diff options
author | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-05-09 14:04:29 +0000 |
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committer | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-05-09 14:04:29 +0000 |
commit | 01b7bec722e18851acfc826ca572d01a127339c1 (patch) | |
tree | e6cef530da4187ac6841d8d682ca1d0797e54ff5 /src/Nerve_GIC | |
parent | aa67dab1eebe3cdba573741857051005ba72cc3b (diff) |
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2408 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 324d557360a52e7181d9cf3c7d77c8445a367808
Diffstat (limited to 'src/Nerve_GIC')
-rw-r--r-- | src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 72 | ||||
-rw-r--r-- | src/Nerve_GIC/example/CMakeLists.txt | 17 | ||||
-rw-r--r-- | src/Nerve_GIC/example/GIC.cpp | 23 | ||||
-rw-r--r-- | src/Nerve_GIC/example/GIC.txt | 57 | ||||
-rw-r--r-- | src/Nerve_GIC/example/MapperDeltaCoord.cpp (renamed from src/Nerve_GIC/example/MapperDelta.cpp) | 9 | ||||
-rw-r--r-- | src/Nerve_GIC/example/MapperDeltaCoord.txt | 125 | ||||
-rw-r--r-- | src/Nerve_GIC/example/MapperDeltaFunc.cpp | 61 | ||||
-rw-r--r-- | src/Nerve_GIC/example/MapperDeltaFunc.txt | 16 | ||||
-rw-r--r-- | src/Nerve_GIC/example/Nerve.cpp | 14 | ||||
-rw-r--r-- | src/Nerve_GIC/example/Nerve.txt | 45 | ||||
-rw-r--r-- | src/Nerve_GIC/example/simple_GIC.cpp | 77 | ||||
-rw-r--r-- | src/Nerve_GIC/include/gudhi/GIC.h | 17 |
12 files changed, 396 insertions, 137 deletions
diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index 0b51e345..44e23983 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -33,9 +33,7 @@ namespace graph_induced_complex { * * @{ * - * \section complexes Graph induced complexes (GIC) and Nerves - * - * GIC and Nerves are simplicial complexes built on top of a point cloud P. + * \section nerves Nerves * * \subsection nervedefinition Nerve definition * @@ -46,78 +44,106 @@ namespace graph_induced_complex { * * \subsection nerveexample Example * - * This example builds the Nerve of a point cloud sampled on a 3D human shape. - * The cover C comes from the preimages of intervals covering the height function. + * This example builds the Nerve of a point cloud sampled on a 3D human shape (human.off). + * The cover C comes from the preimages of intervals (10 intervals with gain 0.3) + * covering the height function (coordinate 2), + * which are then refined into their connected components using the triangulation of the .OFF file. * All intervals have the resolution (either the length or the number of the intervals) * and gain (overlap percentage). * - * \include + * \include Nerve_GIC/Nerve.cpp * * When launching: * - * \code $> + * \code $> ./Nerve ../../../data/points/human.off 2 10 0.3 * \endcode * * the program output is: * - * \include + * \include Nerve_GIC/Nerve.txt + * + * \section gic Graph Induced Complexes (GIC) * - * \section gicdefinition GIC definition + * \subsection gicdefinition GIC definition * * Again, assume you are given a cover C of your point cloud P. Moreover, assume * you are also given a graph G built on top of P. Then, for any clique in G * whose nodes all belong to different elements of C, the GIC includes a corresponding * simplex, whose dimension is the number of nodes in the clique minus one. + * See <a target="_blank" href="https://arxiv.org/abs/1304.0662"> this article </a> + * for more details. * * \subsection gicexample Example * - * This example builds the GIC of a point cloud sampled on a 3D human shape. - * The cover C comes from the preimages of intervals covering the height function, - * and the graph G comes from a Rips complex built with a threshold parameter. + * This example builds the GIC of a point cloud sampled on a 3D human shape (human.off). + * The cover C comes from the preimages of intervals (with length 0.1 and gain 0) + * covering the height function (coordinate 2), + * and the graph G comes from a Rips complex built with threshold 0.1. * Note that if the gain is too big, the number of cliques increases a lot, * which make the computation time much larger. * - * \include + * \include Nerve_GIC/GIC.cpp * * When launching: * - * \code $> + * \code $> ./GIC ../../../data/points/human.off 0.1 2 0.1 0 * \endcode * * the program output is: * - * \include + * \include Nerve_GIC/GIC.txt * * \subsection mapperdeltadefinition Mapper Delta * * If one restricts to the cliques in G whose nodes all belong to preimages of consecutive * intervals (assuming the cover of the height function is minimal, i.e. no more than * two intervals can intersect at a time), the GIC is of dimension one, i.e. a graph. - * We call this graph the Mapper Delta, since it is related to the usual Mapper (see - * <a target="_blank" href="https://arxiv.org/abs/1511.05823"> this article </a>). + * We call this graph the Mapper Delta, since it is related to the usual Mapper. See + * <a target="_blank" href="https://arxiv.org/abs/1511.05823"> this article </a> for more details. * * \subsection mapperdeltaexample Example * * Mapper Delta comes with optimal selection for the Rips threshold, * the resolution and the gain of the function cover. In this example, - * we compute the Mapper Delta of a point cloud sampled on a 3D human shape, + * we compute the Mapper Delta of a point cloud sampled on a 3D human shape (human.off), * where the graph G comes from a Rips complex with optimal threshold, - * and the cover C comes from the preimages of intervals covering the height function, + * and the cover C comes from the preimages of intervals covering the height function (coordinate 2), * with optimal resolution and gain. Note that optimal threshold, resolution and gain * also exist for the Nerve of this cover. * - * \include + * \include Nerve_GIC/MapperDeltaCoord.cpp * * When launching: * - * \code $> + * \code $> ./MapperDeltaCoord ../../../data/points/human.off 2 * \endcode * * the program output is: * - * \include + * \include MapperDeltaCoord.txt + * + * We also provide an example on a set of 72 pictures taken around the same object (lucky_cat.off). + * The function is now the first eigenfunction given by PCA, whose values + * are written in a file (lucky_cat_PCA1). Threshold, resolution and gain are automatically selected as before. + * + * \include Nerve_GIC/MapperDeltaFunc.cpp + * + * When launching: + * + * \code $> ./MapperDeltaFunc ../../../data/points/COIL_database/lucky_cat.off ../../../data/points/COIL_database/lucky_cat_PCA1 + * \endcode + * + * the program output is: + * + * \include MapperDeltaFunc.txt + * + * If you have python and firefox, all the previous .txt files can then be plotted using + * <a target="_blank" href="https://github.com/MLWave/kepler-mapper"> Kepler-Mapper </a> + * with the following: + * + * \code python visu.py && firefox SC_visu.html + * \endcode * - * * \copyright GNU General Public License v3. * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index e4debf2d..d499613d 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -1,8 +1,21 @@ cmake_minimum_required(VERSION 2.6) project(Nerve_GIC_examples) -add_executable ( GIC simple_GIC.cpp ) -target_link_libraries(GIC ${Boost_SYSTEM_LIBRARY}) +add_executable ( Nerve Nerve.cpp ) +target_link_libraries(Nerve ${Boost_SYSTEM_LIBRARY}) + +add_executable ( GIC GIC.cpp ) +target_link_libraries(GIC ${Boost_SYSTEM_LIBRARY}) + +add_executable ( MapperDeltaCoord MapperDeltaCoord.cpp ) +target_link_libraries(MapperDeltaCoord ${Boost_SYSTEM_LIBRARY}) + +add_executable ( MapperDeltaFunc MapperDeltaFunc.cpp ) +target_link_libraries(MapperDeltaFunc ${Boost_SYSTEM_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Nerve ${TBB_LIBRARIES}) target_link_libraries(GIC ${TBB_LIBRARIES}) + target_link_libraries(MapperDeltaCoord ${TBB_LIBRARIES}) + target_link_libraries(MapperDeltaFunc ${TBB_LIBRARIES}) endif()
\ No newline at end of file diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp index 5161a46b..30a485d5 100644 --- a/src/Nerve_GIC/example/GIC.cpp +++ b/src/Nerve_GIC/example/GIC.cpp @@ -3,7 +3,7 @@ void usage(int nbArgs, char * const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; std::cerr << "Usage: " << progName << " filename.off threshold coordinate resolution gain\n"; - std::cerr << " i.e.: " << progName << " ../../data/points/test.off 1.5 1 10 0.3 \n"; + std::cerr << " i.e.: " << progName << " ../../../data/points/human.off 1.5 2 10 0.3 \n"; exit(-1); // ----- >> } @@ -12,7 +12,6 @@ int main(int argc, char **argv) { std::string off_file_name(argv[1]); double threshold = atof(argv[2]); - //std::string func_file_name = argv[3]; int coord = atoi(argv[3]); double resolution = atof(argv[4]); double gain = atof(argv[5]); @@ -30,24 +29,12 @@ int main(int argc, char **argv) { Gudhi::graph_induced_complex::Graph_induced_complex GIC; GIC.set_verbose(verb); - GIC.set_graph_from_automatic_rips(off_file_name); - //GIC.set_graph_from_rips(threshold, off_file_name); - //GIC.set_graph_from_OFF(off_file_name); - + GIC.set_graph_from_rips(threshold, off_file_name); GIC.set_function_from_coordinate(coord, off_file_name); - //GIC.set_function_from_file(func_file_name); - - GIC.set_color_from_coordinate(coord, off_file_name); - //GIC.set_color_from_file(func_file_name); - - GIC.set_automatic_resolution_for_GICMAP(); - GIC.set_gain(); + GIC.set_color_from_coordinate(off_file_name, coord); + GIC.set_resolution_double(resolution); GIC.set_gain(gain); GIC.set_cover_from_function(1); - - //GIC.find_GIC_simplices(); - //GIC.find_Nerve_simplices(); - GIC.find_GICMAP_simplices_with_functional_minimal_cover(); - + GIC.find_GIC_simplices(); GIC.plot_with_KeplerMapper(); Simplex_tree stree; GIC.create_complex(stree); diff --git a/src/Nerve_GIC/example/GIC.txt b/src/Nerve_GIC/example/GIC.txt new file mode 100644 index 00000000..9871cf41 --- /dev/null +++ b/src/Nerve_GIC/example/GIC.txt @@ -0,0 +1,57 @@ +Cloud +Function +0 0 +27 26 +0 -0.949318 240 +1 -0.949346 240 +2 -0.822129 50 +3 -0.822037 51 +4 -0.723847 48 +5 -0.722679 48 +6 -0.625409 57 +7 -0.625771 57 +8 -0.528161 99 +9 -0.528188 99 +10 -0.436343 126 +11 -0.436356 126 +12 -0.330775 194 +13 -0.233638 98 +14 -0.116276 100 +15 -0.129017 144 +16 -0.116513 103 +17 -0.0213554 243 +18 -0.0301512 65 +19 -0.0315443 66 +20 0.0750623 308 +21 0.166778 305 +22 0.270037 307 +23 0.371609 380 +24 0.468078 306 +25 0.567395 312 +26 0.721079 534 +0 3 +1 2 +2 5 +3 4 +4 7 +5 6 +6 9 +7 8 +8 10 +9 11 +10 12 +11 12 +12 13 +13 15 +14 19 +15 17 +16 18 +17 20 +18 20 +19 20 +20 21 +21 22 +22 23 +23 24 +24 25 +25 26 diff --git a/src/Nerve_GIC/example/MapperDelta.cpp b/src/Nerve_GIC/example/MapperDeltaCoord.cpp index 1f8f1582..aa12afe6 100644 --- a/src/Nerve_GIC/example/MapperDelta.cpp +++ b/src/Nerve_GIC/example/MapperDeltaCoord.cpp @@ -3,12 +3,12 @@ void usage(int nbArgs, char * const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; std::cerr << "Usage: " << progName << " filename.off coordinate \n"; - std::cerr << " i.e.: " << progName << " ../../data/points/human.off 2 --v \n"; + std::cerr << " i.e.: " << progName << " ../../../data/points/human.off 2 --v \n"; exit(-1); // ----- >> } int main(int argc, char **argv) { - if ((argc != 6) && (argc != 7)) usage(argc, (argv[0] - 1)); + if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1)); std::string off_file_name(argv[1]); int coord = atoi(argv[2]); @@ -28,9 +28,8 @@ int main(int argc, char **argv) { GIC.set_graph_from_automatic_rips(off_file_name); GIC.set_function_from_coordinate(coord, off_file_name); - GIC.set_color_from_coordinate(coord, off_file_name); - GIC.set_automatic_resolution_for_GICMAP(); - GIC.set_gain(); + GIC.set_color_from_coordinate(off_file_name, coord); + GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain(); GIC.set_cover_from_function(1); GIC.find_GICMAP_simplices_with_functional_minimal_cover(); GIC.plot_with_KeplerMapper(); diff --git a/src/Nerve_GIC/example/MapperDeltaCoord.txt b/src/Nerve_GIC/example/MapperDeltaCoord.txt new file mode 100644 index 00000000..2c2296ea --- /dev/null +++ b/src/Nerve_GIC/example/MapperDeltaCoord.txt @@ -0,0 +1,125 @@ +Cloud +Function +0 0 +61 60 +0 -0.954369 220 +1 -0.954377 220 +2 -0.902361 54 +3 -0.901235 55 +4 -0.84796 27 +5 -0.844637 29 +6 -0.777883 37 +7 -0.778882 39 +8 -0.72868 42 +9 -0.72734 42 +10 -0.677728 48 +11 -0.676848 48 +12 -0.633796 48 +13 -0.634232 48 +14 -0.567924 52 +15 -0.567897 52 +16 -0.52287 77 +17 -0.522897 77 +18 -0.467859 105 +19 -0.467886 105 +20 -0.422377 87 +21 -0.422383 87 +22 -0.363537 80 +23 -0.363508 80 +24 -0.312836 126 +25 -0.267775 84 +26 -0.197152 78 +27 -0.149293 96 +28 -0.134636 48 +29 -0.134463 51 +30 -0.104389 93 +31 -0.108561 96 +32 -0.105219 93 +33 -0.0362235 183 +34 -0.0498358 53 +35 -0.050197 51 +36 -0.000444973 187 +37 0.000472738 42 +38 -0.000214643 42 +39 0.0616246 164 +40 0.0590725 29 +41 0.0590271 31 +42 0.108834 170 +43 0.110991 50 +44 0.110952 50 +45 0.158372 129 +46 0.161945 54 +47 0.161972 54 +48 0.210958 76 +49 0.221521 73 +50 0.221548 73 +51 0.263419 220 +52 0.324345 241 +53 0.371963 311 +54 0.422902 272 +55 0.476693 223 +56 0.530461 246 +57 0.58285 217 +58 0.63636 203 +59 0.690953 230 +60 0.76296 309 +0 3 +1 2 +2 4 +3 5 +4 6 +5 7 +6 9 +7 8 +8 10 +9 11 +10 13 +11 12 +12 14 +13 15 +14 17 +15 16 +16 18 +17 19 +18 20 +19 21 +20 22 +21 23 +22 24 +23 24 +24 25 +25 26 +26 27 +27 31 +28 30 +29 32 +30 35 +31 33 +32 34 +33 36 +34 37 +35 38 +36 39 +37 41 +38 40 +39 42 +40 43 +41 44 +42 45 +43 46 +44 47 +45 48 +46 49 +47 50 +48 51 +49 51 +50 51 +51 52 +52 53 +53 54 +54 55 +55 56 +56 57 +57 58 +58 59 +59 60 diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.cpp b/src/Nerve_GIC/example/MapperDeltaFunc.cpp new file mode 100644 index 00000000..20924b9c --- /dev/null +++ b/src/Nerve_GIC/example/MapperDeltaFunc.cpp @@ -0,0 +1,61 @@ +#include <gudhi/GIC.h> + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " filename.off coordinate \n"; + std::cerr << " i.e.: " << progName << " ../../../data/points/human.off 2 --v \n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1)); + + std::string off_file_name(argv[1]); + std::string func_file_name = argv[2]; + bool verb = 0; if(argc == 4) verb = 1; + + // Type definitions + using Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,\ + boost::property < vertex_filtration_t, Filtration_value >,\ + boost::property < edge_filtration_t, Filtration_value > >; + + // --------------------------------------- + // Init of a Mapper Delta from an OFF file + // --------------------------------------- + + Gudhi::graph_induced_complex::Graph_induced_complex GIC; + GIC.set_verbose(verb); + + GIC.set_graph_from_automatic_rips(off_file_name); + GIC.set_function_from_file(func_file_name); + GIC.set_color_from_file(func_file_name); + GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain(); + GIC.set_cover_from_function(1); + GIC.find_GICMAP_simplices_with_functional_minimal_cover(); + GIC.plot_with_KeplerMapper(); + + Simplex_tree stree; GIC.create_complex(stree); + + std::streambuf* streambufffer = std::cout.rdbuf(); + std::ostream output_stream(streambufffer); + + // ------------------------------------------ + // Display information about the Mapper Delta + // ------------------------------------------ + + if(verb){ + output_stream << "Mapper Delta is of dimension " << stree.dimension() << + " - " << stree.num_simplices() << " simplices - " << + stree.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on Mapper Delta simplices" << std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << std::endl; + } + } + + return 0; +} diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.txt b/src/Nerve_GIC/example/MapperDeltaFunc.txt new file mode 100644 index 00000000..046d2278 --- /dev/null +++ b/src/Nerve_GIC/example/MapperDeltaFunc.txt @@ -0,0 +1,16 @@ +Cloud +Function +0 0 +6 6 +0 -1382.24 20 +1 385.162 3 +2 246.455 12 +3 2204.66 4 +4 2238.94 5 +5 5346.1 39 +0 1 +0 2 +1 3 +2 4 +3 5 +4 5 diff --git a/src/Nerve_GIC/example/Nerve.cpp b/src/Nerve_GIC/example/Nerve.cpp index adcc715d..d4a68c71 100644 --- a/src/Nerve_GIC/example/Nerve.cpp +++ b/src/Nerve_GIC/example/Nerve.cpp @@ -3,16 +3,16 @@ void usage(int nbArgs, char * const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; std::cerr << "Usage: " << progName << " filename.off coordinate resolution gain --v \n"; - std::cerr << " i.e.: " << progName << " ../../data/points/human.off 2 1 0.3 --v \n"; + std::cerr << " i.e.: " << progName << " ../../../data/points/human.off 2 10 0.3 --v \n"; exit(-1); // ----- >> } int main(int argc, char **argv) { - if ((argc != 6) && (argc != 7)) usage(argc, (argv[0] - 1)); + if ((argc != 5) && (argc != 6)) usage(argc, (argv[0] - 1)); std::string off_file_name(argv[1]); int coord = atoi(argv[2]); - double resolution = atof(argv[3]); + int resolution = atoi(argv[3]); double gain = atof(argv[4]); bool verb = 0; if(argc == 6) verb = 1; @@ -28,11 +28,11 @@ int main(int argc, char **argv) { Gudhi::graph_induced_complex::Graph_induced_complex GIC; GIC.set_verbose(verb); + GIC.set_graph_from_OFF(off_file_name); GIC.set_function_from_coordinate(coord, off_file_name); - GIC.set_color_from_coordinate(coord, off_file_name); - GIC.set_resolution_double(resolution); - GIC.set_gain(gain); - GIC.set_cover_from_function(1); + GIC.set_color_from_coordinate(off_file_name, --coord); + GIC.set_resolution_int(resolution); GIC.set_gain(gain); + GIC.set_cover_from_function(0); GIC.find_Nerve_simplices(); GIC.plot_with_KeplerMapper(); diff --git a/src/Nerve_GIC/example/Nerve.txt b/src/Nerve_GIC/example/Nerve.txt new file mode 100644 index 00000000..9ebb2fbb --- /dev/null +++ b/src/Nerve_GIC/example/Nerve.txt @@ -0,0 +1,45 @@ +Cloud +Function +0 0 +21 20 +0 -0.0149926 290 +1 -0.0152551 291 +2 -0.0695028 127 +3 -0.0700955 128 +4 -0.0449554 250 +5 -0.045006 251 +6 -0.0130144 247 +7 -0.0131973 247 +8 0.0766414 127 +9 -0.0118972 165 +10 -0.0121551 165 +11 0.0785204 128 +12 0.0559145 183 +13 -0.0298394 542 +14 0.0569878 181 +15 -0.0201742 388 +16 -0.00110905 208 +17 -0.00131087 208 +18 0.0228028 854 +19 0.0181739 764 +20 0.0307483 597 +0 2 +1 3 +2 5 +3 4 +4 6 +5 7 +6 9 +7 10 +8 12 +9 13 +10 13 +11 14 +12 16 +13 15 +14 17 +15 18 +16 18 +17 18 +18 19 +19 20 diff --git a/src/Nerve_GIC/example/simple_GIC.cpp b/src/Nerve_GIC/example/simple_GIC.cpp deleted file mode 100644 index 5161a46b..00000000 --- a/src/Nerve_GIC/example/simple_GIC.cpp +++ /dev/null @@ -1,77 +0,0 @@ -#include <gudhi/GIC.h> - -void usage(int nbArgs, char * const progName) { - std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " filename.off threshold coordinate resolution gain\n"; - std::cerr << " i.e.: " << progName << " ../../data/points/test.off 1.5 1 10 0.3 \n"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if ((argc != 6) && (argc != 7)) usage(argc, (argv[0] - 1)); - - std::string off_file_name(argv[1]); - double threshold = atof(argv[2]); - //std::string func_file_name = argv[3]; - int coord = atoi(argv[3]); - double resolution = atof(argv[4]); - double gain = atof(argv[5]); - bool verb = 0; if(argc == 7) verb = 1; - - // Type definitions - using Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,\ - boost::property < vertex_filtration_t, Filtration_value >,\ - boost::property < edge_filtration_t, Filtration_value > >; - - // ---------------------------------------------------------------------------- - // Init of a graph induced complex from an OFF file - // ---------------------------------------------------------------------------- - - Gudhi::graph_induced_complex::Graph_induced_complex GIC; - GIC.set_verbose(verb); - - GIC.set_graph_from_automatic_rips(off_file_name); - //GIC.set_graph_from_rips(threshold, off_file_name); - //GIC.set_graph_from_OFF(off_file_name); - - GIC.set_function_from_coordinate(coord, off_file_name); - //GIC.set_function_from_file(func_file_name); - - GIC.set_color_from_coordinate(coord, off_file_name); - //GIC.set_color_from_file(func_file_name); - - GIC.set_automatic_resolution_for_GICMAP(); - GIC.set_gain(); - GIC.set_cover_from_function(1); - - //GIC.find_GIC_simplices(); - //GIC.find_Nerve_simplices(); - GIC.find_GICMAP_simplices_with_functional_minimal_cover(); - - GIC.plot_with_KeplerMapper(); - - Simplex_tree stree; GIC.create_complex(stree); - - std::streambuf* streambufffer = std::cout.rdbuf(); - std::ostream output_stream(streambufffer); - - // ---------------------------------------------------------------------------- - // Display information about the graph induced complex - // ---------------------------------------------------------------------------- - - if(verb){ - output_stream << "Graph induced complex is of dimension " << stree.dimension() << - " - " << stree.num_simplices() << " simplices - " << - stree.num_vertices() << " vertices." << std::endl; - - output_stream << "Iterator on graph induced complex simplices" << std::endl; - for (auto f_simplex : stree.filtration_simplex_range()) { - for (auto vertex : stree.simplex_vertex_range(f_simplex)) { - output_stream << vertex << " "; - } - output_stream << std::endl; - } - } - - return 0; -} diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index abd833e0..c373b25c 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -45,6 +45,7 @@ #include <algorithm> // for std::max #include <cstdint> // for std::uint32_t #include <random> +#include <cassert> #define CONSTANT 10 #define ETA 0.001 @@ -549,7 +550,7 @@ class Graph_induced_complex { * @param[in] off_file_name name of the input .OFF file. * */ - void set_color_from_coordinate(int k = 0, const std::string& off_file_name){ + void set_color_from_coordinate(const std::string& off_file_name, int k = 0){ Points_off_reader<Point> off_reader(off_file_name); int numpts = off_reader.get_point_cloud().size(); for(int i = 0; i < numpts; i++) func_color.insert(std::pair<int,double>(i,off_reader.get_point_cloud()[i][k])); @@ -569,7 +570,7 @@ class Graph_induced_complex { /** \brief Creates a .dot file for neato once the simplicial complex is computed to get a .pdf output. */ void plot_with_neato(){ - char mapp[11] = "mapper.dot"; std::ofstream graphic(mapp); graphic << "graph Mapper {" << std::endl; + char mapp[11] = "SC.dot"; std::ofstream graphic(mapp); graphic << "graph Mapper {" << std::endl; double maxv, minv; maxv = std::numeric_limits<double>::min(); minv = std::numeric_limits<double>::max(); for (std::map<Cover_t,std::pair<int,double> >::iterator iit = cover_color.begin(); iit != cover_color.end(); iit++){ maxv = std::max(maxv, iit->second.second); minv = std::min(minv, iit->second.second); @@ -598,7 +599,7 @@ class Graph_induced_complex { void plot_with_KeplerMapper(){ int num_simplices = simplices.size(); int num_edges = 0; - char mapp[11] = "mapper.txt"; std::ofstream graphic(mapp); + char mapp[11] = "SC.txt"; std::ofstream graphic(mapp); for (int i = 0; i < num_simplices; i++) if (simplices[i].size() == 2) if (cover_color[simplices[i][0]].first > MASK && cover_color[simplices[i][1]].first > MASK) @@ -711,11 +712,17 @@ class Graph_induced_complex { } public: - /** \brief Computes the simplices in the Mapper Delta. + /** \brief Computes the simplices in the Mapper Delta by looking at all the edges of the graph + * and adding the corresponding edges in the Mapper Delta if the images of the endpoints belong + * to consecutive intervals. + * + * \remark WARNING: the output of this function is correct ONLY if the cover is minimal, i.e. + * the gain is less than 0.5!!! + * */ void find_GICMAP_simplices_with_functional_minimal_cover(){ - int v1, v2; + int v1, v2; assert(gain < 0.5); // Loop on all points. for(std::map<int,std::vector<Cover_t> >::iterator it = cover.begin(); it != cover.end(); it++){ |