From 73efba37dfcab3f9b8589cb3b0b80f6d7dd7bd0b Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 4 Oct 2017 10:24:04 +0000 Subject: Document utilies in README files using Markdown + move/rename some utilities Only missing doc for now: Garland_heckbert git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2752 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7ba0113762b6622130835dc9e372acfae29c2db8 --- .../periodic_alpha_complex_3d_persistence.cpp | 268 +++++++++++++++++++++ 1 file changed, 268 insertions(+) create mode 100644 src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp (limited to 'src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp') diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..8140a3c5 --- /dev/null +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -0,0 +1,268 @@ +/* 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 +#include + +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "alpha_complex_3d_helper.h" + +// Traits +using K = CGAL::Exact_predicates_inexact_constructions_kernel; +using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3; +// Vertex type +using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; +using Vb = CGAL::Triangulation_vertex_base_3; +using AsVb = CGAL::Alpha_shape_vertex_base_3; +// Cell type +using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; +using Cb = CGAL::Triangulation_cell_base_3; +using AsCb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; +using Point_3 = PK::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, + CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > >; +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; +using Vertex_list = std::list; + +// 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 Alpha_shape_simplex_tree_pair = std::pair; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< + ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(char * const progName) { + std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" << + "integer > 0] min_persistence[float >= -1.0]\n" << + " path_to_OFF_file is the path to your points cloud in OFF format.\n" << + " path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" << + " x_min y_min z_min x_max y_max z_max\n" << + " In this example, the periodic cube will be " << + "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" << + " For more information, please refer to\n" << + " https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n"; + + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 5) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[3]); + Filtration_value min_persistence = strtof(argv[4], nullptr); + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Read iso_cuboid_3 information from file + std::ifstream iso_cuboid_str(argv[2]); + 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[2] << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector lp = off_reader.get_point_cloud(); + + // Define the periodic cube + P3DT3 pdt(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) + 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(); + 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 + // Maybe need to set it to GENERAL mode + Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree, true); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} -- cgit v1.2.3 From aafe601c247c78a474c6af110ca5b34540a34f44 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 16 Nov 2017 08:31:26 +0000 Subject: Code review : Homogenize alpha shape examples command line git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2887 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8c692434eb48c525047bc34a6fab7d7c1af64d56 --- src/Alpha_complex/utilities/CMakeLists.txt | 19 ++- src/Alpha_complex/utilities/README | 89 +++++++++------ .../utilities/alpha_complex_3d_helper.h | 8 +- .../utilities/alpha_complex_3d_persistence.cpp | 115 ++++++++++++------- .../utilities/alpha_complex_persistence.cpp | 63 +++++----- .../exact_alpha_complex_3d_persistence.cpp | 107 ++++++++++------- .../periodic_alpha_complex_3d_persistence.cpp | 124 ++++++++++++-------- .../weighted_alpha_complex_3d_persistence.cpp | 127 +++++++++++++-------- src/Bottleneck_distance/utilities/CMakeLists.txt | 3 + src/Rips_complex/utilities/README | 3 +- 10 files changed, 406 insertions(+), 252 deletions(-) (limited to 'src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp') diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 18699650..cefc1ad6 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -3,11 +3,11 @@ project(Alpha_complex_utilities) if(CGAL_FOUND) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY}) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp) - target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY}) + target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) - target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY}) + target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) @@ -16,11 +16,11 @@ if(CGAL_FOUND) endif(TBB_FOUND) add_test(NAME Alpha_complex_utilities_alpha_complex_3d_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45") + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "-p" "2" "-m" "0.45") install(TARGETS alpha_complex_3d_persistence DESTINATION bin) install(TARGETS exact_alpha_complex_3d_persistence DESTINATION bin) @@ -28,11 +28,10 @@ if(CGAL_FOUND) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence - ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) @@ -41,7 +40,7 @@ if(CGAL_FOUND) add_test(NAME Alpha_complex_utilities_alpha_complex_persistence COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0") + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "-p" "2" "-m" "0") install(TARGETS alpha_complex_persistence DESTINATION bin) install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/README index 6e7d16b7..c3dd170b 100644 --- a/src/Alpha_complex/utilities/README +++ b/src/Alpha_complex/utilities/README @@ -8,22 +8,24 @@ This program computes the persistent homology with coefficient field Z/pZ of the where `dim` is the dimension of the homological feature, `b` and `d` 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** -`alpha_complex_3d_persistence

` -where -`` is the path to the input point cloud in OFF format. -`

` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer. -`` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +`alpha_complex_3d_persistence [options] ` + +**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** -`alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45` +`alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45` outputs: ``` Simplex_tree dim: 3 -2 0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 ``` Here we retrieve expected Betti numbers on a tore 3D: @@ -48,21 +50,34 @@ Same as `alpha_complex_3d_persistence`, but using exact computation. It is slowe Same as `alpha_complex_3d_persistence`, but using weighted points. **Usage** -`weighted_alpha_complex_3d_persistence

` -where -`` is the path to the input point cloud in OFF format. -`` is the path to the file containing the weights of the points (one value per line). -`

` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer. -`` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +`weighted_alpha_complex_3d_persistence [options] ` +**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` -## `periodic_alpha_complex_3d_persistence` ## -This program computes the persistent homology with coefficient field Z/pZ of the 3D periodic alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention: +outputs: +``` +Simplex_tree dim: 3 +2 0 -1 inf +2 1 -0.931784 0.000103311 +2 1 -0.906588 2.60165e-05 +2 2 -0.43556 0.0393798 +``` -`p dim b d` +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. -where `dim` is the dimension of the homological feature, `b` and `d` 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). + +## `periodic_alpha_complex_3d_persistence` ## +Same as `alpha_complex_3d_persistence`, but using periodic alpha shape 3d. **Usage** `periodic_alpha_complex_3d_persistence

` @@ -72,21 +87,31 @@ where `

` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer. `` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +**Usage** +`./periodic_alpha_complex_3d_persistence [options] input-file cuboid-file` + +**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** -`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` +`periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off ../../data/points/iso_cuboid_3_in_0_1.txt -p 3 -m 1.0` outputs: ``` Periodic Delaunay computed. Simplex_tree dim: 3 -3 0 0 inf -3 1 0.0025 inf -3 1 0.0025 inf -3 1 0.0025 inf -3 2 0.005 inf -3 2 0.005 inf -3 2 0.005 inf -3 3 0.0075 inf +3 0 0 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 2 0.005 inf +3 2 0.005 inf +3 2 0.005 inf +3 3 0.0075 inf ``` Here we retrieve expected Betti numbers on an 3D iso-oriented cuboids: @@ -98,14 +123,12 @@ Betti numbers[3] = 1 ``` N.B.: -* `periodic_alpha_complex_3d_persistence` only accepts OFF files in dimension 3. -* In this example, the periodic cube is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } +* Cuboid file must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsIsoCuboid). * Filtration values are alpha square values. - ## `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. The output diagram contains one bar per line, written with the convention: @@ -119,7 +142,7 @@ where `dim` is the dimension of the homological feature, `b` and `d` are respect **Allowed options** * `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout. +* `-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. diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h index 7865e4ec..6b3b7d5d 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h +++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h @@ -23,7 +23,7 @@ #ifndef ALPHA_COMPLEX_3D_HELPER_H_ #define ALPHA_COMPLEX_3D_HELPER_H_ -template +template Vertex_list from_cell(const Cell_handle& ch) { Vertex_list the_list; for (auto i = 0; i < 4; i++) { @@ -35,7 +35,7 @@ Vertex_list from_cell(const Cell_handle& ch) { return the_list; } -template +template Vertex_list from_facet(const Facet& fct) { Vertex_list the_list; for (auto i = 0; i < 4; i++) { @@ -49,7 +49,7 @@ Vertex_list from_facet(const Facet& fct) { return the_list; } -template +template Vertex_list from_edge(const Edge_3& edg) { Vertex_list the_list; for (auto i = 0; i < 4; i++) { @@ -63,7 +63,7 @@ Vertex_list from_edge(const Edge_3& edg) { return the_list; } -template +template Vertex_list from_vertex(const Vertex_handle& vh) { Vertex_list the_list; #ifdef DEBUG_TRACES diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index f63ff0f6..f2085ab2 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -20,6 +20,7 @@ * along with this program. If not, see . */ +#include #include #include @@ -56,10 +57,10 @@ 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, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; +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; @@ -70,42 +71,28 @@ using Vertex_list = std::list; 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 Alpha_shape_simplex_tree_map = std::map; using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(const std::string& progName) { - std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << - "> 0] min_persistence[float >= -1.0]\n"; - std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; - exit(-1); -} +using Simplex_tree_vector_vertex = std::vector; +using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology; -int main(int argc, char * const argv[]) { - // program args management - if (argc != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, + int &coeff_field_characteristic, Filtration_value &min_persistence); - int coeff_field_characteristic = atoi(argv[2]); +int main(int argc, char **argv) { + std::string off_file_points; + std::string output_file_diag; + int coeff_field_characteristic; + Filtration_value min_persistence; - Filtration_value min_persistence = 0.0; - int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } + program_options(argc, argv, off_file_points, output_file_diag, coeff_field_characteristic, min_persistence); - // Read points from file - std::string offInputFile(argv[1]); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); + 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 " << offInputFile << std::endl; - usage(argv[0]); + std::cerr << "Unable to read file " << off_file_points << std::endl; + exit(-1); } // Retrieve the triangulation @@ -143,28 +130,28 @@ int main(int argc, char * const argv[]) { Filtration_value filtration_max = 0.0; for (auto object_iterator : the_objects) { // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { vertex_list = from_cell(*cell); count_cells++; if (dim_max < 3) { // Cell is of dim 3 dim_max = 3; } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { vertex_list = from_facet(*facet); count_facets++; if (dim_max < 2) { // Facet is of dim 2 dim_max = 2; } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { vertex_list = from_edge(*edge); count_edges++; if (dim_max < 1) { // Edge_3 is of dim 1 dim_max = 1; } - } else if (const Vertex_handle * vertex = CGAL::object_cast(&object_iterator)) { + } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { count_vertices++; vertex_list = from_vertex(*vertex); } @@ -190,7 +177,7 @@ int main(int argc, char * const argv[]) { } } // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); + Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES @@ -211,7 +198,6 @@ int main(int argc, char * const argv[]) { 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; @@ -236,7 +222,58 @@ int main(int argc, char * const argv[]) { pcoh.compute_persistent_cohomology(min_persistence); - pcoh.output_diagram(); + // Output the diagram in filediag + if (output_file_diag.empty()) { + pcoh.output_diagram(); + } else { + std::cout << "Result in file: " << output_file_diag << std::endl; + std::ofstream out(output_file_diag); + pcoh.output_diagram(out); + out.close(); + } return 0; } + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, + int &coeff_field_characteristic, Filtration_value &min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value(&output_file_diag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout")( + "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a 3D Alpha complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index 9e84e91f..2105220a 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -14,12 +14,9 @@ using Simplex_tree = Gudhi::Simplex_tree<>; using Filtration_value = Simplex_tree::Filtration_value; -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & output_file_diag - , Filtration_value & alpha_square_max_value - , int & coeff_field_characteristic - , Filtration_value & min_persistence); +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, + Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, + Filtration_value &min_persistence); int main(int argc, char **argv) { std::string off_file_points; @@ -28,13 +25,13 @@ int main(int argc, char **argv) { int coeff_field_characteristic; Filtration_value min_persistence; - program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, - coeff_field_characteristic, min_persistence); + program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic, + min_persistence); // ---------------------------------------------------------------------------- // Init of an alpha complex from an OFF file // ---------------------------------------------------------------------------- - using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + using Kernel = CGAL::Epick_d; Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(off_file_points); Simplex_tree simplex; @@ -42,17 +39,16 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::cout << "Simplicial complex is of dimension " << simplex.dimension() << - " - " << simplex.num_simplices() << " simplices - " << - simplex.num_vertices() << " vertices." << std::endl; + std::cout << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; // Sort the simplices in the order of the filtration simplex.initialize_filtration(); std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree, - Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex); + Gudhi::persistent_cohomology::Persistent_cohomology pcoh( + simplex); // initializes the coefficient field for homology pcoh.init_coefficients(coeff_field_characteristic); @@ -72,30 +68,26 @@ int main(int argc, char **argv) { return 0; } -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & output_file_diag - , Filtration_value & alpha_square_max_value - , int & coeff_field_characteristic - , Filtration_value & min_persistence) { +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, + Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, + Filtration_value &min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + hidden.add_options()("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("output-file,o", po::value(&output_file_diag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-alpha-square-value,r", - po::value(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), - "Maximal alpha square value for the Alpha complex construction.") - ("field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value(&output_file_diag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout")( + "max-alpha-square-value,r", po::value(&alpha_square_max_value) + ->default_value(std::numeric_limits::infinity()), + "Maximal alpha square value for the Alpha complex construction.")( + "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); po::positional_options_description pos; pos.add("input-file", 1); @@ -104,8 +96,7 @@ void program_options(int argc, char * argv[] all.add(visible).add(hidden); po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), 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")) { diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp index 8ce68406..7919c7fd 100644 --- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp @@ -20,6 +20,7 @@ * along with this program. If not, see . */ +#include #include #include @@ -40,7 +41,7 @@ #include #include -#include "../utilities/alpha_complex_3d_helper.h" +#include "alpha_complex_3d_helper.h" // Alpha_shape_3 templates type definitions using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; @@ -57,10 +58,10 @@ 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, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; +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; @@ -71,42 +72,28 @@ using Vertex_list = std::list; 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 Alpha_shape_simplex_tree_map = std::map; using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(char * const progName) { - std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << - "> 0] min_persistence[float >= -1.0]\n"; - std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; - exit(-1); -} +using Simplex_tree_vector_vertex = std::vector; +using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology; -int main(int argc, char * const argv[]) { - // program args management - if (argc != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, + int &coeff_field_characteristic, Filtration_value &min_persistence); - int coeff_field_characteristic = atoi(argv[2]); +int main(int argc, char **argv) { + std::string off_file_points; + std::string output_file_diag; + int coeff_field_characteristic; + Filtration_value min_persistence; - Filtration_value min_persistence = 0.0; - int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } + program_options(argc, argv, off_file_points, output_file_diag, coeff_field_characteristic, min_persistence); - // Read points from file - std::string offInputFile(argv[1]); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); + 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 " << offInputFile << std::endl; - usage(argv[0]); + std::cerr << "Unable to read file " << off_file_points << std::endl; + exit(-1); } // Retrieve the triangulation @@ -144,28 +131,28 @@ int main(int argc, char * const argv[]) { Filtration_value filtration_max = 0.0; for (auto object_iterator : the_objects) { // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { vertex_list = from_cell(*cell); count_cells++; if (dim_max < 3) { // Cell is of dim 3 dim_max = 3; } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { vertex_list = from_facet(*facet); count_facets++; if (dim_max < 2) { // Facet is of dim 2 dim_max = 2; } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { vertex_list = from_edge(*edge); count_edges++; if (dim_max < 1) { // Edge_3 is of dim 1 dim_max = 1; } - } else if (const Vertex_handle * vertex = CGAL::object_cast(&object_iterator)) { + } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { count_vertices++; vertex_list = from_vertex(*vertex); } @@ -192,7 +179,7 @@ int main(int argc, char * const argv[]) { } // Construction of the simplex_tree // you can also use the_alpha_value_iterator->exact() - Filtration_value filtr = /*std::sqrt*/CGAL::to_double(the_alpha_value_iterator->exact()); + Filtration_value filtr = /*std::sqrt*/ CGAL::to_double(the_alpha_value_iterator->exact()); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES @@ -213,7 +200,6 @@ int main(int argc, char * const argv[]) { 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; @@ -242,3 +228,46 @@ int main(int argc, char * const argv[]) { return 0; } + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, + int &coeff_field_characteristic, Filtration_value &min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value(&output_file_diag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout")( + "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a 3D Alpha complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 8140a3c5..10b62f75 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -20,6 +20,7 @@ * along with this program. If not, see . */ +#include #include #include @@ -63,10 +64,10 @@ using Point_3 = PK::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, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; +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; @@ -77,54 +78,41 @@ using Vertex_list = std::list; 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 Alpha_shape_simplex_tree_map = std::map; using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< - ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(char * const progName) { - std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" << - "integer > 0] min_persistence[float >= -1.0]\n" << - " path_to_OFF_file is the path to your points cloud in OFF format.\n" << - " path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" << - " x_min y_min z_min x_max y_max z_max\n" << - " In this example, the periodic cube will be " << - "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" << - " For more information, please refer to\n" << - " https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n"; - - exit(-1); -} +using Simplex_tree_vector_vertex = std::vector; +using Persistent_cohomology = + Gudhi::persistent_cohomology::Persistent_cohomology; -int main(int argc, char * const argv[]) { - // program args management - if (argc != 5) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &cuboid_file, + std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence); - int coeff_field_characteristic = atoi(argv[3]); - Filtration_value min_persistence = strtof(argv[4], nullptr); +int main(int argc, char **argv) { + std::string off_file_points; + std::string cuboid_file; + std::string output_file_diag; + int coeff_field_characteristic; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, cuboid_file, output_file_diag, coeff_field_characteristic, + min_persistence); - // Read points from file - std::string offInputFile(argv[1]); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); + 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 " << offInputFile << std::endl; - usage(argv[0]); + std::cerr << "Unable to read OFF file " << off_file_points << std::endl; + exit(-1); } // Read iso_cuboid_3 information from file - std::ifstream iso_cuboid_str(argv[2]); + std::ifstream iso_cuboid_str(cuboid_file); 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[2] << std::endl; - usage(argv[0]); + std::cerr << "Unable to read file " << cuboid_file << std::endl; + exit(-1); } // Retrieve the triangulation @@ -168,29 +156,29 @@ int main(int argc, char * const argv[]) { Filtration_value filtration_max = 0.0; for (auto object_iterator : the_objects) { // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { vertex_list = from_cell(*cell); count_cells++; if (dim_max < 3) { // Cell is of dim 3 dim_max = 3; } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { vertex_list = from_facet(*facet); count_facets++; if (dim_max < 2) { // Facet is of dim 2 dim_max = 2; } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { vertex_list = from_edge(*edge); count_edges++; if (dim_max < 1) { // Edge_3 is of dim 1 dim_max = 1; } - } else if (const Alpha_shape_3::Vertex_handle * vertex = - CGAL::object_cast(&object_iterator)) { + } else if (const Alpha_shape_3::Vertex_handle *vertex = + CGAL::object_cast(&object_iterator)) { count_vertices++; vertex_list = from_vertex(*vertex); } @@ -216,7 +204,7 @@ int main(int argc, char * const argv[]) { } } // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); + Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES @@ -237,7 +225,6 @@ int main(int argc, char * const argv[]) { 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; @@ -266,3 +253,50 @@ int main(int argc, char * const argv[]) { return 0; } + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &cuboid_file, + std::string &output_file_diag, int &coeff_field_characteristic, + Filtration_value &min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd ")( + "cuboid-file", po::value(&cuboid_file), + "Name of file describing the periodic domain. Format is: min_hx min_hy min_hz\nmax_hx max_hy max_hz"); + + 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")( + "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + pos.add("cuboid-file", 2); + + 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") || !vm.count("cuboid-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a periodic 3D Alpha complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file cuboid-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp index a4ecf9da..293170f7 100644 --- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp @@ -20,6 +20,7 @@ * along with this program. If not, see . */ +#include #include #include @@ -42,7 +43,7 @@ #include #include -#include "../utilities/alpha_complex_3d_helper.h" +#include "alpha_complex_3d_helper.h" // Traits using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; @@ -60,10 +61,10 @@ using Weighted_point_3 = Gt::Weighted_point; // 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, - CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > >; +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; @@ -74,48 +75,38 @@ using Vertex_list = std::list; 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 Alpha_shape_simplex_tree_map = std::map; using Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< - ST, Gudhi::persistent_cohomology::Field_Zp >; - -void usage(char * const progName) { - std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_weight_file coeff_field_characteristic[integer " << - "> 0] min_persistence[float >= -1.0]\n"; - std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; - std::cerr << " path_to_weight_file is the path to the weights of your points cloud (one value per line.)\n"; - std::cerr << " Weights values are explained on CGAL documentation:\n"; - std::cerr << " https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0\n"; - std::cerr << " https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation\n"; - exit(-1); -} +using Simplex_tree_vector_vertex = std::vector; +using Persistent_cohomology = + Gudhi::persistent_cohomology::Persistent_cohomology; -int main(int argc, char * const argv[]) { - // program args management - if (argc != 5) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &weight_file, + std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence); - int coeff_field_characteristic = atoi(argv[3]); - Filtration_value min_persistence = strtof(argv[4], nullptr); +int main(int argc, char **argv) { + std::string off_file_points; + std::string weight_file; + std::string output_file_diag; + int coeff_field_characteristic; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, weight_file, output_file_diag, coeff_field_characteristic, + min_persistence); - // Read points from file - std::string offInputFile(argv[1]); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); + 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 " << offInputFile << std::endl; - usage(argv[0]); + std::cerr << "Unable to read OFF file " << off_file_points << std::endl; + exit(-1); } // Retrieve the triangulation std::vector lp = off_reader.get_point_cloud(); // Read weights information from file - std::ifstream weights_ifstr(argv[2]); + std::ifstream weights_ifstr(weight_file); std::vector wp; if (weights_ifstr.good()) { double weight = 0.0; @@ -127,12 +118,12 @@ int main(int argc, char * const argv[]) { index++; } if (index != lp.size()) { - std::cerr << "Bad number of weights in file " << argv[2] << std::endl; - usage(argv[0]); + std::cerr << "Bad number of weights in file " << weight_file << std::endl; + exit(-1); } } else { - std::cerr << "Unable to read file " << argv[2] << std::endl; - usage(argv[0]); + std::cerr << "Unable to read weights file " << weight_file << std::endl; + exit(-1); } // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. @@ -167,29 +158,29 @@ int main(int argc, char * const argv[]) { Filtration_value filtration_max = 0.0; for (auto object_iterator : the_objects) { // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast(&object_iterator)) { + if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { vertex_list = from_cell(*cell); count_cells++; if (dim_max < 3) { // Cell is of dim 3 dim_max = 3; } - } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { vertex_list = from_facet(*facet); count_facets++; if (dim_max < 2) { // Facet is of dim 2 dim_max = 2; } - } else if (const Edge_3 * edge = CGAL::object_cast(&object_iterator)) { + } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { vertex_list = from_edge(*edge); count_edges++; if (dim_max < 1) { // Edge_3 is of dim 1 dim_max = 1; } - } else if (const Alpha_shape_3::Vertex_handle * vertex = - CGAL::object_cast(&object_iterator)) { + } else if (const Alpha_shape_3::Vertex_handle *vertex = + CGAL::object_cast(&object_iterator)) { count_vertices++; vertex_list = from_vertex(*vertex); } @@ -215,7 +206,7 @@ int main(int argc, char * const argv[]) { } } // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); + Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES @@ -236,7 +227,6 @@ int main(int argc, char * const argv[]) { 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; @@ -265,3 +255,50 @@ int main(int argc, char * const argv[]) { return 0; } + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &weight_file, + std::string &output_file_diag, int &coeff_field_characteristic, + Filtration_value &min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd ")( + "weight-file", po::value(&weight_file), + "Name of file containing a point weights. Format is one weigt per line: W1\n...\nWn "); + + 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")( + "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + pos.add("weight-file", 2); + + 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") || !vm.count("weight-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a weighted 3D Alpha complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file weight-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Bottleneck_distance/utilities/CMakeLists.txt b/src/Bottleneck_distance/utilities/CMakeLists.txt index cdf76c85..063b6ae3 100644 --- a/src/Bottleneck_distance/utilities/CMakeLists.txt +++ b/src/Bottleneck_distance/utilities/CMakeLists.txt @@ -3,6 +3,9 @@ project(Bottleneck_distance_utilities) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable (bottleneck_read_file bottleneck_read_file.cpp) + if (TBB_FOUND) + target_link_libraries(bottleneck_read_file ${TBB_LIBRARIES}) + endif(TBB_FOUND) add_test(NAME Bottleneck_distance_utilities_Bottleneck_read_file COMMAND $ diff --git a/src/Rips_complex/utilities/README b/src/Rips_complex/utilities/README index 93ec3658..ca10424d 100644 --- a/src/Rips_complex/utilities/README +++ b/src/Rips_complex/utilities/README @@ -13,6 +13,7 @@ where `dim` is the dimension of the homological feature, `b` and `d` are respect **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-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. * `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. * `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. @@ -45,7 +46,7 @@ outputs: ## `rips_distance_matrix_persistence` ## -Same as `rips_persistence` but taking an distance matrix as input. +Same as `rips_persistence` but taking a distance matrix as input. **Example** `rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` -- cgit v1.2.3 From 1b895dd0d76cbe13b92b68b7198f58631678200f Mon Sep 17 00:00:00 2001 From: cjamin Date: Thu, 16 Nov 2017 11:54:36 +0000 Subject: Add missing includes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2890 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9ddda864abff7b9509984dcbc657225ea1c80b1a --- src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp | 2 ++ src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp | 2 ++ src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp | 2 ++ src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp | 2 ++ .../example/weighted_periodic_alpha_complex_3d_persistence.cpp | 2 ++ .../example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp | 2 ++ 6 files changed, 12 insertions(+) (limited to 'src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp') diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index f2085ab2..28daca5e 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -30,6 +30,8 @@ #include #include #include +#include +#include #include #include diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp index 7919c7fd..c69482ab 100644 --- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp @@ -30,6 +30,8 @@ #include #include #include +#include +#include #include #include 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 10b62f75..b480a9ec 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -31,6 +31,8 @@ #include #include #include +#include +#include #include #include diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp index 293170f7..91747a8c 100644 --- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp @@ -31,6 +31,8 @@ #include #include #include +#include +#include #include #include diff --git a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp index 13634ff7..67d830dc 100644 --- a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -30,6 +30,8 @@ #include #include #include +#include +#include #include #include diff --git a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp index ff2eebcb..d8289ba9 100644 --- a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp +++ b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp @@ -28,6 +28,8 @@ #include #include #include +#include +#include #include #include -- cgit v1.2.3