diff options
Diffstat (limited to 'src/common')
-rw-r--r-- | src/common/doc/file_formats.h | 66 | ||||
-rw-r--r-- | src/common/doc/main_page.h | 147 | ||||
-rw-r--r-- | src/common/include/gudhi/Debug_utils.h | 4 | ||||
-rw-r--r-- | src/common/include/gudhi/Unitary_tests_utils.h | 39 | ||||
-rw-r--r-- | src/common/include/gudhi/distance_functions.h | 32 | ||||
-rw-r--r-- | src/common/include/gudhi/graph_simplicial_complex.h | 63 | ||||
-rw-r--r-- | src/common/utilities/README | 26 |
7 files changed, 305 insertions, 72 deletions
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h index d715aa4d..c60ed15a 100644 --- a/src/common/doc/file_formats.h +++ b/src/common/doc/file_formats.h @@ -53,6 +53,72 @@ namespace Gudhi { Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or `Gudhi::read_persistence_intervals_in_dimension()`. + + + \section FileFormatsIsoCuboid Iso-cuboid + + Such a file describes an iso-oriented cuboid with diagonal opposite vertices (min_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is:<br> + \verbatim + min_x min_y [min_z ...] + max_x max_y [max_z ...] + \endverbatim + + Here is a simple sample file in the 3D case: + \verbatim + -1. -1. -1. + 1. 1. 1. + \endverbatim + + + \section FileFormatsPerseus Perseus + + This file format is the format used by the Perseus software + (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda. + The first line contains a number d begin the dimension of the + bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3 + in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8 + 20 4 7 6 5 in the example below). + + \image html "exampleBitmap.png" "Example of a input data." + + The input file for the following complex is: + \verbatim + 2 + 3 + 3 + 1 + 4 + 6 + 8 + 20 + 4 + 7 + 6 + 5 + \endverbatim + + To indicate periodic boundary conditions in a + given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance: + + \verbatim + 2 + -3 + 3 + 1 + 4 + 6 + 8 + 20 + 4 + 7 + 6 + 5 + \endverbatim + + Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. + + Other sample files can be found in the `data/bitmap` folder. + */ } // namespace Gudhi diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 34bf6c22..148ee670 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -99,7 +99,7 @@ <tr> <td width="25%"> <b>Author:</b> Mathieu Carrière<br> - <b>Introduced in:</b> GUDHI 2.0.1<br> + <b>Introduced in:</b> GUDHI 2.1.0<br> <b>Copyright:</b> GPL v3<br> </td> <td width="75%"> @@ -170,6 +170,7 @@ </table> \section Toolbox Toolbox + \subsection BottleneckDistanceToolbox Bottleneck distance \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge" <table border="0"> @@ -229,7 +230,25 @@ <b>User manual:</b> \ref persistent_cohomology - <b>Reference manual:</b> Gudhi::persistent_cohomology::Persistent_cohomology </td> </tr> +</table> + \subsection PersistenceRepresentationsToolbox Persistence representations + \image html "average_landscape.png" "Persistence representations" +<table border="0"> + <tr> + <td width="25%"> + <b>Author:</b> Pawel Dlotko<br> + <b>Introduced in:</b> GUDHI 2.1.0<br> + <b>Copyright:</b> GPL v3<br> + </td> + <td width="75%"> + It contains implementation of various representations of persistence diagrams; diagrams themselves, persistence + landscapes (rigorous and grid version), persistence heath maps, vectors and others. It implements basic + functionalities which are neccessary to use persistence in statistics and machine learning.<br> + <b>User manual:</b> \ref Persistence_representations + </td> + </tr> </table> + */ /*! \page installation GUDHI installation @@ -287,30 +306,38 @@ make doxygen * 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 require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms + * 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="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.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="_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 example requires CGAL version ≥ 4.6.0: - * \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html"> - * Witness_complex/witness_complex_sphere.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="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_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> * @@ -319,8 +346,8 @@ make doxygen * 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_example_8cpp-example.html"> - * Bottleneck_distance/bottleneck_read_file_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"> @@ -341,18 +368,18 @@ make doxygen * <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 example requires the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be + * 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_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> @@ -369,6 +396,16 @@ make doxygen * 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 @@ -377,21 +414,27 @@ make doxygen * * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. * - * The following examples are using Intel® TBB if installed: + * 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/Bitmap_cubical_complex.cpp</a> + * 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/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a> + * 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="_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="_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"> @@ -412,27 +455,31 @@ make doxygen * 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_distance_matrix_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_distance_matrix_persistence.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_8cpp-example.html"> - * Persistent_cohomology/rips_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_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * \li <a href="_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 @@ -456,32 +503,32 @@ make doxygen /*! @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_read_file_example.cpp - * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp - * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.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/alpha_complex_3d_persistence.cpp - * @example Persistent_cohomology/alpha_complex_persistence.cpp * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * @example Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp - * @example Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp - * @example Persistent_cohomology/periodic_alpha_complex_3d_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_distance_matrix_persistence.cpp - * @example Persistent_cohomology/rips_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 @@ -499,9 +546,9 @@ make doxygen * @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_strong_witness_persistence.cpp * @example Witness_complex/example_witness_complex_off.cpp - * @example Witness_complex/example_witness_complex_persistence.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/Debug_utils.h b/src/common/include/gudhi/Debug_utils.h index 8ed3b7b3..90d3cf47 100644 --- a/src/common/include/gudhi/Debug_utils.h +++ b/src/common/include/gudhi/Debug_utils.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -32,7 +32,7 @@ // GUDHI_CHECK throw an exception if expression is false in debug mode, but does nothing in release mode // Could assert in release mode, but cmake sets NDEBUG (for "NO DEBUG") in this mode, means assert does nothing. #ifdef GUDHI_DEBUG - #define GUDHI_CHECK(expression, excpt) if ((expression) == 0) throw excpt + #define GUDHI_CHECK(expression, excpt) ((expression) ? (void) 0 : (throw excpt)) #define GUDHI_CHECK_code(CODE) CODE #else #define GUDHI_CHECK(expression, excpt) (void) 0 diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h new file mode 100644 index 00000000..7ae5d356 --- /dev/null +++ b/src/common/include/gudhi/Unitary_tests_utils.h @@ -0,0 +1,39 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2017 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ +#ifndef UNITARY_TESTS_UTILS_H_ +#define UNITARY_TESTS_UTILS_H_ + +#include <boost/test/unit_test.hpp> + +#include <iostream> + +template<typename FloatingType > +void GUDHI_TEST_FLOAT_EQUALITY_CHECK(FloatingType a, FloatingType b, + FloatingType epsilon = std::numeric_limits<FloatingType>::epsilon()) { +#ifdef DEBUG_TRACES + std::cout << "GUDHI_TEST_FLOAT_EQUALITY_CHECK - " << a << " versus " << b + << " | diff = " << std::fabs(a - b) << " - epsilon = " << epsilon << std::endl; +#endif + BOOST_CHECK(std::fabs(a - b) < epsilon); +} + +#endif // UNITARY_TESTS_UTILS_H_ diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index f6e2ab5a..3a5d1fd5 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -23,9 +23,14 @@ #ifndef DISTANCE_FUNCTIONS_H_ #define DISTANCE_FUNCTIONS_H_ +#include <gudhi/Debug_utils.h> + +#include <boost/range/metafunctions.hpp> + #include <cmath> // for std::sqrt #include <type_traits> // for std::decay #include <iterator> // for std::begin, std::end +#include <utility> namespace Gudhi { @@ -37,16 +42,29 @@ namespace Gudhi { * have the same dimension. */ class Euclidean_distance { public: + // boost::range_value is not SFINAE-friendly so we cannot use it in the return type template< typename Point > - auto operator()(const Point& p1, const Point& p2) const -> typename std::decay<decltype(*std::begin(p1))>::type { - auto it1 = p1.begin(); - auto it2 = p2.begin(); - typename Point::value_type dist = 0.; - for (; it1 != p1.end(); ++it1, ++it2) { - typename Point::value_type tmp = (*it1) - (*it2); + typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type + operator()(const Point& p1, const Point& p2) const { + auto it1 = std::begin(p1); + auto it2 = std::begin(p2); + typedef typename boost::range_value<Point>::type NT; + NT dist = 0; + for (; it1 != std::end(p1); ++it1, ++it2) { + GUDHI_CHECK(it2 != std::end(p2), "inconsistent point dimensions"); + NT tmp = *it1 - *it2; dist += tmp*tmp; } - return std::sqrt(dist); + GUDHI_CHECK(it2 == std::end(p2), "inconsistent point dimensions"); + using std::sqrt; + return sqrt(dist); + } + template< typename T > + T operator() (const std::pair< T, T >& f, const std::pair< T, T >& s) const { + T dx = f.first - s.first; + T dy = f.second - s.second; + using std::sqrt; + return sqrt(dx*dx + dy*dy); } }; diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 5fe7c826..d84421b2 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -28,6 +28,9 @@ #include <utility> // for pair<> #include <vector> #include <map> +#include <tuple> // for std::tie + +namespace Gudhi { /* Edge tag for Boost PropertyGraph. */ struct edge_filtration_t { @@ -39,4 +42,64 @@ struct vertex_filtration_t { typedef boost::vertex_property_tag kind; }; +template <typename SimplicialComplexForProximityGraph> +using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS +, boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > +, boost::property < edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >>; + +/** \brief Computes the proximity graph of the points. + * + * If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the + * distance function between points u and v is smaller than threshold. + * + * \tparam ForwardPointRange furnishes `.begin()` and `.end()` methods. + * + * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where + * `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`. + */ +template< typename SimplicialComplexForProximityGraph + , typename ForwardPointRange + , typename Distance > +Proximity_graph<SimplicialComplexForProximityGraph> compute_proximity_graph( + const ForwardPointRange& points, + typename SimplicialComplexForProximityGraph::Filtration_value threshold, + Distance distance) { + using Vertex_handle = typename SimplicialComplexForProximityGraph::Vertex_handle; + using Filtration_value = typename SimplicialComplexForProximityGraph::Filtration_value; + + std::vector<std::pair< Vertex_handle, Vertex_handle >> edges; + std::vector< Filtration_value > edges_fil; + std::map< Vertex_handle, Filtration_value > vertices; + + Vertex_handle idx_u, idx_v; + Filtration_value fil; + idx_u = 0; + for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { + idx_v = idx_u + 1; + for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { + fil = distance(*it_u, *it_v); + if (fil <= threshold) { + edges.emplace_back(idx_u, idx_v); + edges_fil.push_back(fil); + } + } + ++idx_u; + } + + // Points are labeled from 0 to idx_u-1 + Proximity_graph<SimplicialComplexForProximityGraph> skel_graph(edges.begin(), edges.end(), edges_fil.begin(), idx_u); + + auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); + + typename boost::graph_traits<Proximity_graph<SimplicialComplexForProximityGraph>>::vertex_iterator vi, vi_end; + for (std::tie(vi, vi_end) = boost::vertices(skel_graph); + vi != vi_end; ++vi) { + boost::put(vertex_prop, *vi, 0.); + } + + return skel_graph; +} + +} // namespace Gudhi + #endif // GRAPH_SIMPLICIAL_COMPLEX_H_ diff --git a/src/common/utilities/README b/src/common/utilities/README index dc841521..18fa8cc4 100644 --- a/src/common/utilities/README +++ b/src/common/utilities/README @@ -1,19 +1,19 @@ -======================= off_file_from_shape_generator ================================== +# Pointset generator # -Example of use : +## `off_file_from_shape_generator` ## -*** on|in sphere|cube|curve|torus|klein 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>...` -./off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2 +Warning: "on cube" generator is not available! - => generates a onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2 +Examples: -./off_file_from_shape_generator in sphere inSphere.off 100 2 +* 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 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 - -!! Warning: hypegenerator on cube is not available !! +* 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` |