From 7f3ea79d26c78c8b2107a6a85feba933bd5512ac Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 27 Mar 2018 18:46:18 +0000 Subject: sb_wrapper working git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/toplex_map@3308 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c7400a11583b8b67483974664e410f4c77232fb1 --- src/common/doc/main_page.h | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) (limited to 'src/common/doc/main_page.h') diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index d6569f0c..71655824 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -133,6 +133,23 @@ + \subsection ToplexMapDataStructure Toplex Map + \image html "map.png" "Toplex map representation" + + + + + + \subsection WitnessComplexDataStructure Witness complex \image html "Witness_complex_representation.png" "Witness complex representation"
+ Author: François Godi
+ Introduced in: GUDHI 2.1.0
+ Copyright: GPL v3
+ 		+ The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices) + and secondly of a map which associate any vertex to a set of pointers toward all toplices + containing this vertex. + User manual: \ref toplex_map - Reference manual: Gudhi::Toplex_map +
-- cgit v1.2.3 From 9b8bb34ff06b08119b8fa1e78c260886287c5a92 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 3 Jul 2018 16:08:32 +0000 Subject: Documentation for Alpha complex 3d git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3664 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c6d824cdab7ac5ea79ce458dac666d35a9a21ab7 --- src/Alpha_complex/example/CMakeLists.txt | 10 - .../example/alpha_complex_3d_step_by_step.cpp | 309 +++++++++++++++++++++ src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 120 ++++++-- src/Alpha_complex/utilities/CMakeLists.txt | 2 +- src/Alpha_complex/utilities/alphacomplex.md | 101 ++++--- src/common/doc/examples.h | 4 - src/common/doc/installation.h | 20 +- src/common/doc/main_page.h | 2 +- 8 files changed, 454 insertions(+), 114 deletions(-) create mode 100644 src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp (limited to 'src/common/doc/main_page.h') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 5a66067c..af4bfd74 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -1,16 +1,6 @@ project(Alpha_complex_examples) if(CGAL_FOUND) - add_executable(alpha_complex_3d_step_by_step alpha_complex_3d_step_by_step.cpp) - target_link_libraries(alpha_complex_3d_step_by_step ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(alpha_complex_3d_step_by_step ${TBB_LIBRARIES}) - endif(TBB_FOUND) - - add_test(NAME Alpha_complex_example_alpha_complex_3d_step_by_step COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off") - # need CGAL 4.7 # cmake -DCGAL_DIR=~/workspace/CGAL-4.7 .. if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp b/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp new file mode 100644 index 00000000..d76402e5 --- /dev/null +++ b/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp @@ -0,0 +1,309 @@ +/* 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 + * + * 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 + +#if BOOST_VERSION >= 105400 +#include +#endif + +#include +#include + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +template +Vertex_list from_cell(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; +} + +template +Vertex_list from_facet(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; +} + +template +Vertex_list from_edge(const Edge_3& edg) { + Vertex_list the_list; + for (auto i : {edg.second, edg.third}) { +#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; +} + +template +Vertex_list from_vertex(const 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; +} + +// Alpha_shape_3 templates type definitions +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Vb = CGAL::Alpha_shape_vertex_base_3; +using Fb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using Triangulation_3 = CGAL::Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; + +// From file type definition +using Point_3 = Kernel::Point_3; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = + CGAL::Dispatch_output_iterator, + CGAL::cpp11::tuple >, + std::back_insert_iterator > > >; +using Cell_handle = Alpha_shape_3::Cell_handle; +using Facet = Alpha_shape_3::Facet; +using Edge_3 = Alpha_shape_3::Edge; +using Vertex_handle = Alpha_shape_3::Vertex_handle; + +#if BOOST_VERSION >= 105400 +using Vertex_list = boost::container::static_vector; +#else +using Vertex_list = std::vector; +#endif + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Simplex_tree_vector_vertex = std::vector; + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag); + +int main(int argc, char **argv) { + std::string off_file_points; + std::string output_file_diag; + + program_options(argc, argv, off_file_points, output_file_diag); + + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(off_file_points); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << off_file_points << std::endl; + exit(-1); + } + + // Retrieve the points + std::vector lp = off_reader.get_point_cloud(); + + // 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(); + 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(*cell); + count_cells++; + } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex; + 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.push_back(vertex); + map_cgal_simplex_tree.emplace(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.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 + simplex_tree.insert_simplex(the_simplex, filtr); + GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values"); + ++the_alpha_value_iterator; + } + +#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() << " "; +#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::streambuf* streambufffer; + std::ofstream ouput_file_stream; + if (output_file_diag != std::string()) { + ouput_file_stream.open(output_file_diag); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + output_stream << "Alpha complex is of dimension " << simplex_tree.dimension() << + " - " << simplex_tree.num_simplices() << " simplices - " << + simplex_tree.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + output_stream << " ( "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] "; + output_stream << std::endl; + } + + return 0; +} + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag) { + 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"); + + 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 and displays the 3D Alpha complex defined on a set of input points.\n \n"; + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + exit(-1); + } +} diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 50e344e8..1d171f7d 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -55,6 +55,22 @@ namespace Gudhi { namespace alpha_complex { +/** + * \class Alpha_complex_3d Alpha_complex_3d.h gudhi/Alpha_complex_3d.h + * \brief Alpha complex data structure for 3d specific case. + * + * \ingroup alpha_complex + * + * \details + * The data structure is constructing 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/) from a + * range of points or from an OFF file (cf. Points_off_reader). + * + * Please refer to \ref alpha_complex for examples. + * + * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. + * + */ template class Alpha_complex_3d { using Alpha_shape_3 = typename AlphaComplex3dOptions::Alpha_shape_3; @@ -106,15 +122,24 @@ public: } - /** \brief Alpha_complex constructor from a list of points. -* -* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. -* -* @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d -* -* The type InputPointRange must be a range for which std::begin and -* std::end return input iterators on a Kernel::Point_d. -*/ + /** \brief Alpha_complex constructor from a list of points and associated weights. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * Weights values are explained on CGAL Alpha + * shape and + * Regular + * triangulation documentation. + * + * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. + * + * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] weights Range of weights on points. Points must be in AlphaComplex3dOptions::Point_3 + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * The type WeightRange must be a range for which std::begin and + * std::end return an input iterator on a AlphaComplex3dOptions::Alpha_shape_3::FT. + */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights) { static_assert(AlphaComplex3dOptions::weighted, @@ -148,17 +173,29 @@ public: #endif // DEBUG_TRACES } - /** \brief Alpha_complex constructor from a list of points. -* -* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. -* -* @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d -* -* The type InputPointRange must be a range for which std::begin and -* std::end return input iterators on a Kernel::Point_d. -* -* @exception std::invalid_argument In case the number of simplices is more than Simplex_key type numeric limit. -*/ + /** \brief Alpha_complex constructor from a list of points and an iso-cuboid coordinates. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * + * Refer to the CGAL’s 3D Periodic + * Triangulations User Manual for more details. + * The periodicity is defined by an iso-oriented cuboid with diagonal opposite vertices (x_min, y_min, z_min) and + * (x_max, y_max, z_max). + * + * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. + * + * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] x_min Iso-oriented cuboid x_min. + * @param[in] y_min Iso-oriented cuboid y_min. + * @param[in] z_min Iso-oriented cuboid z_min. + * @param[in] x_max Iso-oriented cuboid x_max. + * @param[in] y_max Iso-oriented cuboid y_max. + * @param[in] z_max Iso-oriented cuboid z_max. + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. + */ template Alpha_complex_3d(const InputPointRange& points, Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, @@ -200,15 +237,40 @@ public: } - /** \brief Alpha_complex constructor from a list of points. -* -* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. -* -* @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d -* -* The type InputPointRange must be a range for which std::begin and -* std::end return input iterators on a Kernel::Point_d. -*/ + /** \brief Alpha_complex constructor from a list of points, associated weights and an iso-cuboid coordinates. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * + * Weights values are explained on CGAL Alpha + * shape and + * Regular + * triangulation documentation. + * + * Refer to the CGAL’s 3D Periodic + * Triangulations User Manual for more details. + * The periodicity is defined by an iso-oriented cuboid with diagonal opposite vertices (x_min, y_min, z_min) and + * (x_max, y_max, z_max). + * + * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. + * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. + * @exception std::invalid_argument In debug mode, if a weight is negative, zero, or greater than 1/64*cuboid length + * squared. + * + * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] weights Range of weights on points. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] x_min Iso-oriented cuboid x_min. + * @param[in] y_min Iso-oriented cuboid y_min. + * @param[in] z_min Iso-oriented cuboid z_min. + * @param[in] x_max Iso-oriented cuboid x_max. + * @param[in] y_max Iso-oriented cuboid y_max. + * @param[in] z_max Iso-oriented cuboid z_max. + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * The type WeightRange must be a range for which std::begin and + * std::end return an input iterator on a AlphaComplex3dOptions::Alpha_shape_3::FT. + * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. + */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights, Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index b43fb6e2..86e761ef 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -15,7 +15,7 @@ if(CGAL_FOUND) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index 0fe98837..7ae5f913 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -12,15 +12,18 @@ Leave the lines above as it is required by the web site generator 'Jekyll' ## alpha_complex_persistence ## -This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud. +This program computes the persistent homology with coefficient field Z/pZ of +the dD alpha complex built from a dD point cloud. The output diagram contains one bar per line, written with the convention: ``` p dim birth death ``` -where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, -and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). +where `dim` is the dimension of the homological feature, `birth` and `death` +are respectively the birth and death of the feature, and `p` is the +characteristic of the field *Z/pZ* used for homology coefficients (`p` must be +a prime number). **Usage** @@ -29,15 +32,20 @@ and `p` is the characteristic of the field *Z/pZ* used for homology coefficients ``` where -`` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). +`` is the path to the input point cloud in +[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). **Allowed options** * `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction. -* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +* `-o [ --output-file ]` Name of file in which the persistence diagram is +written. Default print in standard output. +* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value +for the Alpha complex construction. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the +coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature +to be recorded. Enter a negative value to see zero length intervals. **Example** @@ -51,13 +59,26 @@ N.B.: ## alpha_complex_3d_persistence ## -This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention: +This program computes the persistent homology with coefficient field Z/pZ of +the 3D alpha complex built from a 3D point cloud. +One can use exact computation. It is slower, but it is necessary when points +are on a grid for instance. +Alpha complex 3d can be weighted and/or periodic (refer to the +[CGAL's 3D Periodic Triangulations User Manual]( +https://doc.cgal.org/latest/Periodic_3_triangulation_3/index.html) +for more details). + +The output diagram contains +one bar per line, written with the convention: ``` p dim birth death ``` -where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). +where `dim` is the dimension of the homological feature, `birth` and `death` +are respectively the birth and death of the feature, and `p` is the +characteristic of the field *Z/pZ* used for homology coefficients (`p` must be +a prime number). **Usage** @@ -65,14 +86,25 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are alpha_complex_3d_persistence [options] ``` -where `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). +where `` is the path to the input point cloud in +[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). **Allowed options** * `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +* `-o [ --output-file ]` Name of file in which the persistence diagram is +written. Default print in standard output. +* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient +field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature +to be recorded. Enter a negative value to see zero length intervals. +* `-c [ --cuboid-file ]` is the path to the file describing the periodic domain. +It must be in the format described +[here](/doc/latest/fileformats.html#FileFormatsIsoCuboid). +* `-w [ --weight-file ]` is the path to the file containing the weights of the +points (one value per line). +* `-e [ --exact ]` for the exact computation version (not compatible with +weight and periodic version). **Example** @@ -84,49 +116,16 @@ N.B.: * `alpha_complex_3d_persistence` only accepts OFF files in dimension 3. * Filtration values are alpha square values. - - -## exact_alpha_complex_3d_persistence ## - -Same as `alpha_complex_3d_persistence`, but using exact computation. -It is slower, but it is necessary when points are on a grid for instance. +* Weights values are explained on CGAL +[Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0) +and +[Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation. -## weighted_alpha_complex_3d_persistence ## -Same as `alpha_complex_3d_persistence`, but using weighted points. -**Usage** - -``` - weighted_alpha_complex_3d_persistence [options] -``` - -where - -* `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). -* `` is the path to the file containing the weights of the points (one value per line). -**Allowed options** - -* `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. - -**Example** - -``` - weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights -p 2 -m 0.45 -``` - - -N.B.: - -* Weights values are explained on CGAL [Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0) -and [Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation. -* Filtration values are alpha square values. ## periodic_alpha_complex_3d_persistence ## diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 40f202c7..7c2a8f69 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -53,10 +53,6 @@ * @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 diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 12407c18..8f91e9c1 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -58,10 +58,6 @@ make doxygen * Library (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: * \li * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp * \li * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * @@ -84,8 +80,6 @@ make doxygen * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp * @@ -132,8 +126,8 @@ make doxygen * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp + * \li + * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp * \li @@ -179,12 +173,6 @@ make doxygen * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp * \li * Bitmap_cubical_complex/cubical_complex_persistence.cpp * \li @@ -223,10 +211,6 @@ make doxygen * Persistent_cohomology/rips_multifield_persistence.cpp * \li * Persistent_cohomology/rips_persistence_step_by_step.cpp - * \li - * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp - * \li - * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp * \li diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index db1e80ce..35b84d2e 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -29,7 +29,7 @@ Author: Vincent Rouvreau
Introduced in: GUDHI 1.3.0
Copyright: GPL v3
- Requires: \ref cgal ≥ 4.7.0 and \ref eigen3 + Requires: \ref cgal ≥ 4.11.0 and \ref eigen3
Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
-- cgit v1.2.3 From eef89bb492169faeb57dfdc65222b6a0483cb7c8 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 21 Nov 2018 08:49:55 +0000 Subject: Code review : Use # error instead of static_assert(false, ...) for CGAL version detection Doc review : Better document CGAL types (FT, Weighted_point_3, Point_3, ...) Weighted alpha complex 3d example simplification git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4009 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 187d7a08468c96192b3cb82c93a2df5b425290f9 --- .../benchmark/Alpha_complex_3d_benchmark.cpp | 4 +- .../Weighted_alpha_complex_3d_from_points.cpp | 12 +- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 129 ++++++++++++++------- .../test/Alpha_complex_3d_unit_test.cpp | 2 +- src/common/doc/main_page.h | 7 +- 5 files changed, 94 insertions(+), 60 deletions(-) (limited to 'src/common/doc/main_page.h') diff --git a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp index 96a4baf3..005a712a 100644 --- a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp +++ b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp @@ -116,7 +116,7 @@ void benchmark_weighted_points_on_torus_3D(const std::string& msg) { std::vector points_on_torus = Gudhi::generate_points_on_torus_3D(nb_points, 1.0, 0.5); using Point = typename Weighted_alpha_complex_3d::Point_3; - using Weighted_point = typename Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; + using Weighted_point = typename Weighted_alpha_complex_3d::Weighted_point_3; std::vector points; @@ -207,7 +207,7 @@ void benchmark_weighted_periodic_points(const std::string& msg) { << std::endl; using Point = typename Weighted_periodic_alpha_complex_3d::Point_3; - using Weighted_point = typename Weighted_periodic_alpha_complex_3d::Triangulation_3::Weighted_point; + using Weighted_point = typename Weighted_periodic_alpha_complex_3d::Weighted_point_3; std::vector points; for (double i = 0; i < nb_points; i++) { diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 3a69623f..734b4f37 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -11,21 +11,13 @@ using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Point = Weighted_alpha_complex_3d::Point_3; -using Weighted_point = Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; -using Vector_of_weighted_points = std::vector; -using Vector_of_weights = std::vector; +using Weighted_point = Weighted_alpha_complex_3d::Weighted_point_3; int main(int argc, char **argv) { - if (argc != 1) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - std::cerr << "Usage: " << (argv[0] - 1) << " \n"; - exit(-1); // ----- >> - } - // ---------------------------------------------------------------------------- // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- - Vector_of_weighted_points weighted_points; + std::vector weighted_points; weighted_points.push_back(Weighted_point(Point(1, -1, -1), 4.)); weighted_points.push_back(Weighted_point(Point(-1, 1, -1), 4.)); weighted_points.push_back(Weighted_point(Point(-1, -1, 1), 4.)); diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index ca3c5fc3..c33b9cf8 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -58,7 +58,7 @@ #if CGAL_VERSION_NR < 1041101000 // Make compilation fail - required for external projects - https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/10 -static_assert(false, "Alpha_complex_3d is only available for CGAL >= 4.11"); +# error Alpha_complex_3d is only available for CGAL >= 4.11 #endif namespace Gudhi { @@ -153,7 +153,7 @@ template ::Kernel; - using Exact_tag = typename std::conditional<(Complexity == complexity::FAST), CGAL::Tag_false, CGAL::Tag_true>::type; + using Exact_alpha_comparison_tag = typename std::conditional<(Complexity == complexity::FAST), CGAL::Tag_false, CGAL::Tag_true>::type; using TdsVb = typename std::conditional, CGAL::Triangulation_ds_vertex_base_3<>>::type; @@ -196,7 +196,7 @@ class Alpha_complex_3d { using Tvb = typename std::conditional, CGAL::Triangulation_vertex_base_3>::type; - using Vb = CGAL::Alpha_shape_vertex_base_3; + using Vb = CGAL::Alpha_shape_vertex_base_3; using TdsCb = typename std::conditional, CGAL::Triangulation_ds_cell_base_3<>>::type; @@ -204,43 +204,84 @@ class Alpha_complex_3d { using Tcb = typename std::conditional, CGAL::Triangulation_cell_base_3>::type; - using Cb = CGAL::Alpha_shape_cell_base_3; + using Cb = CGAL::Alpha_shape_cell_base_3; using Tds = CGAL::Triangulation_data_structure_3; // The other way to do a conditional type. Here there 4 possibilities, cannot use std::conditional template - struct Triangulation {}; + struct Triangulation_3 {}; template - struct Triangulation { - using Triangulation_3 = CGAL::Delaunay_triangulation_3; + struct Triangulation_3 { + using Dt = CGAL::Delaunay_triangulation_3; + using Weighted_point_3 = void; }; template - struct Triangulation { - using Triangulation_3 = CGAL::Regular_triangulation_3; + struct Triangulation_3 { + using Dt = CGAL::Regular_triangulation_3; + using Weighted_point_3 = typename Dt::Weighted_point; }; template - struct Triangulation { - using Triangulation_3 = CGAL::Periodic_3_Delaunay_triangulation_3; + struct Triangulation_3 { + using Dt = CGAL::Periodic_3_Delaunay_triangulation_3; + using Weighted_point_3 = void; }; template - struct Triangulation { - using Triangulation_3 = CGAL::Periodic_3_regular_triangulation_3; + struct Triangulation_3 { + using Dt = CGAL::Periodic_3_regular_triangulation_3; + using Weighted_point_3 = typename Dt::Weighted_point; }; - public: - using Triangulation_3 = typename Triangulation::Triangulation_3; - - using Alpha_shape_3 = CGAL::Alpha_shape_3; + /** \brief Is either Delaunay_triangulation_3 (Weighted = false and Periodic = false), + * Regular_triangulation_3 (Weighted = true and Periodic = false), + * Periodic_3_Delaunay_triangulation_3 (Weighted = false and Periodic = true) + * or Periodic_3_regular_triangulation_3 (Weighted = true and Periodic = true). + * + * This type is required by `Gudhi::alpha_complex::Alpha_complex_3d::Alpha_shape_3`. + * */ + using Dt = typename Triangulation_3::Dt; +public: + /** \brief The CGAL 3D Alpha + * Shapes type. + * + * The `Gudhi::alpha_complex::Alpha_complex_3d` is a wrapper on top of this class to ease the standard, weighted + * and/or periodic build of the Alpha complex 3d.*/ + using Alpha_shape_3 = CGAL::Alpha_shape_3; + + /** \brief The alpha values type. + * Must be compatible with double. */ + using FT = typename Alpha_shape_3::FT; + + /** \brief Gives public access to the Point_3 type. Here is a Point_3 constructor example: +\code{.cpp} +using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + +// x0 = 1., y0 = -1.1, z0 = -1.. +Alpha_complex_3d::Point_3 p0(1., -1.1, -1.); +\endcode + * */ using Point_3 = typename Kernel::Point_3; - private: - using Alpha_value_type = typename Alpha_shape_3::FT; + /** \brief Gives public access to the Weighted_point_3 type. A Weighted point can be constructed as follows: +\code{.cpp} +using Weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; + +// x0 = 1., y0 = -1.1, z0 = -1., weight = 4. +Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Point_3(1., -1.1, -1.), 4.); +\endcode + * + * Note: This type is defined to void if Alpha complex is not weighted. + * + * */ + using Weighted_point_3 = typename Triangulation_3::Weighted_point_3; + +private: using Dispatch = - CGAL::Dispatch_output_iterator, + CGAL::Dispatch_output_iterator, CGAL::cpp11::tuple>, - std::back_insert_iterator>>>; + std::back_insert_iterator>>>; using Cell_handle = typename Alpha_shape_3::Cell_handle; using Facet = typename Alpha_shape_3::Facet; @@ -252,12 +293,12 @@ class Alpha_complex_3d { /** \brief Alpha_complex constructor from a list of points. * * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or - * `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * `Alpha_complex_3d::Weighted_point_3`. * * @pre Available if Alpha_complex_3d is not Periodic. * * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a - * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Weighted_point_3`. */ template Alpha_complex_3d(const InputPointRange& points) { @@ -271,15 +312,15 @@ class Alpha_complex_3d { * * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. * - * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` - * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3`. + * @param[in] weights Range of weights on points. Weights shall be in double. * * @pre Available if Alpha_complex_3d is Weighted and not Periodic. * * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a `Alpha_complex_3d::Point_3`. * The type WeightRange must be a range for which std::begin and - * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. + * std::end return an input iterator on a double. */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights) { @@ -288,7 +329,6 @@ class Alpha_complex_3d { GUDHI_CHECK((weights.size() == points.size()), std::invalid_argument("Points number in range different from weights range number")); - using Weighted_point_3 = typename Triangulation_3::Weighted_point; std::vector weighted_points_3; std::size_t index = 0; @@ -307,7 +347,7 @@ class Alpha_complex_3d { * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. * * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or - * `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * `Alpha_complex_3d::Weighted_point_3`. * @param[in] x_min Iso-oriented cuboid x_min. * @param[in] y_min Iso-oriented cuboid y_min. * @param[in] z_min Iso-oriented cuboid z_min. @@ -318,14 +358,14 @@ class Alpha_complex_3d { * @pre Available if Alpha_complex_3d is Periodic. * * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a - * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Weighted_point_3`. * * @note In weighted version, please check weights are greater than zero, and lower than 1/64*cuboid length * squared. */ template - Alpha_complex_3d(const InputPointRange& points, Alpha_value_type x_min, Alpha_value_type y_min, - Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + Alpha_complex_3d(const InputPointRange& points, FT x_min, FT y_min, + FT z_min, FT x_max, FT y_max, FT z_max) { static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. GUDHI_CHECK( @@ -333,7 +373,7 @@ class Alpha_complex_3d { std::invalid_argument("The size of the cuboid in every directions is not the same.")); // Define the periodic cube - Triangulation_3 pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); + Dt pdt(typename Kernel::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) pdt.insert(std::begin(points), std::end(points), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible @@ -354,8 +394,8 @@ class Alpha_complex_3d { * @exception std::invalid_argument In debug mode, if a weight is negative, zero, or greater than 1/64*cuboid length * squared. * - * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` - * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3`. + * @param[in] weights Range of weights on points. Weights shall be in double. * @param[in] x_min Iso-oriented cuboid x_min. * @param[in] y_min Iso-oriented cuboid y_min. * @param[in] z_min Iso-oriented cuboid z_min. @@ -368,12 +408,12 @@ class Alpha_complex_3d { * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a `Alpha_complex_3d::Point_3`. * The type WeightRange must be a range for which std::begin and - * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. - * The type of x_min, y_min, z_min, x_max, y_max and z_max is `Alpha_complex_3d::Alpha_shape_3::FT`. + * std::end return an input iterator on a double. + * The type of x_min, y_min, z_min, x_max, y_max and z_max must be a double. */ template - Alpha_complex_3d(const InputPointRange& points, WeightRange weights, Alpha_value_type x_min, Alpha_value_type y_min, - Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + Alpha_complex_3d(const InputPointRange& points, WeightRange weights, FT x_min, FT y_min, + FT z_min, FT x_max, FT y_max, FT z_max) { static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d"); static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); GUDHI_CHECK((weights.size() == points.size()), @@ -383,7 +423,6 @@ class Alpha_complex_3d { (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::invalid_argument("The size of the cuboid in every directions is not the same.")); - using Weighted_point_3 = typename Triangulation_3::Weighted_point; std::vector weighted_points_3; std::size_t index = 0; @@ -391,7 +430,7 @@ class Alpha_complex_3d { #ifdef GUDHI_DEBUG // Defined in GUDHI_DEBUG to avoid unused variable warning for GUDHI_CHECK - Alpha_value_type maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); + FT maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); #endif while ((index < weights.size()) && (index < points.size())) { @@ -404,7 +443,7 @@ class Alpha_complex_3d { } // Define the periodic cube - Triangulation_3 pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); + Dt pdt(typename Kernel::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) pdt.insert(std::begin(weighted_points_3), std::end(weighted_points_3), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible @@ -453,9 +492,9 @@ class Alpha_complex_3d { std::size_t count_cells = 0; #endif // DEBUG_TRACES std::vector objects; - std::vector alpha_values; + std::vector alpha_values; - Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects), + Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects), std::back_inserter(alpha_values)); alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher); @@ -464,7 +503,7 @@ class Alpha_complex_3d { #endif // DEBUG_TRACES Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - using Alpha_value_iterator = typename std::vector::const_iterator; + using Alpha_value_iterator = typename std::vector::const_iterator; Alpha_value_iterator alpha_value_iterator = alpha_values.begin(); for (auto object_iterator : objects) { Vertex_list vertex_list; diff --git a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp index b818fb2e..e4a45791 100644 --- a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp @@ -228,7 +228,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted, Weighted_alpha_complex_3d, alpha_complex_p_a_w.create_complex(stree); std::cout << "Weighted alpha complex 3d from weighted points" << std::endl; - using Weighted_point_3 = typename Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; + using Weighted_point_3 = typename Weighted_alpha_complex_3d::Weighted_point_3; std::vector weighted_points; diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 35b84d2e..b33a95a1 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -29,7 +29,9 @@ Author: Vincent Rouvreau
Introduced in: GUDHI 1.3.0
Copyright: GPL v3
- Requires: \ref cgal ≥ 4.11.0 and \ref eigen3 + Requires: \ref eigen3 and
+ \ref cgal ≥ 4.7.0 for Alpha_complex
+ \ref cgal ≥ 4.11.0 for Alpha_complex_3d 		Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
@@ -38,7 +40,8 @@ values of the codimension 1 cofaces that make it not Gabriel otherwise. All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into the complex.
- User manual: \ref alpha_complex - Reference manual: Gudhi::alpha_complex::Alpha_complex + User manual: \ref alpha_complex - Reference manual: Gudhi::alpha_complex::Alpha_complex and + Gudhi::alpha_complex::Alpha_complex_3d
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