diff options
Diffstat (limited to 'src/common')
| -rw-r--r-- | src/common/doc/examples.h | 99 | ||||
| -rw-r--r-- | src/common/doc/footer.html | 10 | ||||
| -rw-r--r-- | src/common/doc/header.html | 4 | ||||
| -rw-r--r-- | src/common/doc/installation.h | 263 | ||||
| -rw-r--r-- | src/common/doc/main_page.h | 305 | ||||
| -rw-r--r-- | src/common/include/gudhi/Unitary_tests_utils.h | 1 | ||||
| -rw-r--r-- | src/common/utilities/README | 19 | ||||
| -rw-r--r-- | src/common/utilities/pointsetgenerator.md | 33 |
8 files changed, 404 insertions, 330 deletions
diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h new file mode 100644 index 00000000..40f202c7 --- /dev/null +++ b/src/common/doc/examples.h @@ -0,0 +1,99 @@ +// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments +// In user_version, `find . -name "*.cpp"` in example and utilities folders +/*! @file Examples + * @example Alpha_complex/Alpha_complex_from_off.cpp + * @example Alpha_complex/Alpha_complex_from_points.cpp + * @example Bottleneck_distance/bottleneck_basic_example.cpp + * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp + * @example Witness_complex/example_nearest_landmark_table.cpp + * @example Witness_complex/example_witness_complex_off.cpp + * @example Witness_complex/example_witness_complex_sphere.cpp + * @example Witness_complex/example_strong_witness_complex_off.cpp + * @example Simplex_tree/mini_simplex_tree.cpp + * @example Simplex_tree/graph_expansion_with_blocker.cpp + * @example Simplex_tree/simple_simplex_tree.cpp + * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp + * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp + * @example Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp + * @example Persistent_cohomology/plain_homology.cpp + * @example Persistent_cohomology/persistence_from_file.cpp + * @example Persistent_cohomology/rips_persistence_step_by_step.cpp + * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp + * @example Persistent_cohomology/custom_persistence_sort.cpp + * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp + * @example Persistent_cohomology/rips_multifield_persistence.cpp + * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp + * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp + * @example Skeleton_blocker/Skeleton_blocker_link.cpp + * @example Contraction/Garland_heckbert.cpp + * @example Contraction/Rips_contraction.cpp + * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp + * @example common/example_CGAL_3D_points_off_reader.cpp + * @example common/example_vector_double_points_off_reader.cpp + * @example common/example_CGAL_points_off_reader.cpp + * @example Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp + * @example Rips_complex/example_one_skeleton_rips_from_points.cpp + * @example Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp + * @example Rips_complex/example_rips_complex_from_off_file.cpp + * @example Persistence_representations/persistence_intervals.cpp + * @example Persistence_representations/persistence_vectors.cpp + * @example Persistence_representations/persistence_heat_maps.cpp + * @example Persistence_representations/persistence_landscape_on_grid.cpp + * @example Persistence_representations/persistence_landscape.cpp + * @example Tangential_complex/example_basic.cpp + * @example Tangential_complex/example_with_perturb.cpp + * @example Subsampling/example_custom_kernel.cpp + * @example Subsampling/example_choose_n_farthest_points.cpp + * @example Subsampling/example_sparsify_point_set.cpp + * @example Subsampling/example_pick_n_random_points.cpp + * @example Nerve_GIC/CoordGIC.cpp + * @example Nerve_GIC/Nerve.cpp + * @example Nerve_GIC/FuncGIC.cpp + * @example Nerve_GIC/VoronoiGIC.cpp + * @example Spatial_searching/example_spatial_searching.cpp + * @example Alpha_complex/alpha_complex_3d_persistence.cpp + * @example Alpha_complex/alpha_complex_persistence.cpp + * @example Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp + * @example Bottleneck_distance/bottleneck_distance.cpp + * @example Witness_complex/weak_witness_persistence.cpp + * @example Witness_complex/strong_witness_persistence.cpp + * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp + * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp + * @example common/off_file_from_shape_generator.cpp + * @example Rips_complex/rips_distance_matrix_persistence.cpp + * @example Rips_complex/rips_persistence.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp + * @example Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp + * @example Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp + * @example Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp + * @example Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp + * @example Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp + * @example Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp + * @example Persistence_representations/persistence_heat_maps/create_pssk.cpp + * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp + * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp + * @example Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp + * @example Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp + * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp + * @example Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp + * @example Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp + * @example Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp + * @example Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp + * @example Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp + * @example Persistence_representations/persistence_vectors/average_persistence_vectors.cpp + * @example Persistence_representations/persistence_vectors/create_persistence_vectors.cpp + * @example Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp + * @example Persistence_representations/persistence_landscapes/average_landscapes.cpp + * @example Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp + * @example Persistence_representations/persistence_landscapes/create_landscapes.cpp + * @example Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp + * @example Persistence_representations/persistence_landscapes/plot_landscapes.cpp + */ + diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html index 7b4cdc5c..a557922b 100644 --- a/src/common/doc/footer.html +++ b/src/common/doc/footer.html @@ -6,24 +6,18 @@ <!--BEGIN PROJECT_NAME--> $projectname <!--BEGIN PROJECT_NUMBER--> Version $projectnumber<!--END PROJECT_NUMBER--> <!--BEGIN PROJECT_BRIEF--> - $projectbrief<!--END PROJECT_BRIEF--> +<!--BEGIN PROJECT_BRIEF--> - Copyright : GPL v3<!--END PROJECT_BRIEF--> <!--END PROJECT_NAME--> </td> <td class="network-entypo"> <!--BEGIN GENERATE_TREEVIEW--> $generatedby <a href="http://www.doxygen.org/index.html"> - <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/></a> $doxygenversion + Doxygen</a> $doxygenversion <!--END GENERATE_TREEVIEW--> </td> </tr> </table> -<!--BEGIN !GENERATE_TREEVIEW--> -<hr class="footer"/><address class="footer"><small> tralala -$generatedby  <a href="http://www.doxygen.org/index.html"> -<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/> -</a> $doxygenversion -</small></address> -<!--END !GENERATE_TREEVIEW--> </body> </html> diff --git a/src/common/doc/header.html b/src/common/doc/header.html index 53b5c0a2..9c514381 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -56,6 +56,8 @@ $extrastylesheet <ul class="dropdown"> <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li> <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/file/37113/GUDHI_2.0.0_OSX_UTILS.beta.tar.gz" target="_blank">Utils for Mac OSx</a></li> + <li><a href="https://gforge.inria.fr/frs/download.php/file/37112/GUDHI_2.0.0_WIN64_UTILS.beta.zip" target="_blank">Utils for Win x64</a></li> </ul> </li> <li class="divider"></li> @@ -66,6 +68,8 @@ $extrastylesheet <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li> <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li> + <li><a href="http://gudhi.gforge.inria.fr/utils/">Utilities</a></li> + <li><a href="http://bertrand.michel.perso.math.cnrs.fr/Enseignements/TDA-Gudhi-Python.html" target="_blank">Tutorial</a></li> </ul> </li> <li class="divider"></li> diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h new file mode 100644 index 00000000..25675cc5 --- /dev/null +++ b/src/common/doc/installation.h @@ -0,0 +1,263 @@ +/*! \page installation GUDHI installation + * \tableofcontents + * As GUDHI is a header only library, there is no need to install the library. + * + * Examples of GUDHI headers inclusion can be found in \ref demos. + * + * \section compiling Compiling + * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or + * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. + * + * \subsection demos Demos and examples + * To build the demos and examples, run the following commands in a terminal: +\verbatim cd /path-to-gudhi/ +mkdir build +cd build/ +cmake .. +make \endverbatim + * A list of examples is available <a href="examples.html">here</a>. + * + * \subsection testsuites Test suites + * To test your build, run the following command in a terminal: + * \verbatim make test \endverbatim + * + * \subsection documentationgeneration Documentation + * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required. + * Run the following command in a terminal: +\verbatim +make doxygen +# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/ +# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder` +\endverbatim + * + * \section optionallibrary Optional third-party library + * \subsection gmp GMP + * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision + * arithmetic, operating on signed integers, rational numbers, and floating point numbers. + * + * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic + * Library</a> (GMP) and will not be built if GMP is not installed: + * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> + * Persistent_cohomology/rips_multifield_persistence.cpp</a> + * + * Having GMP version 4.2 or higher installed is recommended. + * + * \subsection cgal CGAL + * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ + * library which provides easy access to efficient and reliable geometric algorithms. + * + * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even + * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version ≥ 4.8.0), thereafter you will be able to compile + * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> + * + * Having CGAL version 4.4.0 or higher installed is recommended. The procedure to install this library according to + * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html + * + * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms + * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> + * + * The following examples/utilities require CGAL version ≥ 4.6.0: + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_strong_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> + * Witness_complex/example_witness_complex_sphere.cpp</a> + * + * The following example requires CGAL version ≥ 4.7.0: + * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_off.cpp</a> + * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> + * Persistent_cohomology/custom_persistence_sort.cpp</a> + * + * The following example requires CGAL version ≥ 4.8.1: + * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> + * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> + * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html"> + * Bottleneck_distance/bottleneck_basic_example.cpp</a> + * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html"> + * Bottleneck_distance/bottleneck_distance.cpp</a> + * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html"> + * Nerve_GIC/CoordGIC.cpp</a> + * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html"> + * Nerve_GIC/FuncGIC.cpp</a> + * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html"> + * Nerve_GIC/Nerve.cpp</a> + * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html"> + * Nerve_GIC/VoronoiGIC.cpp</a> + * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> + * Spatial_searching/example_spatial_searching.cpp</a> + * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> + * Subsampling/example_choose_n_farthest_points.cpp</a> + * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> + * Subsampling/example_custom_kernel.cpp</a> + * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> + * Subsampling/example_pick_n_random_points.cpp</a> + * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> + * Subsampling/example_sparsify_point_set.cpp</a> + * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> + * Tangential_complex/example_basic.cpp</a> + * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> + * Tangential_complex/example_with_perturb.cpp</a> + * + * \subsection eigen3 Eigen3 + * The \ref alpha_complex data structure and few examples requires + * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra: + * matrices, vectors, numerical solvers, and related algorithms. + * + * The following examples/utilities require the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be + * built if Eigen3 is not installed: + * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_off.cpp</a> + * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> + * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> + * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> + * Persistent_cohomology/custom_persistence_sort.cpp</a> + * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> + * Spatial_searching/example_spatial_searching.cpp</a> + * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> + * Subsampling/example_choose_n_farthest_points.cpp</a> + * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> + * Subsampling/example_custom_kernel.cpp</a> + * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> + * Subsampling/example_pick_n_random_points.cpp</a> + * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> + * Subsampling/example_sparsify_point_set.cpp</a> + * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> + * Tangential_complex/example_basic.cpp</a> + * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> + * Tangential_complex/example_with_perturb.cpp</a> + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_strong_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> + * Witness_complex/example_witness_complex_sphere.cpp</a> + * + * \subsection tbb Threading Building Blocks + * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel® TBB</a> lets you easily write parallel + * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have + * future-proof scalability. + * + * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. + * + * The following examples/utilities are using Intel® TBB if installed: + * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_off.cpp</a> + * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> + * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html"> + * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a> + * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html"> + * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a> + * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html"> + * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a> + * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html"> + * Nerve_GIC/CoordGIC.cpp</a> + * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html"> + * Nerve_GIC/FuncGIC.cpp</a> + * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html"> + * Nerve_GIC/Nerve.cpp</a> + * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html"> + * Nerve_GIC/VoronoiGIC.cpp</a> + * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html"> + * Simplex_tree/simple_simplex_tree.cpp</a> + * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> + * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html"> + * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> + * \li <a href="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html"> + * Simplex_tree/graph_expansion_with_blocker.cpp</a> + * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> + * Persistent_cohomology/alpha_complex_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> + * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> + * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html"> + * Persistent_cohomology/persistence_from_file.cpp</a> + * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html"> + * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> + * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> + * Persistent_cohomology/plain_homology.cpp</a> + * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> + * Persistent_cohomology/rips_multifield_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> + * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> + * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> + * Persistent_cohomology/custom_persistence_sort.cpp</a> + * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html"> + * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> + * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html"> + * Rips_complex/example_rips_complex_from_off_file.cpp</a> + * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> + * Rips_complex/rips_distance_matrix_persistence.cpp</a> + * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> + * Rips_complex/rips_persistence.cpp</a> + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_nearest_landmark_table_8cpp-example.html"> + * Witness_complex/example_nearest_landmark_table.cpp</a> + * + * \section Contributions Bug reports and contributions + * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: + * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + * + * GUDHI is open to external contributions. If you want to join our development team, please contact us. + * +*/ + +/*! \page Citation Acknowledging the GUDHI library + * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use + * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages. + * Feel free to contact us in case you have any question or remark on this topic. + * + * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications + * directly related to the GUDHI library. + * \section GudhiBibtex GUDHI bibtex + * \verbinclude biblio/how_to_cite_gudhi.bib +*/ diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 148ee670..b3e9ea03 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -93,7 +93,7 @@ </td> </tr> </table> - \subsection CoverComplexDataStructure Cover Complexes: Nerves and Graph Induced Complexes + \subsection CoverComplexDataStructure Cover Complexes \image html "gicvisu.jpg" "Graph Induced Complex of a point cloud." <table border="0"> <tr> @@ -101,6 +101,7 @@ <b>Author:</b> Mathieu Carrière<br> <b>Introduced in:</b> GUDHI 2.1.0<br> <b>Copyright:</b> GPL v3<br> + <b>Requires:</b> \ref cgal ≥ 4.8.1 </td> <td width="75%"> Nerves and Graph Induced Complexes are cover complexes, i.e. simplicial complexes that provably contain @@ -250,305 +251,3 @@ </table> */ - -/*! \page installation GUDHI installation - * \tableofcontents - * As GUDHI is a header only library, there is no need to install the library. - * - * Examples of GUDHI headers inclusion can be found in \ref demos. - * - * \section compiling Compiling - * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or - * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. - * - * \subsection demos Demos and examples - * To build the demos and examples, run the following commands in a terminal: -\verbatim cd /path-to-gudhi/ -mkdir build -cd build/ -cmake .. -make \endverbatim - * A list of examples is available <a href="examples.html">here</a>. - * - * \subsection testsuites Test suites - * To test your build, run the following command in a terminal: - * \verbatim make test \endverbatim - * - * \subsection documentationgeneration Documentation - * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required. - * Run the following command in a terminal: -\verbatim -make doxygen -# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/ -# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder` -\endverbatim - * - * \section optionallibrary Optional third-party library - * \subsection gmp GMP - * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision - * arithmetic, operating on signed integers, rational numbers, and floating point numbers. - * - * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic - * Library</a> (GMP) and will not be built if GMP is not installed: - * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_persistence.cpp</a> - * - * Having GMP version 4.2 or higher installed is recommended. - * - * \subsection cgal CGAL - * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ - * library which provides easy access to efficient and reliable geometric algorithms. - * - * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even - * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version ≥ 4.8.0), thereafter you will be able to compile - * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> - * - * Having CGAL version 4.4.0 or higher installed is recommended. The procedure to install this library according to - * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html - * - * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms - * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: - * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - * - * The following examples/utilities require CGAL version ≥ 4.6.0: - * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_strong_witness_complex_off.cpp</a> - * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_witness_complex_off.cpp</a> - * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> - * Witness_complex/example_witness_complex_sphere.cpp</a> - * - * The following example requires CGAL version ≥ 4.7.0: - * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * - * The following example requires CGAL version ≥ 4.8.1: - * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> - * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> - * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html"> - * Bottleneck_distance/bottleneck_basic_example.cpp</a> - * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html"> - * Bottleneck_distance/bottleneck_distance.cpp</a> - * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> - * Spatial_searching/example_spatial_searching.cpp</a> - * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> - * Subsampling/example_choose_n_farthest_points.cpp</a> - * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> - * Subsampling/example_custom_kernel.cpp</a> - * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> - * Subsampling/example_pick_n_random_points.cpp</a> - * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> - * Subsampling/example_sparsify_point_set.cpp</a> - * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> - * Tangential_complex/example_basic.cpp</a> - * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> - * Tangential_complex/example_with_perturb.cpp</a> - * - * \subsection eigen3 Eigen3 - * The \ref alpha_complex data structure and few examples requires - * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra: - * matrices, vectors, numerical solvers, and related algorithms. - * - * The following examples/utilities require the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be - * built if Eigen3 is not installed: - * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> - * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> - * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> - * Spatial_searching/example_spatial_searching.cpp</a> - * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> - * Subsampling/example_choose_n_farthest_points.cpp</a> - * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> - * Subsampling/example_custom_kernel.cpp</a> - * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> - * Subsampling/example_pick_n_random_points.cpp</a> - * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> - * Subsampling/example_sparsify_point_set.cpp</a> - * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> - * Tangential_complex/example_basic.cpp</a> - * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> - * Tangential_complex/example_with_perturb.cpp</a> - * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_strong_witness_complex_off.cpp</a> - * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_witness_complex_off.cpp</a> - * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> - * Witness_complex/example_witness_complex_sphere.cpp</a> - * - * \subsection tbb Threading Building Blocks - * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel® TBB</a> lets you easily write parallel - * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have - * future-proof scalability. - * - * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. - * - * The following examples/utilities are using Intel® TBB if installed: - * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html"> - * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a> - * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html"> - * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a> - * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html"> - * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a> - * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html"> - * Simplex_tree/simple_simplex_tree.cpp</a> - * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html"> - * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - * \li <a href="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html"> - * Simplex_tree/graph_expansion_with_blocker.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> - * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> - * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html"> - * Persistent_cohomology/persistence_from_file.cpp</a> - * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html"> - * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> - * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> - * Persistent_cohomology/plain_homology.cpp</a> - * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> - * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> - * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html"> - * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> - * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html"> - * Rips_complex/example_rips_complex_from_off_file.cpp</a> - * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> - * Rips_complex/rips_distance_matrix_persistence.cpp</a> - * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> - * Rips_complex/rips_persistence.cpp</a> - * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="_witness_complex_2example_nearest_landmark_table_8cpp-example.html"> - * Witness_complex/example_nearest_landmark_table.cpp</a> - * - * \section Contributions Bug reports and contributions - * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: - * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim - * - * GUDHI is open to external contributions. If you want to join our development team, please contact us. - * -*/ - -/*! \page Citation Acknowledging the GUDHI library - * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use - * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages. - * Feel free to contact us in case you have any question or remark on this topic. - * - * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications - * directly related to the GUDHI library. - * \section GudhiBibtex GUDHI bibtex - * \verbinclude biblio/how_to_cite_gudhi.bib -*/ - -// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments -/*! @file Examples - * @example Alpha_complex/Alpha_complex_from_off.cpp - * @example Alpha_complex/Alpha_complex_from_points.cpp - * @example Alpha_complex/alpha_complex_3d_persistence.cpp - * @example Alpha_complex/alpha_complex_persistence.cpp - * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp - * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp - * @example Bottleneck_distance/bottleneck_basic_example.cpp - * @example Bottleneck_distance/bottleneck_distance.cpp - * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp - * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * @example common/example_CGAL_3D_points_off_reader.cpp - * @example common/example_CGAL_points_off_reader.cpp - * @example Contraction/Garland_heckbert.cpp - * @example Contraction/Rips_contraction.cpp - * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.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/custom_persistence_sort.cpp - * @example Persistent_cohomology/rips_persistence_step_by_step.cpp - * @example Rips_complex/example_one_skeleton_rips_from_points.cpp - * @example Rips_complex/example_rips_complex_from_off_file.cpp - * @example Rips_complex/rips_persistence.cpp - * @example Rips_complex/rips_distance_matrix_persistence.cpp - * @example Simplex_tree/mini_simplex_tree.cpp - * @example Simplex_tree/simple_simplex_tree.cpp - * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp - * @example Simplex_tree/graph_expansion_with_blocker.cpp - * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp - * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp - * @example Skeleton_blocker/Skeleton_blocker_link.cpp - * @example Spatial_searching/example_spatial_searching.cpp - * @example Subsampling/example_choose_n_farthest_points.cpp - * @example Subsampling/example_custom_kernel.cpp - * @example Subsampling/example_pick_n_random_points.cpp - * @example Subsampling/example_sparsify_point_set.cpp - * @example Tangential_complex/example_basic.cpp - * @example Tangential_complex/example_with_perturb.cpp - * @example Witness_complex/example_nearest_landmark_table.cpp - * @example Witness_complex/example_strong_witness_complex_off.cpp - * @example Witness_complex/example_witness_complex_off.cpp - * @example Witness_complex/example_witness_complex_sphere.cpp - * @example Witness_complex/weak_witness_persistence.cpp - * @example Witness_complex/strong_witness_persistence.cpp - */ - diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h index 7ae5d356..8394a062 100644 --- a/src/common/include/gudhi/Unitary_tests_utils.h +++ b/src/common/include/gudhi/Unitary_tests_utils.h @@ -25,6 +25,7 @@ #include <boost/test/unit_test.hpp> #include <iostream> +#include <limits> // for std::numeric_limits<> template<typename FloatingType > void GUDHI_TEST_FLOAT_EQUALITY_CHECK(FloatingType a, FloatingType b, diff --git a/src/common/utilities/README b/src/common/utilities/README deleted file mode 100644 index 18fa8cc4..00000000 --- a/src/common/utilities/README +++ /dev/null @@ -1,19 +0,0 @@ -# Pointset generator # - -## `off_file_from_shape_generator` ## - -Generates a pointset and save it in an OFF file. Command-line is: -`off_file_from_shape_generator on|in sphere|cube|curve|torus|klein <filename> <num_points> <dimension> <parameter1> <parameter2>...` - -Warning: "on cube" generator is not available! - -Examples: - -* Generate an onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2: -`off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2` - -* Generate an inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default): -`off_file_from_shape_generator in sphere inSphere.off 100 2` - -* Generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8: -`off_file_from_shape_generator in cube inCube.off 10000 3 5.8` diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md new file mode 100644 index 00000000..284715d4 --- /dev/null +++ b/src/common/utilities/pointsetgenerator.md @@ -0,0 +1,33 @@ + + +# common # + +## off_file_from_shape_generator ## + +Generates a pointset and save it in an OFF file. Command-line is: + +``` +off_file_from_shape_generator on|in sphere|cube|curve|torus|klein <filename> <num_points> <dimension> <parameter1> <parameter2>... +``` + +Warning: "on cube" generator is not available! + +**Examples** + +``` +off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2 +``` + +* Generates an onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2. + +``` +off_file_from_shape_generator in sphere inSphere.off 100 2 +``` + +* Generates an inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default). + +``` +off_file_from_shape_generator in cube inCube.off 10000 3 5.8 +``` + +* Generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8. |