diff options
Diffstat (limited to 'src')
3 files changed, 75 insertions, 17 deletions
diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 6993b0ad..ac72dcc4 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -3,6 +3,7 @@ * library for computational topology. * * Author(s): Vincent Rouvreau + * Pawel Dlotko - 2017 - Swansea University, UK * * Copyright (C) 2014 INRIA * @@ -112,6 +113,12 @@ int main(int argc, char **argv) { std::cerr << "Unable to read file " << cuboid_file << std::endl; exit(-1); } + //Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. + if ((x_max-x_min != y_max-y_min) || (x_max-x_min != z_max-z_min) || (z_max-z_min != y_max-y_min)) + { + std::cerr << "The size of the cuboid in every directions is not the same." << std::endl; + exit(-1); + } // Retrieve the points std::vector<Point_3> lp = off_reader.get_point_cloud(); @@ -121,7 +128,12 @@ int main(int argc, char **argv) { // Heuristic for inserting large point sets (if pts is reasonably large) pdt.insert(lp.begin(), lp.end(), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible - if (pdt.is_triangulation_in_1_sheet()) pdt.convert_to_1_sheeted_covering(); + if (pdt.is_triangulation_in_1_sheet()) { + pdt.convert_to_1_sheeted_covering(); + } else { + std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; + exit(-1); + } std::cout << "Periodic Delaunay computed." << std::endl; // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp index 282b9180..f7a89454 100644 --- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -3,6 +3,7 @@ * library for computational topology. * * Author(s): Vincent Rouvreau + * Pawel Dlotko - 2017 - Swansea University, UK * * Copyright (C) 2014 INRIA * @@ -113,6 +114,24 @@ int main(int argc, char* const argv[]) { // Retrieve the points std::vector<Point_3> lp = off_reader.get_point_cloud(); + // Read iso_cuboid_3 information from file + std::ifstream iso_cuboid_str(argv[3]); + double x_min, y_min, z_min, x_max, y_max, z_max; + if (iso_cuboid_str.good()) { + iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max; + } else { + std::cerr << "Unable to read file " << argv[3] << std::endl; + usage(argv[0]); + } + //Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. + if ((x_max-x_min != y_max-y_min) || (x_max-x_min != z_max-z_min) || (z_max-z_min != y_max-y_min)) + { + std::cerr << "The size of the cuboid in every directions is not the same." << std::endl; + exit(-1); + } + + double maximal_possible_weigth = 0.015625 * (x_max-x_min) * (x_max-x_min); + // Read weights information from file std::ifstream weights_ifstr(argv[2]); std::vector<Weighted_point_3> wp; @@ -122,6 +141,14 @@ int main(int argc, char* const argv[]) { wp.reserve(lp.size()); // Attempt read the weight in a double format, return false if it fails while ((weights_ifstr >> weight) && (index < lp.size())) { + if (weight >= maximal_possible_weigth) + { + std::cerr << "At line " << (index + 1) << ", the weight (" << weight + << ") is more or equal to maximal possible weight (" << maximal_possible_weigth + << ") = 1/64*cuboid length squared, which is not an acceptable input." << std::endl; + exit(-1); + } + wp.push_back(Weighted_point_3(lp[index], weight)); index++; } @@ -134,23 +161,18 @@ int main(int argc, char* const argv[]) { usage(argv[0]); } - // Read iso_cuboid_3 information from file - std::ifstream iso_cuboid_str(argv[3]); - double x_min, y_min, z_min, x_max, y_max, z_max; - if (iso_cuboid_str.good()) { - iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max; - } else { - std::cerr << "Unable to read file " << argv[3] << std::endl; - usage(argv[0]); - } - // Define the periodic cube P3RT3 prt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); // Heuristic for inserting large point sets (if pts is reasonably large) prt.insert(wp.begin(), wp.end(), true); // As prt won't be modified anymore switch to 1-sheeted cover if possible - if (prt.is_triangulation_in_1_sheet()) prt.convert_to_1_sheeted_covering(); - std::cout << "Periodic Delaunay computed." << std::endl; + if (prt.is_triangulation_in_1_sheet()) { + prt.convert_to_1_sheeted_covering(); + } else { + std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; + exit(-1); + } + std::cout << "Weighted Periodic Delaunay computed." << std::endl; // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode // Maybe need to set it to GENERAL mode diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 62bbbfc5..5059bc33 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -165,7 +165,7 @@ outputs its persistence diagram. \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. -\code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 \endcode +\code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 2 0 0 inf 2 1 0.0682162 1.0001 @@ -177,7 +177,7 @@ Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> computes the persistent \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. Here, as CGAL computes the exact values, it is slower, but it is necessary when points are on a grid for instance. -\code $> ./exact_alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off 2 0.1 \endcode +\code $> ./exact_alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off -p 2 -m 0.1 \endcode \code Simplex_tree dim: 3 2 0 0 inf 2 2 0.0002 0.2028 \endcode @@ -187,7 +187,7 @@ Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> computes the persist \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the weighted alpha complex on points sampling from an OFF file and a weights file. \code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off -../../data/points/tore3D_300.weights 2 0.45 \endcode +../../data/points/tore3D_300.weights -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 2 0 -1 inf 2 1 -0.931784 0.000103311 @@ -208,8 +208,10 @@ Simplex_tree dim: 3 \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. +The second parameter is a \ref FileFormatsIsoCuboid file with coordinates of the periodic cuboid. +Note that the lengths of the sides of the periodic cuboid have to be the same. \code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off -../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 \endcode +../../data/points/iso_cuboid_3_in_0_1.txt -p 3 -m 1.0 \endcode \code Periodic Delaunay computed. Simplex_tree dim: 3 3 0 0 inf @@ -221,6 +223,28 @@ Simplex_tree dim: 3 3 2 0.005 inf 3 3 0.0075 inf \endcode +\li <a href="_persistent_cohomology_2weighted_periodic_alpha_complex_3d_persistence_8cpp-example.html"> +Persistent_cohomology/weighted_periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on weighted points from an OFF file. The +additional parameters of this program are:<br> +(a) The file with the weights of points. The file consist of a sequence of numbers (as many as points). +Note that the weight of each single point have to be bounded by 1/64 times the square of the diameter of +the cuboid.<br> +(b) A \ref FileFormatsIsoCuboid file with coordinates of the periodic cuboid. +Note that the lengths of the sides of the periodic cuboid have to be the same.<br> +\code $> ./weighted_periodic_alpha_complex_3d_persistence ../../data/points/shifted_sphere.off +../../data/points/shifted_sphere.weights ../../data/points/iso_cuboid_3_in_0_10.txt 3 1.0 \endcode +\code Weighted Periodic Delaunay computed. +Simplex_tree dim: 3 +3 0 -0.0001 inf +3 1 16.0264 inf +3 1 16.0273 inf +3 1 16.0303 inf +3 2 36.8635 inf +3 2 36.8704 inf +3 2 36.8838 inf +3 3 58.6783 inf \endcode + \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> Persistent_cohomology/plain_homology.cpp</a> computes the plain homology of a simple simplicial complex without filtration values. |