct - BOOST_CHECK(!off_writer.is_valid()); - - delete triangulation; -} - diff --git a/src/common/test/points_off_reader_unit_test.cpp b/src/common/test/points_off_reader_unit_test.cpp new file mode 100644 index 00000000..73e19cbc --- /dev/null +++ b/src/common/test/points_off_reader_unit_test.cpp @@ -0,0 +1,78 @@ +/* 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) 2015 INRIA Saclay (France) + * + * 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 . + */ + +#include + +// For CGAL points type in dimension d +// cf. http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Point__d.html +#include + +#include +#include +#include + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "points_off_read_write" +#include + +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; +typedef typename Kernel::Point_d Point_d; + +BOOST_AUTO_TEST_CASE( points_doc_test ) +{ + // Read the OFF file (input file name given as parameter) and triangulates points + Gudhi::Points_off_reader off_reader("alphacomplexdoc.off"); + // Check the read operation was correct + BOOST_CHECK(off_reader.is_valid()); + + // Retrieve the triangulation + std::vector point_cloud = off_reader.get_point_cloud(); + BOOST_CHECK(point_cloud.size() == 7); + + std::vector expected_points; + std::vector point = {1.0, 1.0}; + expected_points.push_back(Point_d(2, point.begin(), point.end())); + point = {7.0, 0.0}; + expected_points.push_back(Point_d(2, point.begin(), point.end())); + point = {4.0, 6.0}; + expected_points.push_back(Point_d(2, point.begin(), point.end())); + point = {9.0, 6.0}; + expected_points.push_back(Point_d(2, point.begin(), point.end())); + point = {0.0, 14.0}; + expected_points.push_back(Point_d(2, point.begin(), point.end())); + point = {2.0, 19.0}; + expected_points.push_back(Point_d(2, point.begin(), point.end())); + point = {9.0, 17.0}; + expected_points.push_back(Point_d(2, point.begin(), point.end())); + + BOOST_CHECK(point_cloud == expected_points); +} + +BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_read_test ) +{ + Gudhi::Points_off_reader off_reader("some_impossible_weird_file_name.off"); + // Check the read operation was correct + BOOST_CHECK(!off_reader.is_valid()); + + std::vector point_cloud = off_reader.get_point_cloud(); + BOOST_CHECK(point_cloud.size() == 0); +} -- cgit v1.2.3