From bef47576f91c005417ac589b91f6c236fa5a1b60 Mon Sep 17 00:00:00 2001 From: pdlotko Date: Thu, 30 Jun 2016 07:59:24 +0000 Subject: removing files again git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@1361 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9d7b3d461e8de61bed508754106ed3d8f2af0aab --- CMakeLists.txt | 3 +++ 1 file changed, 3 insertions(+) (limited to 'CMakeLists.txt') diff --git a/CMakeLists.txt b/CMakeLists.txt index 9e85be8a..e22be07b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -111,6 +111,7 @@ endif() include_directories(src/Simplex_tree/include/) include_directories(src/Skeleton_blocker/include/) include_directories(src/Witness_complex/include/) + include_directories(src/Gudhi_stat/include/) add_subdirectory(src/common/example) add_subdirectory(src/common/test) @@ -127,6 +128,8 @@ endif() add_subdirectory(src/Bitmap_cubical_complex/example) add_subdirectory(src/Alpha_complex/example) add_subdirectory(src/Alpha_complex/test) + add_subdirectory(src/Gudhi_stat/test) + add_subdirectory(src/Gudhi_stat/example) # data points generator add_subdirectory(data/points/generator) -- cgit v1.2.3 From 7a6ebbd6c26306bca806bbc8c08f74a13c63fca6 Mon Sep 17 00:00:00 2001 From: pdlotko Date: Tue, 11 Oct 2016 07:43:50 +0000 Subject: adding answert to Vincent's comments git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@1688 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3e90519425010bfedae7af946238188fee6cf420 --- CMakeLists.txt | 1 + src/Gudhi_stat/example/CMakeLists.txt | 98 ---------- src/Gudhi_stat/example/persistence_heat_maps.cpp | 2 +- src/Gudhi_stat/example/persistence_intervals.cpp | 2 +- src/Gudhi_stat/example/persistence_landscape.cpp | 2 +- .../example/persistence_landscape_on_grid.cpp | 2 +- .../average_persistence_heat_maps.cpp | 73 -------- .../compute_distance_of_persistence_heat_maps.cpp | 107 ----------- ...ute_scalar_product_of_persistence_heat_maps.cpp | 91 --------- .../create_persistence_heat_maps.cpp | 79 -------- ...aps_weighted_by_arctan_of_their_persistence.cpp | 79 -------- ...eat_maps_weighted_by_distance_from_diagonal.cpp | 79 -------- ..._weighted_by_squared_distance_from_diagonal.cpp | 79 -------- .../persistence_heat_maps/create_pssk.cpp | 77 -------- .../plot_persistence_heat_map.cpp | 44 ----- .../example/utilities/persistence_intervals/aaa | 51 ----- .../persistence_intervals/aaa_Gnuplot_script | 208 --------------------- ...te_birth_death_range_in_persistence_diagram.cpp | 72 ------- .../compute_number_of_dominant_intervals.cpp | 57 ------ .../plot_histogram_of_intervals_lengths.cpp | 69 ------- .../plot_persistence_Betti_numebrs.cpp | 93 --------- .../plot_persistence_intervals.cpp | 59 ------ .../persistence_landscapes/average_landscapes.cpp | 75 -------- .../compute_distance_of_landscapes.cpp | 109 ----------- .../compute_scalar_product_of_landscapes.cpp | 92 --------- .../persistence_landscapes/create_landscapes.cpp | 56 ------ .../persistence_landscapes/plot_landscapes.cpp | 50 ----- .../average_landscapes_on_grid.cpp | 74 -------- .../compute_distance_of_landscapes_on_grid.cpp | 107 ----------- ...ompute_scalar_product_of_landscapes_on_grid.cpp | 91 --------- .../create_landscapes_on_grid.cpp | 80 -------- .../plot_landscapes_on_grid.cpp | 55 ------ .../average_persistence_vectors.cpp | 75 -------- .../compute_distance_of_persistence_vectors.cpp | 108 ----------- ...mpute_scalar_product_of_persistence_vectors.cpp | 97 ---------- .../create_persistence_vectors.cpp | 57 ------ .../plot_persistence_vectors.cpp | 51 ----- src/Gudhi_stat/example/vector_representation.cpp | 2 +- .../Abs_Real_valued_topological_data.h | 2 +- .../gudhi/abstract_classes/Abs_Topological_data.h | 10 +- .../Abs_Topological_data_with_averages.h | 9 +- .../Abs_Topological_data_with_distances.h | 9 +- .../Abs_Topological_data_with_scalar_product.h | 7 +- .../Abs_Vectorized_topological_data.h | 10 +- .../include/gudhi/concretizations/PSSK.h | 2 +- .../gudhi/concretizations/Persistence_heat_maps.h | 14 +- .../gudhi/concretizations/Persistence_intervals.h | 7 +- .../gudhi/concretizations/Persistence_landscape.h | 6 +- .../Persistence_landscape_on_grid.h | 42 +++-- .../concretizations/Vector_distances_in_diagram.h | 124 ++++++------ .../concretizations/read_persitence_from_file.h | 20 +- src/Gudhi_stat/test/persistence_heat_maps_test.cpp | 2 +- src/Gudhi_stat/test/persistence_intervals_test.cpp | 2 +- .../test/persistence_lanscapes_on_grid_test.cpp | 2 +- src/Gudhi_stat/test/persistence_lanscapes_test.cpp | 2 +- src/Gudhi_stat/test/vector_representation_test.cpp | 4 +- src/Gudhi_stat/utilities/CMakeLists.txt | 103 ++++++++++ .../average_persistence_heat_maps.cpp | 73 ++++++++ .../compute_distance_of_persistence_heat_maps.cpp | 107 +++++++++++ ...ute_scalar_product_of_persistence_heat_maps.cpp | 91 +++++++++ .../create_persistence_heat_maps.cpp | 79 ++++++++ ...aps_weighted_by_arctan_of_their_persistence.cpp | 79 ++++++++ ...eat_maps_weighted_by_distance_from_diagonal.cpp | 79 ++++++++ ..._weighted_by_squared_distance_from_diagonal.cpp | 79 ++++++++ .../persistence_heat_maps/create_pssk.cpp | 77 ++++++++ .../plot_persistence_heat_map.cpp | 44 +++++ ...te_birth_death_range_in_persistence_diagram.cpp | 72 +++++++ .../compute_number_of_dominant_intervals.cpp | 57 ++++++ .../plot_histogram_of_intervals_lengths.cpp | 69 +++++++ .../plot_persistence_Betti_numebrs.cpp | 93 +++++++++ .../plot_persistence_intervals.cpp | 59 ++++++ .../persistence_landscapes/average_landscapes.cpp | 75 ++++++++ .../compute_distance_of_landscapes.cpp | 109 +++++++++++ .../compute_scalar_product_of_landscapes.cpp | 92 +++++++++ .../persistence_landscapes/create_landscapes.cpp | 56 ++++++ .../persistence_landscapes/plot_landscapes.cpp | 50 +++++ .../average_landscapes_on_grid.cpp | 74 ++++++++ .../compute_distance_of_landscapes_on_grid.cpp | 107 +++++++++++ ...ompute_scalar_product_of_landscapes_on_grid.cpp | 91 +++++++++ .../create_landscapes_on_grid.cpp | 80 ++++++++ .../plot_landscapes_on_grid.cpp | 55 ++++++ .../average_persistence_vectors.cpp | 75 ++++++++ .../compute_distance_of_persistence_vectors.cpp | 108 +++++++++++ ...mpute_scalar_product_of_persistence_vectors.cpp | 97 ++++++++++ .../create_persistence_vectors.cpp | 57 ++++++ .../plot_persistence_vectors.cpp | 51 +++++ 86 files changed, 2494 insertions(+), 2721 deletions(-) delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/create_pssk.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_intervals/aaa delete mode 100644 src/Gudhi_stat/example/utilities/persistence_intervals/aaa_Gnuplot_script delete mode 100644 src/Gudhi_stat/example/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_intervals/plot_persistence_intervals.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes/average_landscapes.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes/create_landscapes.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes/plot_landscapes.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_vectors/average_persistence_vectors.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_vectors/create_persistence_vectors.cpp delete mode 100644 src/Gudhi_stat/example/utilities/persistence_vectors/plot_persistence_vectors.cpp create mode 100644 src/Gudhi_stat/utilities/CMakeLists.txt create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp (limited to 'CMakeLists.txt') diff --git a/CMakeLists.txt b/CMakeLists.txt index d7078489..488f1d62 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -145,6 +145,7 @@ else() add_subdirectory(src/Alpha_complex/test) add_subdirectory(src/Gudhi_stat/test) add_subdirectory(src/Gudhi_stat/example) + add_subdirectory(src/Gudhi_stat/utilities) # data points generator add_subdirectory(data/points/generator) diff --git a/src/Gudhi_stat/example/CMakeLists.txt b/src/Gudhi_stat/example/CMakeLists.txt index 613e4d26..5ae6cd6a 100644 --- a/src/Gudhi_stat/example/CMakeLists.txt +++ b/src/Gudhi_stat/example/CMakeLists.txt @@ -17,103 +17,5 @@ add_executable ( persistence_heat_maps persistence_heat_maps.cpp ) target_link_libraries(persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) -##UTILITIES: - -#persitence diagrams -add_executable ( plot_persistence_intervals utilities/persistence_intervals/plot_persistence_intervals.cpp ) -target_link_libraries( plot_persistence_intervals ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_birth_death_range_in_persistence_diagram utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp ) -target_link_libraries( compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_number_of_dominant_intervals utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp ) -target_link_libraries( compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY}) - -add_executable ( plot_histogram_of_intervals_lengths utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp ) -target_link_libraries( plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY}) - -add_executable ( plot_persistence_Betti_numebrs utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp ) -target_link_libraries( plot_persistence_Betti_numebrs ${Boost_SYSTEM_LIBRARY}) - -#when we have bottleneck and wasserstein distance computations, add suitable programs here. - - -#persitence landscapes -add_executable ( average_landscapes utilities/persistence_landscapes/average_landscapes.cpp ) -target_link_libraries(average_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_executable ( create_landscapes utilities/persistence_landscapes/create_landscapes.cpp ) -target_link_libraries(create_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_executable ( plot_landscapes utilities/persistence_landscapes/plot_landscapes.cpp ) -target_link_libraries(plot_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_distance_of_landscapes utilities/persistence_landscapes/compute_distance_of_landscapes.cpp ) -target_link_libraries(compute_distance_of_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_scalar_product_of_landscapes utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp ) -target_link_libraries(compute_scalar_product_of_landscapes ${Boost_SYSTEM_LIBRARY}) - -#persitence landscapes on a grid -add_executable ( average_landscapes_on_grid utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp ) -target_link_libraries(average_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_executable ( create_landscapes_on_grid utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp ) -target_link_libraries(create_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_executable ( plot_landscapes_on_grid utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp ) -target_link_libraries(plot_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_distance_of_landscapes_on_grid utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp ) -target_link_libraries(compute_distance_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_scalar_product_of_landscapes_on_grid utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp ) -target_link_libraries(compute_scalar_product_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -#persitence heat maps -add_executable ( average_persistence_heat_maps utilities/persistence_heat_maps/average_persistence_heat_maps.cpp ) -target_link_libraries(average_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_executable ( create_persistence_heat_maps utilities/persistence_heat_maps/create_persistence_heat_maps.cpp ) -target_link_libraries(create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_executable ( plot_persistence_heat_map utilities/persistence_heat_maps/plot_persistence_heat_map.cpp ) -target_link_libraries(plot_persistence_heat_map ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_distance_of_persistence_heat_maps utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp ) -target_link_libraries(compute_distance_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_scalar_product_of_persistence_heat_maps utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp ) -target_link_libraries(compute_scalar_product_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_executable ( create_pssk utilities/persistence_heat_maps/create_pssk.cpp ) -target_link_libraries(create_pssk ${Boost_SYSTEM_LIBRARY}) - -add_executable ( create_persistence_heat_maps_weighted_by_distance_from_diagonal utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp ) -target_link_libraries(create_persistence_heat_maps_weighted_by_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) - -add_executable ( create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp ) -target_link_libraries(create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) - -add_executable ( create_persistence_heat_maps_weighted_by_arctan_of_their_persistence utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp ) -target_link_libraries(create_persistence_heat_maps_weighted_by_arctan_of_their_persistence ${Boost_SYSTEM_LIBRARY}) - - -#persitence vectors -add_executable ( average_persistence_vectors utilities/persistence_vectors/average_persistence_vectors.cpp ) -target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_executable ( create_persistence_vectors utilities/persistence_vectors/create_persistence_vectors.cpp ) -target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_distance_of_persistence_vectors utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp ) -target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_executable ( compute_scalar_product_of_persistence_vectors utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp ) -target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_executable ( plot_persistence_vectors utilities/persistence_vectors/plot_persistence_vectors.cpp ) -target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - diff --git a/src/Gudhi_stat/example/persistence_heat_maps.cpp b/src/Gudhi_stat/example/persistence_heat_maps.cpp index cd0c4113..e336ab44 100644 --- a/src/Gudhi_stat/example/persistence_heat_maps.cpp +++ b/src/Gudhi_stat/example/persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/example/persistence_intervals.cpp b/src/Gudhi_stat/example/persistence_intervals.cpp index cbd4020d..5357def7 100644 --- a/src/Gudhi_stat/example/persistence_intervals.cpp +++ b/src/Gudhi_stat/example/persistence_intervals.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/example/persistence_landscape.cpp b/src/Gudhi_stat/example/persistence_landscape.cpp index a5b726c7..3204148b 100644 --- a/src/Gudhi_stat/example/persistence_landscape.cpp +++ b/src/Gudhi_stat/example/persistence_landscape.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp b/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp index 2807d76f..e1a0ba5d 100644 --- a/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp +++ b/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp deleted file mode 100644 index d90e78e1..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp +++ /dev/null @@ -1,73 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program computes average persistence landscape of persistence landscapes created based on persistence diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; - std::vector< const char* > filenames; - - if ( argc == 1 ) - { - std::cout << "No input files given, the program will now terminate \n"; - return 1; - } - - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - std::cout << "Creating persistence landscapes...\n"; - std::vector< Abs_Topological_data_with_averages* > maps; - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - Persistence_heat_maps* l = new Persistence_heat_maps; - l->load_from_file( filenames[i] ); - maps.push_back( (Abs_Topological_data_with_averages*)l ); - } - - Persistence_heat_maps av; - av.compute_average( maps ); - - av.print_to_file( "average.mps" ); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - delete maps[i]; - } - - std::cout << "Done \n"; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp deleted file mode 100644 index 10d6f04c..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp +++ /dev/null @@ -1,107 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute dsitance of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the two landscapes. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence landscapes.\n"; - - if ( argc < 3 ) - { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - int p = atoi( argv[1] ); - - std::vector< const char* > filenames; - for ( int i = 2 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Abs_Topological_data_with_distances* > maps; - maps.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - Persistence_heat_maps* l = new Persistence_heat_maps; - l->load_from_file( filenames[file_no] ); - maps.push_back( (Abs_Topological_data_with_distances*)l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > distance( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - distance[i] = v; - } - - //and now we can compute the distnaces: - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - for ( size_t j = i ; j != filenames.size() ; ++j ) - { - distance[i][j] = distance[j][i] = ((Persistence_heat_maps*)maps[i])->distance( maps[j] , p ) ; - } - } - - //and now output the result to the screen and a file: - ofstream out; - out.open( "distance" ); - for ( size_t i = 0 ; i != distance.size() ; ++i ) - { - for ( size_t j = 0 ; j != distance.size() ; ++j ) - { - cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - cout << endl; - out << endl; - } - out.close(); - - return 0; -} - - - - - - - diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp deleted file mode 100644 index cd529f10..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp +++ /dev/null @@ -1,91 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; - - std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Persistence_heat_maps* > maps; - maps.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - Persistence_heat_maps* l = new Persistence_heat_maps; - l->load_from_file( filenames[file_no] ); - maps.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > scalar_product( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - scalar_product[i] = v; - } - - //and now we can compute the scalar product: - for ( size_t i = 0 ; i != maps.size() ; ++i ) - { - for ( size_t j = i ; j != maps.size() ; ++j ) - { - scalar_product[i][j] = scalar_product[j][i] = ((Persistence_heat_maps*)maps[i])->compute_scalar_product( maps[j] ) ; - } - } - - //and now output the result to the screen and a file: - ofstream out; - out.open( "scalar_product" ); - for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) - { - for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) - { - cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - cout << endl; - out << endl; - } - out.close(); - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp deleted file mode 100644 index 3d8dc2e8..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp +++ /dev/null @@ -1,79 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - - -int main( int argc , char** argv ) -{ - std::cout << "This program creates persistence heat map of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if ( argc < 5 ) - { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - size_t size_of_grid = (size_t)atoi( argv[1] ); - double min_ = atof( argv[2] ); - double max_ = atof( argv[3] ); - size_t stdiv = atof( argv[4] ); - - std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - - - std::cout << "Creating persistence heat maps...\n"; - std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; - Persistence_heat_maps l( filenames[i] , filter, constant_function, false , size_of_grid , min_ , max_ ); - - std::stringstream ss; - ss << filenames[i] << ".mps"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp deleted file mode 100644 index 253320ff..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp +++ /dev/null @@ -1,79 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - - -int main( int argc , char** argv ) -{ - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the arcus tangens of their persistence.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if ( argc < 5 ) - { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - size_t size_of_grid = (size_t)atoi( argv[1] ); - double min_ = atof( argv[2] ); - double max_ = atof( argv[3] ); - size_t stdiv = atof( argv[4] ); - - std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - - - std::cout << "Creating persistence heat maps...\n"; - std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; - Persistence_heat_maps l( filenames[i] , filter, arc_tan_of_persistence_of_point, false , size_of_grid , min_ , max_ ); - - std::stringstream ss; - ss << filenames[i] << ".mps"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp deleted file mode 100644 index d7f4fbdd..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp +++ /dev/null @@ -1,79 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - - -int main( int argc , char** argv ) -{ - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the distance of a center from the diagonal.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if ( argc < 5 ) - { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - size_t size_of_grid = (size_t)atoi( argv[1] ); - double min_ = atof( argv[2] ); - double max_ = atof( argv[3] ); - size_t stdiv = atof( argv[4] ); - - std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - - - std::cout << "Creating persistence heat maps...\n"; - std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; - Persistence_heat_maps l( filenames[i] , filter, distance_from_diagonal, false , size_of_grid , min_ , max_ ); - - std::stringstream ss; - ss << filenames[i] << ".mps"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp deleted file mode 100644 index eac0d067..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp +++ /dev/null @@ -1,79 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - - -int main( int argc , char** argv ) -{ - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the square of distance of a center from the diagonal.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if ( argc < 5 ) - { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - size_t size_of_grid = (size_t)atoi( argv[1] ); - double min_ = atof( argv[2] ); - double max_ = atof( argv[3] ); - size_t stdiv = atof( argv[4] ); - - std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - - - std::cout << "Creating persistence heat maps...\n"; - std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; - Persistence_heat_maps l( filenames[i] , filter, squared_distance_from_diagonal, false , size_of_grid , min_ , max_ ); - - std::stringstream ss; - ss << filenames[i] << ".mps"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_pssk.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_pssk.cpp deleted file mode 100644 index ccd884ec..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/create_pssk.cpp +++ /dev/null @@ -1,77 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - - -int main( int argc , char** argv ) -{ - std::cout << "This program creates PSSK of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if ( argc < 5 ) - { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - size_t size_of_grid = (size_t)atoi( argv[1] ); - double min_ = atof( argv[2] ); - double max_ = atof( argv[3] ); - size_t stdiv = atof( argv[4] ); - - std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - std::cout << "Creating persistence heat maps...\n"; - std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; - PSSK l( filenames[i] , filter , size_of_grid , min_ , max_ ); - - std::stringstream ss; - ss << filenames[i] << ".pssk"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Gudhi_stat/example/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp deleted file mode 100644 index b85a502b..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp +++ /dev/null @@ -1,44 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape file \n"; - Persistence_heat_maps l; - l.load_from_file( argv[1] ); - l.plot( argv[1] ); - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_intervals/aaa b/src/Gudhi_stat/example/utilities/persistence_intervals/aaa deleted file mode 100644 index 5aed2ec0..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_intervals/aaa +++ /dev/null @@ -1,51 +0,0 @@ -0.254583 0.837489 -0.25491 0.410985 -0.262238 0.405964 -0.233498 0.338685 -0.253282 0.344571 -0.249923 0.339748 -0.179532 0.263873 -0.247402 0.323782 -0.181315 0.249492 -0.160746 0.22547 -0.170367 0.232149 -0.192048 0.253065 -0.27298 0.333994 -0.202383 0.260308 -0.278325 0.329157 -0.176624 0.226215 -0.200184 0.249281 -0.275607 0.323516 -0.178408 0.224032 -0.319435 0.362706 -0.184347 0.226301 -0.19342 0.23356 -0.143554 0.180648 -0.313975 0.34917 -0.260887 0.29465 -0.206395 0.23344 -0.272846 0.298156 -0.222294 0.246925 -0.272951 0.295696 -0.235421 0.257957 -0.277907 0.29913 -0.16591 0.186925 -0.223042 0.243167 -0.435025 0.454885 -0.151992 0.169807 -0.138011 0.155776 -0.218083 0.235837 -0.219364 0.237079 -0.297063 0.313899 -0.282666 0.298727 -0.24199 0.256381 -0.302722 0.316677 -0.160453 0.174076 -0.157689 0.169984 -0.192957 0.204705 -0.153738 0.165306 -0.226448 0.237898 -0.243627 0.252613 -0.210126 0.21907 -0.172082 0.177708 -0.232291 0.234521 diff --git a/src/Gudhi_stat/example/utilities/persistence_intervals/aaa_Gnuplot_script b/src/Gudhi_stat/example/utilities/persistence_intervals/aaa_Gnuplot_script deleted file mode 100644 index 3ff83e9c..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_intervals/aaa_Gnuplot_script +++ /dev/null @@ -1,208 +0,0 @@ -set xrange [0.131016 : 0.844554] -set yrange [0 : 16.16] -plot '-' using 1:2 notitle with lp -0.138011 0 -0.138011 1 -0.143554 1 -0.143554 2 -0.151992 2 -0.151992 3 -0.153738 3 -0.153738 4 -0.155776 4 -0.155776 3 -0.157689 3 -0.157689 4 -0.160453 4 -0.160453 5 -0.160746 5 -0.160746 6 -0.165306 6 -0.165306 5 -0.16591 5 -0.16591 6 -0.169807 6 -0.169807 5 -0.169984 5 -0.169984 4 -0.170367 4 -0.170367 5 -0.172082 5 -0.172082 6 -0.174076 6 -0.174076 5 -0.176624 5 -0.176624 6 -0.177708 6 -0.177708 5 -0.178408 5 -0.178408 6 -0.179532 6 -0.179532 7 -0.180648 7 -0.180648 6 -0.181315 6 -0.181315 7 -0.184347 7 -0.184347 8 -0.186925 8 -0.186925 7 -0.192048 7 -0.192048 8 -0.192957 8 -0.192957 9 -0.19342 9 -0.19342 10 -0.200184 10 -0.200184 11 -0.202383 11 -0.202383 12 -0.204705 12 -0.204705 11 -0.206395 11 -0.206395 12 -0.210126 12 -0.210126 13 -0.218083 13 -0.218083 14 -0.21907 14 -0.21907 13 -0.219364 13 -0.219364 14 -0.222294 14 -0.222294 15 -0.223042 15 -0.223042 16 -0.224032 16 -0.224032 15 -0.22547 15 -0.22547 14 -0.226215 14 -0.226215 13 -0.226301 13 -0.226301 12 -0.226448 12 -0.226448 13 -0.232149 13 -0.232149 12 -0.232291 12 -0.232291 13 -0.23344 13 -0.23344 12 -0.233498 12 -0.233498 13 -0.23356 13 -0.23356 12 -0.234521 12 -0.234521 11 -0.235421 11 -0.235421 12 -0.235837 12 -0.235837 11 -0.237079 11 -0.237079 10 -0.237898 10 -0.237898 9 -0.24199 9 -0.24199 10 -0.243167 10 -0.243167 9 -0.243627 9 -0.243627 10 -0.246925 10 -0.246925 9 -0.247402 9 -0.247402 10 -0.249281 10 -0.249281 9 -0.249492 9 -0.249492 8 -0.249923 8 -0.249923 9 -0.252613 9 -0.252613 8 -0.253065 8 -0.253065 7 -0.253282 7 -0.253282 8 -0.254583 8 -0.254583 9 -0.25491 9 -0.25491 10 -0.256381 10 -0.256381 9 -0.257957 9 -0.257957 8 -0.260308 8 -0.260308 7 -0.260887 7 -0.260887 8 -0.262238 8 -0.262238 9 -0.263873 9 -0.263873 8 -0.272846 8 -0.272846 9 -0.272951 9 -0.272951 10 -0.27298 10 -0.27298 11 -0.275607 11 -0.275607 12 -0.277907 12 -0.277907 13 -0.278325 13 -0.278325 14 -0.282666 14 -0.282666 15 -0.29465 15 -0.29465 14 -0.295696 14 -0.295696 13 -0.297063 13 -0.297063 14 -0.298156 14 -0.298156 13 -0.298727 13 -0.298727 12 -0.29913 12 -0.29913 11 -0.302722 11 -0.302722 12 -0.313899 12 -0.313899 11 -0.313975 11 -0.313975 12 -0.316677 12 -0.316677 11 -0.319435 11 -0.319435 12 -0.323516 12 -0.323516 11 -0.323782 11 -0.323782 10 -0.329157 10 -0.329157 9 -0.333994 9 -0.333994 8 -0.338685 8 -0.338685 7 -0.339748 7 -0.339748 6 -0.344571 6 -0.344571 5 -0.34917 5 -0.34917 4 -0.362706 4 -0.362706 3 -0.405964 3 -0.405964 2 -0.410985 2 -0.410985 1 -0.435025 1 -0.435025 2 -0.454885 2 -0.454885 1 -0.837489 1 -0.837489 0 - diff --git a/src/Gudhi_stat/example/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Gudhi_stat/example/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp deleted file mode 100644 index dba0984a..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp +++ /dev/null @@ -1,72 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -using namespace std; - - -int main( int argc , char** argv ) -{ - //std::cout << "This program compute minimum birth and the maximum death time for a collection of persistence intervals \n"; - //if ( argc != 2 ) - //{ - // cout << "To run this program, please provide the name of a file with persistence diagram \n"; - // return 1; - //} - //Persistence_intervals p( argv[1] ); - //std::pair min_max_ = p.min_max(); - //cout << "Birth-death range : min: " << min_max_.first << ", max: " << min_max_.second << endl; - - std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - double min_ = std::numeric_limits::max(); - double max_ = -std::numeric_limits::max(); - - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - std::cout << "Creating diagram based on a file : " << filenames[file_no] << std::endl; - Persistence_intervals p( filenames[file_no] ); - std::pair min_max_ = p.min_max(); - if ( min_max_.first < min_ )min_ = min_max_.first; - if ( min_max_.second > max_ )max_ = min_max_.second; - } - cout << "Birth-death range : min: " << min_ << ", max: " << max_ << endl; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Gudhi_stat/example/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp deleted file mode 100644 index 6e6a9c88..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp +++ /dev/null @@ -1,57 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -using namespace std; - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of this program. \n"; - if ( argc != 3 ) - { - cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n"; - return 1; - } - - Persistence_intervals p( argv[1] ); - std::vector< std::pair > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) ); - cout << "Here are the dominant intervals : " << endl; - for ( size_t i = 0 ; i != dominant_intervals.size() ; ++i ) - { - cout << " " << dominant_intervals[i].first<< "," << dominant_intervals[i].second << " "<< endl; - } - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Gudhi_stat/example/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp deleted file mode 100644 index dd2f3f99..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp +++ /dev/null @@ -1,69 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -using namespace std; - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter of this program. \n"; - if ( argc != 3 ) - { - cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n"; - return 1; - } - - Persistence_intervals p( argv[1] ); - std::vector< std::pair > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) ); - std::vector< size_t > histogram = p.histograms_of_lengths( 10 ); - - std::stringstream gnuplot_script; - gnuplot_script << argv[1] << "_Gnuplot_script"; - ofstream out; - out.open( gnuplot_script.str().c_str() ); - - out << "set style data histogram" << std::endl; - out << "set style histogram cluster gap 1" << std::endl; - out << "set style fill solid border -1" << std::endl; - out << "plot '-' notitle" << std::endl; - for ( size_t i = 0 ; i != histogram.size() ; ++i ) - { - out << histogram[i] << std::endl; - } - out << endl; - std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; - out.close(); - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp b/src/Gudhi_stat/example/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp deleted file mode 100644 index 33ff7bce..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp +++ /dev/null @@ -1,93 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -using namespace std; - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with persistence intervals. \n"; - if ( argc != 2 ) - { - cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n"; - return 1; - } - - - - std::stringstream gnuplot_script; - gnuplot_script << argv[1] << "_Gnuplot_script"; - ofstream out; - out.open( gnuplot_script.str().c_str() ); - - Persistence_intervals p( argv[1] ); - std::vector< std::pair< double , size_t > > pbns = p.compute_persistent_betti_numbers(); - - //set up the ranges so that we see the image well. - double xRangeBegin = pbns[0].first; - double xRangeEnd = pbns[ pbns.size()-1 ].first; - double yRangeBegin = 0; - double yRangeEnd = 0; - for ( size_t i = 0 ; i != pbns.size() ; ++i ) - { - if ( pbns[i].second > yRangeEnd )yRangeEnd = pbns[i].second; - } - xRangeBegin -= (xRangeEnd -xRangeBegin)/100.0; - xRangeEnd += (xRangeEnd -xRangeBegin)/100.0; - yRangeEnd += yRangeEnd/100; - - - out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << endl; - out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << endl; - out << "plot '-' using 1:2 notitle with lp " << std::endl; - double previous_y = 0; - for ( size_t i = 0 ; i != pbns.size() ; ++i ) - { - out << pbns[i].first << " " << previous_y << endl; - out << pbns[i].first << " " << pbns[i].second << std::endl; - previous_y = pbns[i].second; - } - out << endl; - out.close(); - - //for ( size_t i = 0 ; i != pbns.size() ; ++i ) - //{ - // cout << pbns[i].first << " " << pbns[i].second << std::endl; - //} - - std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Gudhi_stat/example/utilities/persistence_intervals/plot_persistence_intervals.cpp deleted file mode 100644 index c4dd7284..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_intervals/plot_persistence_intervals.cpp +++ /dev/null @@ -1,59 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - - -double epsilon = 0.0000005; - -using namespace std; - - -int main( int argc , char** argv ) -{ - if ( argc != 2 ) - { - cout << "To run this program, please provide the name of a file with persistence diagram \n"; - return 1; - } - Persistence_intervals b( argv[1] ); - b.plot( argv[1] ); - return 0; -} - - - - - - - diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes/average_landscapes.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes/average_landscapes.cpp deleted file mode 100644 index 418244d2..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes/average_landscapes.cpp +++ /dev/null @@ -1,75 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program computes average persistence landscape of persistence landscapes created based on persistence diagrams provided as an input (you must create them first).\n"; - std::cout << "Please call this program with the names of files with persistence landscapes. The program will create a persistence landscape which will be their average \n"; - std::vector< const char* > filenames; - - if ( argc == 1 ) - { - std::cout << "No input files given, the program will now terminate \n"; - return 1; - } - - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - std::cout << "Creating persistence landscapes...\n"; - std::vector< Abs_Topological_data_with_averages* > lands; - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - Persistence_landscape* l = new Persistence_landscape; - l->load_landscape_from_file( filenames[i] ); - lands.push_back( (Abs_Topological_data_with_averages*)l ); - } - - Persistence_landscape av; - av.compute_average( lands ); - - av.print_to_file( "average.land" ); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - delete lands[i]; - } - - std::cout << "Done \n"; - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp deleted file mode 100644 index 12a4b3bd..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp +++ /dev/null @@ -1,109 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute distance of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the given landscapes. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence landscapes."; - - if ( argc < 3 ) - { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - int p = atoi( argv[1] ); - - std::vector< const char* > filenames; - for ( int i = 2 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Persistence_landscape > landscaspes; - landscaspes.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - std::cout << "Loading persistence landscape from a file : " << filenames[file_no] << std::endl; - Persistence_landscape l; - l.load_landscape_from_file( filenames[file_no] ); - landscaspes.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > distance( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - distance[i] = v; - } - - //and now we can compute the distances: - for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) - { - for ( size_t j = i ; j != landscaspes.size() ; ++j ) - { - distance[i][j] = distance[j][i] = compute_discance_of_landscapes( landscaspes[i], landscaspes[j] , p ) ; - - } - } - - //and now output the result to the screen and a file: - ofstream out; - out.open( "distance" ); - for ( size_t i = 0 ; i != distance.size() ; ++i ) - { - for ( size_t j = 0 ; j != distance.size() ; ++j ) - { - cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - cout << endl; - out << endl; - } - out.close(); - - return 0; -} - - - - - - - diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp deleted file mode 100644 index ac64a798..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp +++ /dev/null @@ -1,92 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; - - std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Persistence_landscape > landscaspes; - landscaspes.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - std::cout << "Reading persistence landscape from a file : " << filenames[file_no] << std::endl; - Persistence_landscape l; - l.load_landscape_from_file( filenames[file_no] ); - landscaspes.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > scalar_product( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - scalar_product[i] = v; - } - - //and now we can compute the scalar product: - for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) - { - for ( size_t j = i ; j != landscaspes.size() ; ++j ) - { - scalar_product[i][j] = scalar_product[j][i] = compute_inner_product( landscaspes[i], landscaspes[j] ) ; - } - } - - //and now output the result to the screen and a file: - ofstream out; - out.open( "scalar_product" ); - for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) - { - for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) - { - cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - cout << endl; - out << endl; - } - out.close(); - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes/create_landscapes.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes/create_landscapes.cpp deleted file mode 100644 index 5152a033..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes/create_landscapes.cpp +++ /dev/null @@ -1,56 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program creates persistence landscapes of diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; - std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - std::cout << "Creating persistence landscapes...\n"; - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - Persistence_landscape l( filenames[i] , 1 ); - std::stringstream ss; - ss << filenames[i] << ".land"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes/plot_landscapes.cpp deleted file mode 100644 index 559fc096..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes/plot_landscapes.cpp +++ /dev/null @@ -1,50 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape file \n"; - Persistence_landscape l; - l.load_landscape_from_file( argv[1] ); - - std::stringstream ss; - ss << argv[1] << "_gnuplot_script"; - l.plot( ss.str().c_str() ); - - std::cout << "Done \n"; - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp deleted file mode 100644 index 7c3b8db2..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp +++ /dev/null @@ -1,74 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program computes average persistence landscape on grid of persistence landscapes on grid created based on persistence diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; - std::vector< const char* > filenames; - - if ( argc == 1 ) - { - std::cout << "No input files given, the program will now terminate \n"; - return 1; - } - - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - std::cout << "Creating persistence landscapes...\n"; - std::vector< Abs_Topological_data_with_averages* > lands; - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - Persistence_landscape_on_grid* l = new Persistence_landscape_on_grid; - l->load_landscape_from_file( filenames[i] ); - lands.push_back( (Abs_Topological_data_with_averages*)l ); - } - - Persistence_landscape_on_grid av; - av.compute_average( lands ); - - av.print_to_file( "average.g_land" ); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - delete lands[i]; - } - - std::cout << "Done \n"; - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp deleted file mode 100644 index 20cb52c9..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp +++ /dev/null @@ -1,107 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute dsitance of persistence landscapes on grid stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the the landscapes on grid. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence landscapes on grid.\n"; - - if ( argc < 3 ) - { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - int p = atoi( argv[1] ); - - std::vector< const char* > filenames; - for ( int i = 2 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Persistence_landscape_on_grid > landscaspes; - landscaspes.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - Persistence_landscape_on_grid l; - l.load_landscape_from_file( filenames[file_no] ); - landscaspes.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > distance( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - distance[i] = v; - } - - //and now we can compute the scalar product: - for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) - { - for ( size_t j = i ; j != landscaspes.size() ; ++j ) - { - distance[i][j] = distance[j][i] = compute_discance_of_landscapes_on_grid( landscaspes[i], landscaspes[j] , p ) ; - } - } - - //and now output the result to the screen and a file: - ofstream out; - out.open( "distance" ); - for ( size_t i = 0 ; i != distance.size() ; ++i ) - { - for ( size_t j = 0 ; j != distance.size() ; ++j ) - { - cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - cout << endl; - out << endl; - } - out.close(); - - return 0; -} - - - - - - - diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp deleted file mode 100644 index 056710ff..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp +++ /dev/null @@ -1,91 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute scalar product of persistence landscapes on grid stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes on grid.\n"; - - std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Persistence_landscape_on_grid > landscaspes; - landscaspes.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - Persistence_landscape_on_grid l; - l.load_landscape_from_file( filenames[file_no] ); - landscaspes.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > scalar_product( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - scalar_product[i] = v; - } - - //and now we can compute the scalar product: - for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) - { - for ( size_t j = i ; j != landscaspes.size() ; ++j ) - { - scalar_product[i][j] = scalar_product[j][i] = compute_inner_product( landscaspes[i], landscaspes[j] ) ; - } - } - - //and now output the result to the screen and a file: - ofstream out; - out.open( "scalar_product" ); - for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) - { - for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) - { - cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - cout << endl; - out << endl; - } - out.close(); - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp deleted file mode 100644 index 2ac74eb3..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp +++ /dev/null @@ -1,80 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program creates persistence landscape on grid of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if ( argc < 4 ) - { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - size_t size_of_grid = (size_t)atoi( argv[1] ); - double min_ = atof( argv[2] ); - double max_ = atof( argv[3] ); - - std::vector< const char* > filenames; - for ( int i = 4 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - std::cout << "Creating persistence landscapes...\n"; - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::cout << "Creating persistence landscape on a grid based on a file : " << filenames[i] << std::endl; - Persistence_landscape_on_grid l; - if ( (min_ != -1) || (max_ != -1) ) - { - l = Persistence_landscape_on_grid( filenames[i] , min_ , max_ , size_of_grid ); - } - else - { - //(min_ == -1) && (max_ == -1), in this case the program will find min_ and max_ based on the data. - l = Persistence_landscape_on_grid( filenames[i] , size_of_grid ); - } - std::stringstream ss; - ss << filenames[i] << ".g_land"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp deleted file mode 100644 index 54b8367b..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp +++ /dev/null @@ -1,55 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape on grid file \n"; - if ( argc == 1 ) - { - std::cout << "Wrong parameters of a program call, the program will now terminate \n"; - return 1; - } - Persistence_landscape_on_grid l; - l.load_landscape_from_file( argv[1] ); - - std::stringstream ss; - ss << argv[1] << "_gnuplot_script"; - l.plot( ss.str().c_str() ); - - std::cout << "Done \n"; - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Gudhi_stat/example/utilities/persistence_vectors/average_persistence_vectors.cpp deleted file mode 100644 index 1b269e9c..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_vectors/average_persistence_vectors.cpp +++ /dev/null @@ -1,75 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program computes average persistence vector of persistence vectors created based on persistence diagrams provided as an input. \n"; - std::cout << "Please call this program with the names of files with persistence diagrams \n"; - std::vector< const char* > filenames; - - if ( argc == 1 ) - { - std::cout << "No input files given, the program will now terminate \n"; - return 1; - } - - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - std::cout << "Reading persistence vectors...\n"; - std::vector< Abs_Topological_data_with_averages* > lands; - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - Vector_distances_in_diagram< euclidean_distance >* l = new Vector_distances_in_diagram< euclidean_distance >; - l->load_from_file( filenames[i] ); - lands.push_back( (Abs_Topological_data_with_averages*)l ); - } - - Vector_distances_in_diagram< euclidean_distance > av; - av.compute_average( lands ); - - av.print_to_file( "average.vect" ); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - delete lands[i]; - } - - std::cout << "Done \n"; - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Gudhi_stat/example/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp deleted file mode 100644 index 72026497..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ /dev/null @@ -1,108 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an interger p. The program compute l^p distance of the vectors. For l^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n"; - - if ( argc < 3 ) - { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - int p = atoi( argv[1] ); - - std::vector< const char* > filenames; - for ( int i = 2 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Vector_distances_in_diagram< euclidean_distance >* > vectors; - vectors.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - //cerr << filenames[file_no] << endl; - Vector_distances_in_diagram< euclidean_distance >* l = new Vector_distances_in_diagram< euclidean_distance >; - l->load_from_file( filenames[file_no] ); - vectors.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > distance( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - distance[i] = v; - } - - //and now we can compute the distances: - for ( size_t i = 0 ; i != vectors.size() ; ++i ) - { - for ( size_t j = i+1 ; j != vectors.size() ; ++j ) - { - distance[i][j] = distance[j][i] = ((Vector_distances_in_diagram< euclidean_distance >*)vectors[i])->distance( vectors[j] , p ) ; - } - } - - //and now output the result to the screen and a file: - ofstream out; - out.open( "distance" ); - for ( size_t i = 0 ; i != distance.size() ; ++i ) - { - for ( size_t j = 0 ; j != distance.size() ; ++j ) - { - cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - cout << endl; - out << endl; - } - out.close(); - - return 0; -} - - - - - - - diff --git a/src/Gudhi_stat/example/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Gudhi_stat/example/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp deleted file mode 100644 index 16192d52..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp +++ /dev/null @@ -1,97 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence vectors.\n"; - - std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Vector_distances_in_diagram< euclidean_distance >* > vectors; - vectors.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - Vector_distances_in_diagram< euclidean_distance >* l = new Vector_distances_in_diagram< euclidean_distance >; - l->load_from_file( filenames[file_no] ); - vectors.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > scalar_product( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - scalar_product[i] = v; - } - - //and now we can compute the scalar product: - for ( size_t i = 0 ; i != vectors.size() ; ++i ) - { - for ( size_t j = i ; j != vectors.size() ; ++j ) - { - scalar_product[i][j] = scalar_product[j][i] = ((Vector_distances_in_diagram< euclidean_distance >*)vectors[i])->compute_scalar_product( vectors[j] ) ; - } - } - - //and now output the result to the screen and a file: - ofstream out; - out.open( "scalar_product" ); - for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) - { - for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) - { - cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - cout << endl; - out << endl; - } - out.close(); - - //cleaning up - for ( size_t i = 0 ; i != vectors.size() ; ++i ) - { - delete vectors[i]; - } - - return 0; -} diff --git a/src/Gudhi_stat/example/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Gudhi_stat/example/utilities/persistence_vectors/create_persistence_vectors.cpp deleted file mode 100644 index 99015e41..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_vectors/create_persistence_vectors.cpp +++ /dev/null @@ -1,57 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program creates persistence vectors of diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; - std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::cerr << "Creatign persistence vectors based on a file : " << filenames[i] << std::endl; - Vector_distances_in_diagram< euclidean_distance > l( filenames[i] , -1 ); - std::stringstream ss; - ss << filenames[i] << ".vect"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; -} - diff --git a/src/Gudhi_stat/example/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Gudhi_stat/example/utilities/persistence_vectors/plot_persistence_vectors.cpp deleted file mode 100644 index ad6c06e2..00000000 --- a/src/Gudhi_stat/example/utilities/persistence_vectors/plot_persistence_vectors.cpp +++ /dev/null @@ -1,51 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) - * - * 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 - - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - -#include -#include - - -int main( int argc , char** argv ) -{ - std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the name of file with persistence vector. \n"; - if ( argc != 2 ) - { - std::cout << "Wrong number of parameters, the program will now terminate. \n"; - return 1; - } - Vector_distances_in_diagram< euclidean_distance > l; - l.load_from_file( argv[1] ); - l.plot( argv[1] ); - - return 0; -} - diff --git a/src/Gudhi_stat/example/vector_representation.cpp b/src/Gudhi_stat/example/vector_representation.cpp index 358de1b0..0581baf4 100644 --- a/src/Gudhi_stat/example/vector_representation.cpp +++ b/src/Gudhi_stat/example/vector_representation.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Real_valued_topological_data.h b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Real_valued_topological_data.h index 9b313e62..09c2cf85 100644 --- a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Real_valued_topological_data.h +++ b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Real_valued_topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data.h b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data.h index 0e3db722..e38ae2df 100644 --- a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data.h +++ b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -20,10 +20,10 @@ * along with this program. If not, see . */ -//#ifndef ABS_Topological_data_H_ -//#define ABS_Topological_data_H_ +#ifndef ABS_Topological_data_H_ +#define ABS_Topological_data_H_ + -#pragma once namespace Gudhi { @@ -44,4 +44,4 @@ class Abs_Topological_data }//namespace Gudhi_stat }//namespace Gudhi -//#endif +#endif diff --git a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_averages.h b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_averages.h index 88220e73..8585a62c 100644 --- a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_averages.h +++ b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_averages.h @@ -5,7 +5,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -23,14 +23,13 @@ #ifndef Abs_Topological_data_with_averages_H_ #define Abs_Topological_data_with_averages_H_ +#include + namespace Gudhi { namespace Gudhi_stat { - -#include - /** * This is an abstract container to store topological information. Most typically, this information will be some representation of persistent homology. @@ -46,7 +45,7 @@ public: //2) Function returns Abs_Topological_data*, and compute the average of all the objects in the vector, plus (*this). //virtual Abs_Topological_data* compute_average( std::vector< Abs_Topological_data_with_averages* > to_average ) = 0; //At the moment I will try to implement option (1). - virtual void compute_average( std::vector< Abs_Topological_data_with_averages* > to_average ) = 0; + virtual void compute_average( const std::vector< Abs_Topological_data_with_averages* >& to_average ) = 0; virtual ~Abs_Topological_data_with_averages(){} protected: }; diff --git a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_distances.h b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_distances.h index 2725c2c6..5b683268 100644 --- a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_distances.h +++ b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_distances.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -23,14 +23,15 @@ #ifndef Abs_Topological_data_with_distances_H_ #define Abs_Topological_data_with_distances_H_ +//#include "Abs_Topological_data.h" +#include + + namespace Gudhi { namespace Gudhi_stat { -//with this path it do not find the files -//#include -#include "Abs_Topological_data.h" /** * This is an abstract container to store topological information. Most typically, this information will be some representation of persistent homology. diff --git a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h index b5e5b175..819b1376 100644 --- a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h +++ b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Topological_data_with_scalar_product.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -23,13 +23,14 @@ #ifndef Abs_Topological_data_with_scalar_product_H #define Abs_Topological_data_with_scalar_product_H_ +#include + + namespace Gudhi { namespace Gudhi_stat { -#include - /** * This is an abstract container to store topological information. Most typically, this information will be some representation of persistent homology. **/ diff --git a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Vectorized_topological_data.h b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Vectorized_topological_data.h index df423688..2f352428 100644 --- a/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Vectorized_topological_data.h +++ b/src/Gudhi_stat/include/gudhi/abstract_classes/Abs_Vectorized_topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -24,17 +24,13 @@ #define Abs_Vectorized_topological_data_H_ #include +#include "Abs_Topological_data.h" +#include namespace Gudhi { namespace Gudhi_stat { - -//with this path it do not find the files -//#include -#include "Abs_Topological_data.h" -#include - using namespace std; /** diff --git a/src/Gudhi_stat/include/gudhi/concretizations/PSSK.h b/src/Gudhi_stat/include/gudhi/concretizations/PSSK.h index 61597ee2..8168b7a7 100644 --- a/src/Gudhi_stat/include/gudhi/concretizations/PSSK.h +++ b/src/Gudhi_stat/include/gudhi/concretizations/PSSK.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_heat_maps.h b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_heat_maps.h index afb0da87..89254f16 100644 --- a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_heat_maps.h +++ b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_heat_maps.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -19,6 +19,9 @@ * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ + +#ifndef Persistence_heat_maps_H +#define Persistence_heat_maps_H //standard include #include @@ -36,7 +39,7 @@ #include #include #include -#include +#include @@ -311,7 +314,7 @@ public: std::vector vectorize( int number_of_function ); double distance( const Abs_Topological_data_with_distances* second_ , double power = 1); double project_to_R( int number_of_function ); - void compute_average( std::vector< Abs_Topological_data_with_averages* > to_average ); + void compute_average( const std::vector< Abs_Topological_data_with_averages* >& to_average ); double compute_scalar_product( const Abs_Topological_data_with_scalar_product* second_ ); protected: @@ -740,7 +743,7 @@ double Persistence_heat_maps::project_to_R( int number_of_function ) return result; } -void Persistence_heat_maps::compute_average( std::vector< Abs_Topological_data_with_averages* > to_average ) +void Persistence_heat_maps::compute_average( const std::vector< Abs_Topological_data_with_averages* >& to_average ) { std::vector maps; maps.reserve( to_average.size() ); @@ -779,3 +782,6 @@ double Persistence_heat_maps::compute_scalar_product( const Abs_Topological_data }//namespace Gudhi_stat }//namespace Gudhi + + +#endif diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_intervals.h b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_intervals.h index e0db0070..f694541b 100644 --- a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_intervals.h +++ b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_intervals.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -517,7 +517,8 @@ std::vector< double > Persistence_intervals::k_n_n( size_t k , size_t where_to_c } std::vector< double > distances_from_diagonal( this->intervals.size() ); std::fill( distances_from_diagonal.begin() , distances_from_diagonal.end() , 0 ); - for ( size_t i = 0 ; i != this->intervals.size() ; ++i ) + + for ( size_t i = 0 ; i != this->intervals.size() ; ++i ) { std::vector< double > distancesFromI; for ( size_t j = i+1 ; j != this->intervals.size() ; ++j ) @@ -602,7 +603,7 @@ std::vector< double > Persistence_intervals::k_n_n( size_t k , size_t where_to_c std::sort( result.begin() , result.end() , std::greater() ); result.resize( std::min( result.size() , where_to_cut ) ); - return result; + return result; } diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape.h b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape.h index 82ee5878..f5f96d34 100644 --- a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape.h +++ b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -42,7 +42,7 @@ #include #include #include -#include +#include using namespace std; @@ -446,7 +446,7 @@ public: } return v; } - void compute_average( std::vector< Abs_Topological_data_with_averages* > to_average ) + void compute_average( const std::vector< Abs_Topological_data_with_averages* >& to_average ) { bool dbg = false; diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape_on_grid.h b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape_on_grid.h index 7afd515d..8afab347 100644 --- a/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape_on_grid.h +++ b/src/Gudhi_stat/include/gudhi/concretizations/Persistence_landscape_on_grid.h @@ -1,3 +1,25 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 . + */ + #ifndef Persistence_landscape_on_grid_H_ #define Persistence_landscape_on_grid_H_ @@ -20,6 +42,7 @@ #include #include #include +#include @@ -47,23 +70,6 @@ struct greater bool operator()(T const &a, T const &b) const { return a > b; } }; -//double epsi = std::numeric_limits::epsilon(); -double epsi = 0.000005; - - -/** - * A procedure used to compare doubles. Typically gien two doubles A and B, comparing A == B is not good idea. In this case, we use the procedure almostEqual with the epsi defined at - * the top of the file. Setting up the epsi give the user a tolerance on what should be consider equal. -**/ -inline bool almost_equal( double a , double b ) -{ - if ( fabs(a-b) < epsi ) - return true; - return false; -} - - - class Persistence_landscape_on_grid : public Abs_Vectorized_topological_data , @@ -739,7 +745,7 @@ public: /** * A function to compute averaged persistence landscape on a grid, based on vector of persistence landscapes on grid (projected to Abs_Topological_data_with_averages*, since this is a concretization of a virtual method. **/ - void compute_average( std::vector< Abs_Topological_data_with_averages* > to_average ) + void compute_average( const std::vector< Abs_Topological_data_with_averages* >& to_average ) { bool dbg = false; diff --git a/src/Gudhi_stat/include/gudhi/concretizations/Vector_distances_in_diagram.h b/src/Gudhi_stat/include/gudhi/concretizations/Vector_distances_in_diagram.h index 5870c652..951d8717 100644 --- a/src/Gudhi_stat/include/gudhi/concretizations/Vector_distances_in_diagram.h +++ b/src/Gudhi_stat/include/gudhi/concretizations/Vector_distances_in_diagram.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -20,7 +20,7 @@ * along with this program. If not, see . */ -#pragma once + #ifndef Vector_distances_in_diagram_H #define Vector_distances_in_diagram_H @@ -38,7 +38,7 @@ #include #include #include -#include +#include using namespace std; namespace Gudhi @@ -88,7 +88,7 @@ public: /** * The constructor that takes as an input a multiset of persistence intervals (given as vector of birth-death pairs). The second parameter is the desiered length of the output vectors. **/ - Vector_distances_in_diagram( std::vector< std::pair< double , double > > intervals , size_t where_to_cut ); + Vector_distances_in_diagram( const std::vector< std::pair< double , double > >& intervals , size_t where_to_cut ); /** * The constructor taking as an input a file with birth-death pairs. The second parameter is the desiered length of the output vectors. @@ -112,9 +112,9 @@ public: template friend ostream& operator << ( ostream& out , const Vector_distances_in_diagram& d ) { - for ( size_t i = 0 ; i != std::min( d.sorted_vector_of_distnaces.size() , d.where_to_cut) ; ++i ) + for ( size_t i = 0 ; i != std::min( d.sorted_vector_of_distances.size() , d.where_to_cut) ; ++i ) { - out << d.sorted_vector_of_distnaces[i] << " "; + out << d.sorted_vector_of_distances[i] << " "; } return out; } @@ -124,14 +124,14 @@ public: **/ inline double vector_in_position( size_t position ) { - if ( position >= this->sorted_vector_of_distnaces.size() )throw("Wrong position in accessing Vector_distances_in_diagram::sorted_vector_of_distnaces\n"); - return this->sorted_vector_of_distnaces[position]; + if ( position >= this->sorted_vector_of_distances.size() )throw("Wrong position in accessing Vector_distances_in_diagram::sorted_vector_of_distances\n"); + return this->sorted_vector_of_distances[position]; } /** * Return a size of a vector. **/ - inline size_t size()const{return this->sorted_vector_of_distnaces.size();} + inline size_t size()const{return this->sorted_vector_of_distances.size();} /** * Write a vector to a file. @@ -156,10 +156,10 @@ public: **/ bool operator == ( const Vector_distances_in_diagram& second ) { - if ( this->sorted_vector_of_distnaces.size() != second.sorted_vector_of_distnaces.size() )return false; - for ( size_t i = 0 ; i != this->sorted_vector_of_distnaces.size() ; ++i ) + if ( this->sorted_vector_of_distances.size() != second.sorted_vector_of_distances.size() )return false; + for ( size_t i = 0 ; i != this->sorted_vector_of_distances.size() ; ++i ) { - if ( !almost_equal(this->sorted_vector_of_distnaces[i] , second.sorted_vector_of_distnaces[i]) )return false; + if ( !almost_equal(this->sorted_vector_of_distances[i] , second.sorted_vector_of_distances[i]) )return false; } return true; } @@ -183,7 +183,7 @@ public: /** * Compute a average of two persistent vectors. **/ - void compute_average( std::vector< Abs_Topological_data_with_averages* > to_average ); + void compute_average( const std::vector< Abs_Topological_data_with_averages* >& to_average ); /** * Compute a distance of two persistent vectors. @@ -200,7 +200,7 @@ public: **/ std::vector< double > output_for_visualization() { - return this->sorted_vector_of_distnaces; + return this->sorted_vector_of_distances; } /** @@ -216,9 +216,9 @@ public: out << "set style histogram cluster gap 1" << std::endl; out << "set style fill solid border -1" << std::endl; out << "plot '-' notitle" << std::endl; - for ( size_t i = 0 ; i != this->sorted_vector_of_distnaces.size() ; ++i ) + for ( size_t i = 0 ; i != this->sorted_vector_of_distances.size() ; ++i ) { - out << this->sorted_vector_of_distnaces[i] << std::endl; + out << this->sorted_vector_of_distances[i] << std::endl; } out << endl; out.close(); @@ -228,12 +228,12 @@ public: private: std::vector< std::pair< double , double > > intervals; - std::vector< double > sorted_vector_of_distnaces; + std::vector< double > sorted_vector_of_distances; - void compute_sorted_vector_of_distnaces_via_heap( size_t where_to_cut ); - void compute_sorted_vector_of_distnaces_via_vector_sorting( size_t where_to_cut ); + void compute_sorted_vector_of_distances_via_heap( size_t where_to_cut ); + void compute_sorted_vector_of_distances_via_vector_sorting( size_t where_to_cut ); - Vector_distances_in_diagram( const std::vector< double >& sorted_vector_of_distnaces_ ):sorted_vector_of_distnaces(sorted_vector_of_distnaces_) + Vector_distances_in_diagram( const std::vector< double >& sorted_vector_of_distances_ ):sorted_vector_of_distances(sorted_vector_of_distances_) { this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); } @@ -241,19 +241,19 @@ private: void set_up_numbers_of_functions_for_vectorization_and_projections_to_reals() { //warning, this function can be only called after filling in the intervals vector. - this->number_of_functions_for_vectorization = this->sorted_vector_of_distnaces.size(); - this->number_of_functions_for_projections_to_reals = this->sorted_vector_of_distnaces.size(); + this->number_of_functions_for_vectorization = this->sorted_vector_of_distances.size(); + this->number_of_functions_for_projections_to_reals = this->sorted_vector_of_distances.size(); } }; template -Vector_distances_in_diagram::Vector_distances_in_diagram( std::vector< std::pair< double,double > > intervals_ , size_t where_to_cut ):Abs_Vectorized_topological_data(where_to_cut) +Vector_distances_in_diagram::Vector_distances_in_diagram( const std::vector< std::pair< double,double > >& intervals_ , size_t where_to_cut ):Abs_Vectorized_topological_data(where_to_cut) { std::vector< std::pair< double,double > > i( intervals_ ); this->intervals = i; - //this->compute_sorted_vector_of_distnaces_via_heap( where_to_cut ); - this->compute_sorted_vector_of_distnaces_via_vector_sorting(where_to_cut); + //this->compute_sorted_vector_of_distances_via_heap( where_to_cut ); + this->compute_sorted_vector_of_distances_via_vector_sorting(where_to_cut); this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); } @@ -262,8 +262,8 @@ Vector_distances_in_diagram::Vector_distances_in_diagram( const Vector_distan { std::vector< std::pair< double,double > > inter( org.intervals ); this->intervals = inter; - std::vector< double > sorted_vector_of_distnaces( org.sorted_vector_of_distnaces ); - this->sorted_vector_of_distnaces = sorted_vector_of_distnaces; + std::vector< double > sorted_vector_of_distances( org.sorted_vector_of_distances ); + this->sorted_vector_of_distances = sorted_vector_of_distances; set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); } @@ -273,8 +273,8 @@ Vector_distances_in_diagram& Vector_distances_in_diagram::operator =( cons { std::vector< std::pair< double , double > > inter( org.intervals ); this->intervals = inter; - std::vector< double > sorted_vector_of_distnaces( org.sorted_vector_of_distnaces ); - this->sorted_vector_of_distnaces = sorted_vector_of_distnaces; + std::vector< double > sorted_vector_of_distances( org.sorted_vector_of_distances ); + this->sorted_vector_of_distances = sorted_vector_of_distances; return *this; } @@ -288,13 +288,13 @@ Vector_distances_in_diagram::Vector_distances_in_diagram( const char* filenam //std::vector< std::pair< double , double > > intervals = read_gudhi_file( filename , dimension ); this->intervals = intervals; - this->compute_sorted_vector_of_distnaces_via_heap( where_to_cut ); - //this->compute_sorted_vector_of_distnaces_via_vector_sorting( where_to_cut ); + this->compute_sorted_vector_of_distances_via_heap( where_to_cut ); + //this->compute_sorted_vector_of_distances_via_vector_sorting( where_to_cut ); set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); } template < typename F> -void Vector_distances_in_diagram::compute_sorted_vector_of_distnaces_via_heap( size_t where_to_cut ) +void Vector_distances_in_diagram::compute_sorted_vector_of_distances_via_heap( size_t where_to_cut ) { bool dbg = false; @@ -387,14 +387,14 @@ void Vector_distances_in_diagram::compute_sorted_vector_of_distnaces_via_heap std::cout << endl; } - this->sorted_vector_of_distnaces = heap; + this->sorted_vector_of_distances = heap; } template < typename F> -void Vector_distances_in_diagram::compute_sorted_vector_of_distnaces_via_vector_sorting( size_t where_to_cut ) +void Vector_distances_in_diagram::compute_sorted_vector_of_distances_via_vector_sorting( size_t where_to_cut ) { std::vector< double > distances; distances.reserve( (size_t)(0.5 * this->intervals.size() * ( this->intervals.size() - 1 ) + this->intervals.size()) ); @@ -421,7 +421,7 @@ void Vector_distances_in_diagram::compute_sorted_vector_of_distnaces_via_vect std::sort( distances.begin() , distances.end() , std::greater() ); if ( distances.size() > where_to_cut )distances.resize( where_to_cut ); - this->sorted_vector_of_distnaces = distances; + this->sorted_vector_of_distances = distances; } @@ -436,13 +436,13 @@ double Vector_distances_in_diagram::project_to_R( int number_of_function ) double result = 0; for ( size_t i = 0 ; i != number_of_function ; ++i ) { - result += sorted_vector_of_distnaces[i]; + result += sorted_vector_of_distances[i]; } return result; } template -void Vector_distances_in_diagram::compute_average( std::vector< Abs_Topological_data_with_averages* > to_average ) +void Vector_distances_in_diagram::compute_average( const std::vector< Abs_Topological_data_with_averages* >& to_average ) { if ( to_average.size() == 0 ) @@ -455,9 +455,9 @@ void Vector_distances_in_diagram::compute_average( std::vector< Abs_Topologic for ( size_t i = 0 ; i != to_average.size() ; ++i ) { Vector_distances_in_diagram* current = (Vector_distances_in_diagram*)to_average[i]; - if ( current->sorted_vector_of_distnaces.size() > maximal_length_of_vector ) + if ( current->sorted_vector_of_distances.size() > maximal_length_of_vector ) { - maximal_length_of_vector = current->sorted_vector_of_distnaces.size(); + maximal_length_of_vector = current->sorted_vector_of_distances.size(); } } @@ -467,9 +467,9 @@ void Vector_distances_in_diagram::compute_average( std::vector< Abs_Topologic for ( size_t i = 0 ; i != to_average.size() ; ++i ) { Vector_distances_in_diagram* current = (Vector_distances_in_diagram*)to_average[i]; - for ( size_t j = 0 ; j != current->sorted_vector_of_distnaces.size() ; ++j ) + for ( size_t j = 0 ; j != current->sorted_vector_of_distances.size() ; ++j ) { - av[j] += current->sorted_vector_of_distnaces[j]; + av[j] += current->sorted_vector_of_distances[j]; } } @@ -477,7 +477,7 @@ void Vector_distances_in_diagram::compute_average( std::vector< Abs_Topologic { av[i] /= (double)to_average.size(); } - this->sorted_vector_of_distnaces = av; + this->sorted_vector_of_distances = av; this->where_to_cut = av.size(); } @@ -498,40 +498,40 @@ double Vector_distances_in_diagram::distance( const Abs_Topological_data_with double result = 0; - for ( size_t i = 0 ; i != std::min(this->sorted_vector_of_distnaces.size(), second_->sorted_vector_of_distnaces.size()) ; ++i ) + for ( size_t i = 0 ; i != std::min(this->sorted_vector_of_distances.size(), second_->sorted_vector_of_distances.size()) ; ++i ) { if ( power == 1 ) { if ( dbg ) { - cerr << "|" << this->sorted_vector_of_distnaces[i] << " - " << second_->sorted_vector_of_distnaces[i] << " | : " << fabs( this->sorted_vector_of_distnaces[i] - second_->sorted_vector_of_distnaces[i] ) << endl; + cerr << "|" << this->sorted_vector_of_distances[i] << " - " << second_->sorted_vector_of_distances[i] << " | : " << fabs( this->sorted_vector_of_distances[i] - second_->sorted_vector_of_distances[i] ) << endl; } - result += fabs( this->sorted_vector_of_distnaces[i] - second_->sorted_vector_of_distnaces[i] ); + result += fabs( this->sorted_vector_of_distances[i] - second_->sorted_vector_of_distances[i] ); } else { - result += std::pow( fabs( this->sorted_vector_of_distnaces[i] - second_->sorted_vector_of_distnaces[i] ) , power ); + result += std::pow( fabs( this->sorted_vector_of_distances[i] - second_->sorted_vector_of_distances[i] ) , power ); if ( dbg ) { - cerr << "| " << this->sorted_vector_of_distnaces[i] << " - " << second_->sorted_vector_of_distnaces[i] << " : " << fabs( this->sorted_vector_of_distnaces[i] - second_->sorted_vector_of_distnaces[i] ) << endl; + cerr << "| " << this->sorted_vector_of_distances[i] << " - " << second_->sorted_vector_of_distances[i] << " : " << fabs( this->sorted_vector_of_distances[i] - second_->sorted_vector_of_distances[i] ) << endl; } } } - if ( this->sorted_vector_of_distnaces.size() != second_->sorted_vector_of_distnaces.size() ) + if ( this->sorted_vector_of_distances.size() != second_->sorted_vector_of_distances.size() ) { - if ( this->sorted_vector_of_distnaces.size() > second_->sorted_vector_of_distnaces.size() ) + if ( this->sorted_vector_of_distances.size() > second_->sorted_vector_of_distances.size() ) { - for ( size_t i = second_->sorted_vector_of_distnaces.size() ; i != this->sorted_vector_of_distnaces.size() ; ++i ) + for ( size_t i = second_->sorted_vector_of_distances.size() ; i != this->sorted_vector_of_distances.size() ; ++i ) { - result += fabs( this->sorted_vector_of_distnaces[i] ); + result += fabs( this->sorted_vector_of_distances[i] ); } } else { - //this->sorted_vector_of_distnaces.size() < second_->sorted_vector_of_distnaces.size() - for ( size_t i = this->sorted_vector_of_distnaces.size() ; i != second_->sorted_vector_of_distnaces.size() ; ++i ) + //this->sorted_vector_of_distances.size() < second_->sorted_vector_of_distances.size() + for ( size_t i = this->sorted_vector_of_distances.size() ; i != second_->sorted_vector_of_distances.size() ; ++i ) { - result += fabs( second_->sorted_vector_of_distnaces[i] ); + result += fabs( second_->sorted_vector_of_distances[i] ); } } } @@ -550,10 +550,10 @@ std::vector Vector_distances_in_diagram::vectorize( int number_of_fun if ( number_of_function > this->number_of_functions_for_vectorization )throw "Wrong index of a function in a method Vector_distances_in_diagram::vectorize"; if ( number_of_function < 0 )throw "Wrong index of a function in a method Vector_distances_in_diagram::vectorize"; - std::vector< double > result( std::min( (size_t)number_of_function , this->sorted_vector_of_distnaces.size() ) ); - for ( size_t i = 0 ; i != std::min( (size_t)number_of_function , this->sorted_vector_of_distnaces.size() ) ; ++i ) + std::vector< double > result( std::min( (size_t)number_of_function , this->sorted_vector_of_distances.size() ) ); + for ( size_t i = 0 ; i != std::min( (size_t)number_of_function , this->sorted_vector_of_distances.size() ) ; ++i ) { - result[i] = this->sorted_vector_of_distnaces[i]; + result[i] = this->sorted_vector_of_distances[i]; } return result; } @@ -565,9 +565,9 @@ void Vector_distances_in_diagram::write_to_file( const char* filename ) std::ofstream out; out.open( filename ); - for ( size_t i = 0 ; i != this->sorted_vector_of_distnaces.size() ; ++i ) + for ( size_t i = 0 ; i != this->sorted_vector_of_distances.size() ; ++i ) { - out << this->sorted_vector_of_distnaces[i] << " "; + out << this->sorted_vector_of_distances[i] << " "; } out.close(); @@ -590,7 +590,7 @@ void Vector_distances_in_diagram::load_from_file( const char* filename ) { in >> number; if ( in.eof() )break; - this->sorted_vector_of_distnaces.push_back(number); + this->sorted_vector_of_distances.push_back(number); } in.close(); } @@ -601,9 +601,9 @@ double Vector_distances_in_diagram::compute_scalar_product( const Abs_Topolog Vector_distances_in_diagram* second_vector = (Vector_distances_in_diagram*)second; double result = 0; - for ( size_t i = 0 ; i != std::min(this->sorted_vector_of_distnaces.size(),second_vector->sorted_vector_of_distnaces.size()) ; ++i ) + for ( size_t i = 0 ; i != std::min(this->sorted_vector_of_distances.size(),second_vector->sorted_vector_of_distances.size()) ; ++i ) { - result += this->sorted_vector_of_distnaces[i] * second_vector->sorted_vector_of_distnaces[i]; + result += this->sorted_vector_of_distances[i] * second_vector->sorted_vector_of_distances[i]; } return result; } diff --git a/src/Gudhi_stat/include/gudhi/concretizations/read_persitence_from_file.h b/src/Gudhi_stat/include/gudhi/concretizations/read_persitence_from_file.h index d2e6ec3c..03446289 100644 --- a/src/Gudhi_stat/include/gudhi/concretizations/read_persitence_from_file.h +++ b/src/Gudhi_stat/include/gudhi/concretizations/read_persitence_from_file.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -35,7 +35,12 @@ namespace Gudhi namespace Gudhi_stat { - +/** + * This method reads persistence from standalone file. The format of the file is as follows: + * In every line there are two numbers which denotes birth and death of a persistence interval. The file is not supposed to contains any nonwhite characters excet from digits. In particular symbols + * like 'inf' are not allowed. + * If begin of the interval is greater than the end of the interval, those two numbers are swapped. +**/ std::vector< std::pair< double , double > > read_standard_file( const char* filename ) { bool dbg = false; @@ -78,6 +83,17 @@ std::vector< std::pair< double , double > > read_standard_file( const char* file return barcode; }//read_standard_file + + +/** + * This procedure reads Gudhi style file. The format of a Gudhi style file is as follows: + * Each line consist of the following information: + * A prime number p indicating that the class is nontrivial over Z_p field. + * A positive numebr, being a dimension of a persistence class + * A birth and a death time of a class. + * Death time may be infitnity, in which case a string 'inf' is used. + * If begin of the interval is greater than the end of the interval, those two numbers are swapped. +**/ std::vector< std::pair< double , double > > read_gudhi_file( const char* filename , size_t dimension = 0 ) { bool dbg = false; diff --git a/src/Gudhi_stat/test/persistence_heat_maps_test.cpp b/src/Gudhi_stat/test/persistence_heat_maps_test.cpp index 505b1912..c4c97d72 100644 --- a/src/Gudhi_stat/test/persistence_heat_maps_test.cpp +++ b/src/Gudhi_stat/test/persistence_heat_maps_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/test/persistence_intervals_test.cpp b/src/Gudhi_stat/test/persistence_intervals_test.cpp index 70e20ed0..f86300fa 100644 --- a/src/Gudhi_stat/test/persistence_intervals_test.cpp +++ b/src/Gudhi_stat/test/persistence_intervals_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp index 7d0b58a5..d7d72d6b 100644 --- a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp +++ b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/test/persistence_lanscapes_test.cpp b/src/Gudhi_stat/test/persistence_lanscapes_test.cpp index 8a7d0ce1..9506410a 100644 --- a/src/Gudhi_stat/test/persistence_lanscapes_test.cpp +++ b/src/Gudhi_stat/test/persistence_lanscapes_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 diff --git a/src/Gudhi_stat/test/vector_representation_test.cpp b/src/Gudhi_stat/test/vector_representation_test.cpp index e87d1b23..44801ad9 100644 --- a/src/Gudhi_stat/test/vector_representation_test.cpp +++ b/src/Gudhi_stat/test/vector_representation_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * Copyright (C) 2015 INRIA (France) * * 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 @@ -22,7 +22,7 @@ #include -#include +#include #include #define BOOST_TEST_DYN_LINK diff --git a/src/Gudhi_stat/utilities/CMakeLists.txt b/src/Gudhi_stat/utilities/CMakeLists.txt new file mode 100644 index 00000000..d75acc43 --- /dev/null +++ b/src/Gudhi_stat/utilities/CMakeLists.txt @@ -0,0 +1,103 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + + + +#persitence diagrams +add_executable ( persistence_intervals/plot_persistence_intervals persistence_intervals/plot_persistence_intervals.cpp ) +target_link_libraries( persistence_intervals/plot_persistence_intervals ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_intervals/compute_birth_death_range_in_persistence_diagram persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp ) +target_link_libraries( persistence_intervals/compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_intervals/compute_number_of_dominant_intervals persistence_intervals/compute_number_of_dominant_intervals.cpp ) +target_link_libraries( persistence_intervals/compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_intervals/plot_histogram_of_intervals_lengths persistence_intervals/plot_histogram_of_intervals_lengths.cpp ) +target_link_libraries( persistence_intervals/plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_intervals/plot_persistence_Betti_numebrs persistence_intervals/plot_persistence_Betti_numebrs.cpp ) +target_link_libraries( persistence_intervals/plot_persistence_Betti_numebrs ${Boost_SYSTEM_LIBRARY}) + +#when we have bottleneck and wasserstein distance computations, add suitable programs here. + + +#persitence landscapes +add_executable ( persistence_landscapes/average_landscapes persistence_landscapes/average_landscapes.cpp ) +target_link_libraries(persistence_landscapes/average_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscapes/create_landscapes persistence_landscapes/create_landscapes.cpp ) +target_link_libraries(persistence_landscapes/create_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscapes/plot_landscapes persistence_landscapes/plot_landscapes.cpp ) +target_link_libraries(persistence_landscapes/plot_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscapes/compute_distance_of_landscapes persistence_landscapes/compute_distance_of_landscapes.cpp ) +target_link_libraries(persistence_landscapes/compute_distance_of_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscapes/compute_scalar_product_of_landscapes persistence_landscapes/compute_scalar_product_of_landscapes.cpp ) +target_link_libraries(persistence_landscapes/compute_scalar_product_of_landscapes ${Boost_SYSTEM_LIBRARY}) + +#persitence landscapes on a grid +add_executable ( persistence_landscapes_on_grid/average_landscapes_on_grid persistence_landscapes_on_grid/average_landscapes_on_grid.cpp ) +target_link_libraries(persistence_landscapes_on_grid/average_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscapes_on_grid/create_landscapes_on_grid persistence_landscapes_on_grid/create_landscapes_on_grid.cpp ) +target_link_libraries(persistence_landscapes_on_grid/create_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscapes_on_grid/plot_landscapes_on_grid persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp ) +target_link_libraries(persistence_landscapes_on_grid/plot_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp ) +target_link_libraries(persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp ) +target_link_libraries(persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +#persitence heat maps +add_executable ( persistence_heat_maps/average_persistence_heat_maps persistence_heat_maps/average_persistence_heat_maps.cpp ) +target_link_libraries(persistence_heat_maps/average_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps/create_persistence_heat_maps persistence_heat_maps/create_persistence_heat_maps.cpp ) +target_link_libraries(persistence_heat_maps/create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps/plot_persistence_heat_map persistence_heat_maps/plot_persistence_heat_map.cpp ) +target_link_libraries(persistence_heat_maps/plot_persistence_heat_map ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps/compute_distance_of_persistence_heat_maps persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp ) +target_link_libraries(persistence_heat_maps/compute_distance_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp ) +target_link_libraries(persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps/create_pssk persistence_heat_maps/create_pssk.cpp ) +target_link_libraries(persistence_heat_maps/create_pssk ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp ) +target_link_libraries(persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp ) +target_link_libraries(persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp ) +target_link_libraries(persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence ${Boost_SYSTEM_LIBRARY}) + + +#persitence vectors +add_executable ( persistence_vectors/average_persistence_vectors persistence_vectors/average_persistence_vectors.cpp ) +target_link_libraries(persistence_vectors/average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_vectors/create_persistence_vectors persistence_vectors/create_persistence_vectors.cpp ) +target_link_libraries(persistence_vectors/create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_vectors/compute_distance_of_persistence_vectors persistence_vectors/compute_distance_of_persistence_vectors.cpp ) +target_link_libraries(persistence_vectors/compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_vectors/compute_scalar_product_of_persistence_vectors persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp ) +target_link_libraries(persistence_vectors/compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_vectors/plot_persistence_vectors persistence_vectors/plot_persistence_vectors.cpp ) +target_link_libraries(persistence_vectors/plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + + + diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp new file mode 100644 index 00000000..811e4557 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp @@ -0,0 +1,73 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program computes average persistence landscape of persistence landscapes created based on persistence diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; + std::vector< const char* > filenames; + + if ( argc == 1 ) + { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Creating persistence landscapes...\n"; + std::vector< Abs_Topological_data_with_averages* > maps; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Persistence_heat_maps* l = new Persistence_heat_maps; + l->load_from_file( filenames[i] ); + maps.push_back( (Abs_Topological_data_with_averages*)l ); + } + + Persistence_heat_maps av; + av.compute_average( maps ); + + av.print_to_file( "average.mps" ); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + delete maps[i]; + } + + std::cout << "Done \n"; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp new file mode 100644 index 00000000..e462f009 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp @@ -0,0 +1,107 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute dsitance of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the two landscapes. For L^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence landscapes.\n"; + + if ( argc < 3 ) + { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + int p = atoi( argv[1] ); + + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Abs_Topological_data_with_distances* > maps; + maps.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + Persistence_heat_maps* l = new Persistence_heat_maps; + l->load_from_file( filenames[file_no] ); + maps.push_back( (Abs_Topological_data_with_distances*)l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > distance( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + distance[i] = v; + } + + //and now we can compute the distnaces: + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + for ( size_t j = i ; j != filenames.size() ; ++j ) + { + distance[i][j] = distance[j][i] = ((Persistence_heat_maps*)maps[i])->distance( maps[j] , p ) ; + } + } + + //and now output the result to the screen and a file: + ofstream out; + out.open( "distance" ); + for ( size_t i = 0 ; i != distance.size() ; ++i ) + { + for ( size_t j = 0 ; j != distance.size() ; ++j ) + { + cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + cout << endl; + out << endl; + } + out.close(); + + return 0; +} + + + + + + + diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp new file mode 100644 index 00000000..c9ffa22e --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp @@ -0,0 +1,91 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Persistence_heat_maps* > maps; + maps.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + Persistence_heat_maps* l = new Persistence_heat_maps; + l->load_from_file( filenames[file_no] ); + maps.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > scalar_product( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + scalar_product[i] = v; + } + + //and now we can compute the scalar product: + for ( size_t i = 0 ; i != maps.size() ; ++i ) + { + for ( size_t j = i ; j != maps.size() ; ++j ) + { + scalar_product[i][j] = scalar_product[j][i] = ((Persistence_heat_maps*)maps[i])->compute_scalar_product( maps[j] ) ; + } + } + + //and now output the result to the screen and a file: + ofstream out; + out.open( "scalar_product" ); + for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) + { + for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) + { + cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + cout << endl; + out << endl; + } + out.close(); + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp new file mode 100644 index 00000000..2cc00b87 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -0,0 +1,79 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence heat map of diagrams provided as an input.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if ( argc < 5 ) + { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi( argv[1] ); + double min_ = atof( argv[2] ); + double max_ = atof( argv[3] ); + size_t stdiv = atof( argv[4] ); + + std::vector< const char* > filenames; + for ( int i = 5 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + + + std::cout << "Creating persistence heat maps...\n"; + std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l( filenames[i] , filter, constant_function, false , size_of_grid , min_ , max_ ); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp new file mode 100644 index 00000000..ae579329 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp @@ -0,0 +1,79 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the arcus tangens of their persistence.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if ( argc < 5 ) + { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi( argv[1] ); + double min_ = atof( argv[2] ); + double max_ = atof( argv[3] ); + size_t stdiv = atof( argv[4] ); + + std::vector< const char* > filenames; + for ( int i = 5 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + + + std::cout << "Creating persistence heat maps...\n"; + std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l( filenames[i] , filter, arc_tan_of_persistence_of_point, false , size_of_grid , min_ , max_ ); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp new file mode 100644 index 00000000..7877d699 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp @@ -0,0 +1,79 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the distance of a center from the diagonal.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if ( argc < 5 ) + { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi( argv[1] ); + double min_ = atof( argv[2] ); + double max_ = atof( argv[3] ); + size_t stdiv = atof( argv[4] ); + + std::vector< const char* > filenames; + for ( int i = 5 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + + + std::cout << "Creating persistence heat maps...\n"; + std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l( filenames[i] , filter, distance_from_diagonal, false , size_of_grid , min_ , max_ ); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp new file mode 100644 index 00000000..67972afe --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp @@ -0,0 +1,79 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the square of distance of a center from the diagonal.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if ( argc < 5 ) + { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi( argv[1] ); + double min_ = atof( argv[2] ); + double max_ = atof( argv[3] ); + size_t stdiv = atof( argv[4] ); + + std::vector< const char* > filenames; + for ( int i = 5 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + + + std::cout << "Creating persistence heat maps...\n"; + std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l( filenames[i] , filter, squared_distance_from_diagonal, false , size_of_grid , min_ , max_ ); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp new file mode 100644 index 00000000..1fc9d263 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp @@ -0,0 +1,77 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates PSSK of diagrams provided as an input.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if ( argc < 5 ) + { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi( argv[1] ); + double min_ = atof( argv[2] ); + double max_ = atof( argv[3] ); + size_t stdiv = atof( argv[4] ); + + std::vector< const char* > filenames; + for ( int i = 5 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector< std::vector > filter = create_Gaussian_filter(stdiv,1); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + PSSK l( filenames[i] , filter , size_of_grid , min_ , max_ ); + + std::stringstream ss; + ss << filenames[i] << ".pssk"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp new file mode 100644 index 00000000..6b67ea57 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -0,0 +1,44 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape file \n"; + Persistence_heat_maps l; + l.load_from_file( argv[1] ); + l.plot( argv[1] ); + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp new file mode 100644 index 00000000..2c55a806 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -0,0 +1,72 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +using namespace std; + + +int main( int argc , char** argv ) +{ + //std::cout << "This program compute minimum birth and the maximum death time for a collection of persistence intervals \n"; + //if ( argc != 2 ) + //{ + // cout << "To run this program, please provide the name of a file with persistence diagram \n"; + // return 1; + //} + //Persistence_intervals p( argv[1] ); + //std::pair min_max_ = p.min_max(); + //cout << "Birth-death range : min: " << min_max_.first << ", max: " << min_max_.second << endl; + + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + double min_ = std::numeric_limits::max(); + double max_ = -std::numeric_limits::max(); + + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + std::cout << "Creating diagram based on a file : " << filenames[file_no] << std::endl; + Persistence_intervals p( filenames[file_no] ); + std::pair min_max_ = p.min_max(); + if ( min_max_.first < min_ )min_ = min_max_.first; + if ( min_max_.second > max_ )max_ = min_max_.second; + } + cout << "Birth-death range : min: " << min_ << ", max: " << max_ << endl; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp new file mode 100644 index 00000000..b29aea3a --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -0,0 +1,57 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +using namespace std; + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of this program. \n"; + if ( argc != 3 ) + { + cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n"; + return 1; + } + + Persistence_intervals p( argv[1] ); + std::vector< std::pair > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) ); + cout << "Here are the dominant intervals : " << endl; + for ( size_t i = 0 ; i != dominant_intervals.size() ; ++i ) + { + cout << " " << dominant_intervals[i].first<< "," << dominant_intervals[i].second << " "<< endl; + } + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp new file mode 100644 index 00000000..99f7e640 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -0,0 +1,69 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +using namespace std; + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter of this program. \n"; + if ( argc != 3 ) + { + cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n"; + return 1; + } + + Persistence_intervals p( argv[1] ); + std::vector< std::pair > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) ); + std::vector< size_t > histogram = p.histograms_of_lengths( 10 ); + + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_Gnuplot_script"; + ofstream out; + out.open( gnuplot_script.str().c_str() ); + + out << "set style data histogram" << std::endl; + out << "set style histogram cluster gap 1" << std::endl; + out << "set style fill solid border -1" << std::endl; + out << "plot '-' notitle" << std::endl; + for ( size_t i = 0 ; i != histogram.size() ; ++i ) + { + out << histogram[i] << std::endl; + } + out << endl; + std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + out.close(); + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp new file mode 100644 index 00000000..e23a4f20 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp @@ -0,0 +1,93 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +using namespace std; + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with persistence intervals. \n"; + if ( argc != 2 ) + { + cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n"; + return 1; + } + + + + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_Gnuplot_script"; + ofstream out; + out.open( gnuplot_script.str().c_str() ); + + Persistence_intervals p( argv[1] ); + std::vector< std::pair< double , size_t > > pbns = p.compute_persistent_betti_numbers(); + + //set up the ranges so that we see the image well. + double xRangeBegin = pbns[0].first; + double xRangeEnd = pbns[ pbns.size()-1 ].first; + double yRangeBegin = 0; + double yRangeEnd = 0; + for ( size_t i = 0 ; i != pbns.size() ; ++i ) + { + if ( pbns[i].second > yRangeEnd )yRangeEnd = pbns[i].second; + } + xRangeBegin -= (xRangeEnd -xRangeBegin)/100.0; + xRangeEnd += (xRangeEnd -xRangeBegin)/100.0; + yRangeEnd += yRangeEnd/100; + + + out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << endl; + out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << endl; + out << "plot '-' using 1:2 notitle with lp " << std::endl; + double previous_y = 0; + for ( size_t i = 0 ; i != pbns.size() ; ++i ) + { + out << pbns[i].first << " " << previous_y << endl; + out << pbns[i].first << " " << pbns[i].second << std::endl; + previous_y = pbns[i].second; + } + out << endl; + out.close(); + + //for ( size_t i = 0 ; i != pbns.size() ; ++i ) + //{ + // cout << pbns[i].first << " " << pbns[i].second << std::endl; + //} + + std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp new file mode 100644 index 00000000..5950240e --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -0,0 +1,59 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + + +double epsilon = 0.0000005; + +using namespace std; + + +int main( int argc , char** argv ) +{ + if ( argc != 2 ) + { + cout << "To run this program, please provide the name of a file with persistence diagram \n"; + return 1; + } + Persistence_intervals b( argv[1] ); + b.plot( argv[1] ); + return 0; +} + + + + + + + diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp new file mode 100644 index 00000000..895146f5 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes/average_landscapes.cpp @@ -0,0 +1,75 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program computes average persistence landscape of persistence landscapes created based on persistence diagrams provided as an input (you must create them first).\n"; + std::cout << "Please call this program with the names of files with persistence landscapes. The program will create a persistence landscape which will be their average \n"; + std::vector< const char* > filenames; + + if ( argc == 1 ) + { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Creating persistence landscapes...\n"; + std::vector< Abs_Topological_data_with_averages* > lands; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Persistence_landscape* l = new Persistence_landscape; + l->load_landscape_from_file( filenames[i] ); + lands.push_back( (Abs_Topological_data_with_averages*)l ); + } + + Persistence_landscape av; + av.compute_average( lands ); + + av.print_to_file( "average.land" ); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + delete lands[i]; + } + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp new file mode 100644 index 00000000..34ec0bfa --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -0,0 +1,109 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute distance of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the given landscapes. For L^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence landscapes."; + + if ( argc < 3 ) + { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + int p = atoi( argv[1] ); + + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Persistence_landscape > landscaspes; + landscaspes.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + std::cout << "Loading persistence landscape from a file : " << filenames[file_no] << std::endl; + Persistence_landscape l; + l.load_landscape_from_file( filenames[file_no] ); + landscaspes.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > distance( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + distance[i] = v; + } + + //and now we can compute the distances: + for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) + { + for ( size_t j = i ; j != landscaspes.size() ; ++j ) + { + distance[i][j] = distance[j][i] = compute_discance_of_landscapes( landscaspes[i], landscaspes[j] , p ) ; + + } + } + + //and now output the result to the screen and a file: + ofstream out; + out.open( "distance" ); + for ( size_t i = 0 ; i != distance.size() ; ++i ) + { + for ( size_t j = 0 ; j != distance.size() ; ++j ) + { + cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + cout << endl; + out << endl; + } + out.close(); + + return 0; +} + + + + + + + diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp new file mode 100644 index 00000000..443240ff --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp @@ -0,0 +1,92 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Persistence_landscape > landscaspes; + landscaspes.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + std::cout << "Reading persistence landscape from a file : " << filenames[file_no] << std::endl; + Persistence_landscape l; + l.load_landscape_from_file( filenames[file_no] ); + landscaspes.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > scalar_product( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + scalar_product[i] = v; + } + + //and now we can compute the scalar product: + for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) + { + for ( size_t j = i ; j != landscaspes.size() ; ++j ) + { + scalar_product[i][j] = scalar_product[j][i] = compute_inner_product( landscaspes[i], landscaspes[j] ) ; + } + } + + //and now output the result to the screen and a file: + ofstream out; + out.open( "scalar_product" ); + for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) + { + for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) + { + cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + cout << endl; + out << endl; + } + out.close(); + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp new file mode 100644 index 00000000..fe96a067 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp @@ -0,0 +1,56 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence landscapes of diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Creating persistence landscapes...\n"; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Persistence_landscape l( filenames[i] , 1 ); + std::stringstream ss; + ss << filenames[i] << ".land"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp new file mode 100644 index 00000000..e035e4aa --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes/plot_landscapes.cpp @@ -0,0 +1,50 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape file \n"; + Persistence_landscape l; + l.load_landscape_from_file( argv[1] ); + + std::stringstream ss; + ss << argv[1] << "_gnuplot_script"; + l.plot( ss.str().c_str() ); + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp new file mode 100644 index 00000000..3b580181 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp @@ -0,0 +1,74 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program computes average persistence landscape on grid of persistence landscapes on grid created based on persistence diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; + std::vector< const char* > filenames; + + if ( argc == 1 ) + { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Creating persistence landscapes...\n"; + std::vector< Abs_Topological_data_with_averages* > lands; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Persistence_landscape_on_grid* l = new Persistence_landscape_on_grid; + l->load_landscape_from_file( filenames[i] ); + lands.push_back( (Abs_Topological_data_with_averages*)l ); + } + + Persistence_landscape_on_grid av; + av.compute_average( lands ); + + av.print_to_file( "average.g_land" ); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + delete lands[i]; + } + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp new file mode 100644 index 00000000..1813e297 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp @@ -0,0 +1,107 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute dsitance of persistence landscapes on grid stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the the landscapes on grid. For L^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence landscapes on grid.\n"; + + if ( argc < 3 ) + { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + int p = atoi( argv[1] ); + + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Persistence_landscape_on_grid > landscaspes; + landscaspes.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + Persistence_landscape_on_grid l; + l.load_landscape_from_file( filenames[file_no] ); + landscaspes.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > distance( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + distance[i] = v; + } + + //and now we can compute the scalar product: + for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) + { + for ( size_t j = i ; j != landscaspes.size() ; ++j ) + { + distance[i][j] = distance[j][i] = compute_discance_of_landscapes_on_grid( landscaspes[i], landscaspes[j] , p ) ; + } + } + + //and now output the result to the screen and a file: + ofstream out; + out.open( "distance" ); + for ( size_t i = 0 ; i != distance.size() ; ++i ) + { + for ( size_t j = 0 ; j != distance.size() ; ++j ) + { + cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + cout << endl; + out << endl; + } + out.close(); + + return 0; +} + + + + + + + diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp new file mode 100644 index 00000000..33e111d5 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp @@ -0,0 +1,91 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute scalar product of persistence landscapes on grid stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence landscapes on grid.\n"; + + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Persistence_landscape_on_grid > landscaspes; + landscaspes.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + Persistence_landscape_on_grid l; + l.load_landscape_from_file( filenames[file_no] ); + landscaspes.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > scalar_product( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + scalar_product[i] = v; + } + + //and now we can compute the scalar product: + for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) + { + for ( size_t j = i ; j != landscaspes.size() ; ++j ) + { + scalar_product[i][j] = scalar_product[j][i] = compute_inner_product( landscaspes[i], landscaspes[j] ) ; + } + } + + //and now output the result to the screen and a file: + ofstream out; + out.open( "scalar_product" ); + for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) + { + for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) + { + cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + cout << endl; + out << endl; + } + out.close(); + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp new file mode 100644 index 00000000..f6545e44 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp @@ -0,0 +1,80 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence landscape on grid of diagrams provided as an input.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if ( argc < 4 ) + { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi( argv[1] ); + double min_ = atof( argv[2] ); + double max_ = atof( argv[3] ); + + std::vector< const char* > filenames; + for ( int i = 4 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Creating persistence landscapes...\n"; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cout << "Creating persistence landscape on a grid based on a file : " << filenames[i] << std::endl; + Persistence_landscape_on_grid l; + if ( (min_ != -1) || (max_ != -1) ) + { + l = Persistence_landscape_on_grid( filenames[i] , min_ , max_ , size_of_grid ); + } + else + { + //(min_ == -1) && (max_ == -1), in this case the program will find min_ and max_ based on the data. + l = Persistence_landscape_on_grid( filenames[i] , size_of_grid ); + } + std::stringstream ss; + ss << filenames[i] << ".g_land"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp new file mode 100644 index 00000000..c12c3862 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp @@ -0,0 +1,55 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape on grid file \n"; + if ( argc == 1 ) + { + std::cout << "Wrong parameters of a program call, the program will now terminate \n"; + return 1; + } + Persistence_landscape_on_grid l; + l.load_landscape_from_file( argv[1] ); + + std::stringstream ss; + ss << argv[1] << "_gnuplot_script"; + l.plot( ss.str().c_str() ); + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp new file mode 100644 index 00000000..3262b157 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -0,0 +1,75 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program computes average persistence vector of persistence vectors created based on persistence diagrams provided as an input. \n"; + std::cout << "Please call this program with the names of files with persistence diagrams \n"; + std::vector< const char* > filenames; + + if ( argc == 1 ) + { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Reading persistence vectors...\n"; + std::vector< Abs_Topological_data_with_averages* > lands; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Vector_distances_in_diagram< euclidean_distance >* l = new Vector_distances_in_diagram< euclidean_distance >; + l->load_from_file( filenames[i] ); + lands.push_back( (Abs_Topological_data_with_averages*)l ); + } + + Vector_distances_in_diagram< euclidean_distance > av; + av.compute_average( lands ); + + av.print_to_file( "average.vect" ); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + delete lands[i]; + } + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp new file mode 100644 index 00000000..33d92a72 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -0,0 +1,108 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The first parameter of a program is an interger p. The program compute l^p distance of the vectors. For l^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n"; + + if ( argc < 3 ) + { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + int p = atoi( argv[1] ); + + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Vector_distances_in_diagram< euclidean_distance >* > vectors; + vectors.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + //cerr << filenames[file_no] << endl; + Vector_distances_in_diagram< euclidean_distance >* l = new Vector_distances_in_diagram< euclidean_distance >; + l->load_from_file( filenames[file_no] ); + vectors.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > distance( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + distance[i] = v; + } + + //and now we can compute the distances: + for ( size_t i = 0 ; i != vectors.size() ; ++i ) + { + for ( size_t j = i+1 ; j != vectors.size() ; ++j ) + { + distance[i][j] = distance[j][i] = ((Vector_distances_in_diagram< euclidean_distance >*)vectors[i])->distance( vectors[j] , p ) ; + } + } + + //and now output the result to the screen and a file: + ofstream out; + out.open( "distance" ); + for ( size_t i = 0 ; i != distance.size() ; ++i ) + { + for ( size_t j = 0 ; j != distance.size() ; ++j ) + { + cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + cout << endl; + out << endl; + } + out.close(); + + return 0; +} + + + + + + + diff --git a/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp new file mode 100644 index 00000000..5bea2765 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -0,0 +1,97 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence vectors.\n"; + + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Vector_distances_in_diagram< euclidean_distance >* > vectors; + vectors.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + Vector_distances_in_diagram< euclidean_distance >* l = new Vector_distances_in_diagram< euclidean_distance >; + l->load_from_file( filenames[file_no] ); + vectors.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > scalar_product( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + scalar_product[i] = v; + } + + //and now we can compute the scalar product: + for ( size_t i = 0 ; i != vectors.size() ; ++i ) + { + for ( size_t j = i ; j != vectors.size() ; ++j ) + { + scalar_product[i][j] = scalar_product[j][i] = ((Vector_distances_in_diagram< euclidean_distance >*)vectors[i])->compute_scalar_product( vectors[j] ) ; + } + } + + //and now output the result to the screen and a file: + ofstream out; + out.open( "scalar_product" ); + for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) + { + for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) + { + cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + cout << endl; + out << endl; + } + out.close(); + + //cleaning up + for ( size_t i = 0 ; i != vectors.size() ; ++i ) + { + delete vectors[i]; + } + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp new file mode 100644 index 00000000..8e309b11 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -0,0 +1,57 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence vectors of diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cerr << "Creatign persistence vectors based on a file : " << filenames[i] << std::endl; + Vector_distances_in_diagram< euclidean_distance > l( filenames[i] , -1 ); + std::stringstream ss; + ss << filenames[i] << ".vect"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} + diff --git a/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp new file mode 100644 index 00000000..53f53654 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -0,0 +1,51 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include +#include + + +int main( int argc , char** argv ) +{ + std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the name of file with persistence vector. \n"; + if ( argc != 2 ) + { + std::cout << "Wrong number of parameters, the program will now terminate. \n"; + return 1; + } + Vector_distances_in_diagram< euclidean_distance > l; + l.load_from_file( argv[1] ); + l.plot( argv[1] ); + + return 0; +} + -- cgit v1.2.3 From 318c309206f1cffcc17c9333bb6ac9e2f90b7610 Mon Sep 17 00:00:00 2001 From: pdlotko Date: Fri, 31 Mar 2017 13:22:29 +0000 Subject: solved problem with cmake. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2294 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 34fc791c80d9e66ab18e992f73bbf3252b3d5e1e --- CMakeLists.txt | 5 + src/Gudhi_stat/include/gudhi/bootstrap.h | 17 ++- src/Gudhi_stat/utilities/CMakeLists.txt | 103 +------------------ src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp | 81 --------------- src/Gudhi_stat/utilities/Hausdorff_subsampling.cpp | 114 +++++++++++++++++++++ .../utilities/persistence_heat_maps/CMakeLists.txt | 31 ++++++ .../utilities/persistence_intervals/CMakeLists.txt | 22 ++++ .../plot_persistence_intervals.cpp | 4 +- .../persistence_landscapes/CMakeLists.txt | 21 ++++ .../persistence_landscapes_on_grid/CMakeLists.txt | 22 ++++ .../utilities/persistence_vectors/CMakeLists.txt | 20 ++++ 11 files changed, 254 insertions(+), 186 deletions(-) delete mode 100644 src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp create mode 100644 src/Gudhi_stat/utilities/Hausdorff_subsampling.cpp create mode 100644 src/Gudhi_stat/utilities/persistence_heat_maps/CMakeLists.txt create mode 100644 src/Gudhi_stat/utilities/persistence_intervals/CMakeLists.txt create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes/CMakeLists.txt create mode 100644 src/Gudhi_stat/utilities/persistence_landscapes_on_grid/CMakeLists.txt create mode 100644 src/Gudhi_stat/utilities/persistence_vectors/CMakeLists.txt (limited to 'CMakeLists.txt') diff --git a/CMakeLists.txt b/CMakeLists.txt index 488f1d62..bb412421 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -146,6 +146,11 @@ else() add_subdirectory(src/Gudhi_stat/test) add_subdirectory(src/Gudhi_stat/example) add_subdirectory(src/Gudhi_stat/utilities) + add_subdirectory(src/Gudhi_stat/utilities/persistence_heat_maps) + add_subdirectory(src/Gudhi_stat/utilities/persistence_intervals) + add_subdirectory(src/Gudhi_stat/utilities/persistence_landscapes) + add_subdirectory(src/Gudhi_stat/utilities/persistence_landscapes_on_grid) + add_subdirectory(src/Gudhi_stat/utilities/persistence_vectors) # data points generator add_subdirectory(data/points/generator) diff --git a/src/Gudhi_stat/include/gudhi/bootstrap.h b/src/Gudhi_stat/include/gudhi/bootstrap.h index 629240ed..dde08130 100644 --- a/src/Gudhi_stat/include/gudhi/bootstrap.h +++ b/src/Gudhi_stat/include/gudhi/bootstrap.h @@ -1,4 +1,4 @@ -/* This file is part of the Gudhi Library. The Gudhi library +/* Thicharacteristic_of_all_pointss file is part of the Gudhi Library. The Gudhi library * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * @@ -135,14 +135,21 @@ double bootstrap( size_t number_of_points , CharacteristicFunction f , DistanceB // ); // #endif + //size_t position_of_quantile = floor(2*(1-quantile)*vector_of_distances.size()); + + size_t position_of_quantile = floor(quantile*vector_of_distances.size()); if ( position_of_quantile ) --position_of_quantile; if ( dbg ) { - std::cout << "position_of_quantile : " << position_of_quantile << ", and here is the array : " << std::endl; + std::cerr << "quantile : " << quantile << std::endl; + std::cerr << "position_of_quantile : " << position_of_quantile << std::endl; + + std::sort( vector_of_distances.begin() , vector_of_distances.end() ); + //std::cout << "position_of_quantile : " << position_of_quantile << ", and here is the array : " << std::endl; for ( size_t i = 0 ; i != vector_of_distances.size() ; ++i ) { - std::cout << vector_of_distances[i] << std::endl; + std::cout << vector_of_distances[i] << " " ; } std::cout << std::endl; } @@ -150,6 +157,10 @@ double bootstrap( size_t number_of_points , CharacteristicFunction f , DistanceB //now we need to sort the vector_of_distances and find the quantile: std::nth_element (vector_of_distances.begin(), vector_of_distances.begin()+position_of_quantile, vector_of_distances.end()); + + //for Hausdorff bootrstra I have to multily it by 2. + //In case of other bootsraps, I do not have to do it. We need a special variable saying if Ineed this multiplication or not.//This should be done outside the bootstrap, since the fact hat we need it do not come from bootstrab, but from geometry of bottleneck distance + if ( dbg )std::cout << "Result : " << vector_of_distances[ position_of_quantile ] << std::endl; return vector_of_distances[ position_of_quantile ]; diff --git a/src/Gudhi_stat/utilities/CMakeLists.txt b/src/Gudhi_stat/utilities/CMakeLists.txt index b7989a96..235d5d2e 100644 --- a/src/Gudhi_stat/utilities/CMakeLists.txt +++ b/src/Gudhi_stat/utilities/CMakeLists.txt @@ -3,103 +3,6 @@ project(GUDHI_STAT) -#persitence diagrams -add_executable ( persistence_intervals/plot_persistence_intervals persistence_intervals/plot_persistence_intervals.cpp ) -target_link_libraries( persistence_intervals/plot_persistence_intervals ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_intervals/compute_birth_death_range_in_persistence_diagram persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp ) -target_link_libraries( persistence_intervals/compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_intervals/compute_number_of_dominant_intervals persistence_intervals/compute_number_of_dominant_intervals.cpp ) -target_link_libraries( persistence_intervals/compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_intervals/plot_histogram_of_intervals_lengths persistence_intervals/plot_histogram_of_intervals_lengths.cpp ) -target_link_libraries( persistence_intervals/plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_intervals/plot_persistence_Betti_numebrs persistence_intervals/plot_persistence_Betti_numebrs.cpp ) -target_link_libraries( persistence_intervals/plot_persistence_Betti_numebrs ${Boost_SYSTEM_LIBRARY}) - -#when we have bottleneck and wasserstein distance computations, add suitable programs here. - - -#persitence landscapes -add_executable ( persistence_landscapes/average_landscapes persistence_landscapes/average_landscapes.cpp ) -target_link_libraries(persistence_landscapes/average_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_landscapes/create_landscapes persistence_landscapes/create_landscapes.cpp ) -target_link_libraries(persistence_landscapes/create_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_landscapes/plot_landscapes persistence_landscapes/plot_landscapes.cpp ) -target_link_libraries(persistence_landscapes/plot_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_landscapes/compute_distance_of_landscapes persistence_landscapes/compute_distance_of_landscapes.cpp ) -target_link_libraries(persistence_landscapes/compute_distance_of_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_landscapes/compute_scalar_product_of_landscapes persistence_landscapes/compute_scalar_product_of_landscapes.cpp ) -target_link_libraries(persistence_landscapes/compute_scalar_product_of_landscapes ${Boost_SYSTEM_LIBRARY}) - -#persitence landscapes on a grid -add_executable ( persistence_landscapes_on_grid/average_landscapes_on_grid persistence_landscapes_on_grid/average_landscapes_on_grid.cpp ) -target_link_libraries(persistence_landscapes_on_grid/average_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_landscapes_on_grid/create_landscapes_on_grid persistence_landscapes_on_grid/create_landscapes_on_grid.cpp ) -target_link_libraries(persistence_landscapes_on_grid/create_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_landscapes_on_grid/plot_landscapes_on_grid persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp ) -target_link_libraries(persistence_landscapes_on_grid/plot_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp ) -target_link_libraries(persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp ) -target_link_libraries(persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -#persitence heat maps -add_executable ( persistence_heat_maps/average_persistence_heat_maps persistence_heat_maps/average_persistence_heat_maps.cpp ) -target_link_libraries(persistence_heat_maps/average_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_heat_maps/create_persistence_heat_maps persistence_heat_maps/create_persistence_heat_maps.cpp ) -target_link_libraries(persistence_heat_maps/create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_heat_maps/plot_persistence_heat_map persistence_heat_maps/plot_persistence_heat_map.cpp ) -target_link_libraries(persistence_heat_maps/plot_persistence_heat_map ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_heat_maps/compute_distance_of_persistence_heat_maps persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp ) -target_link_libraries(persistence_heat_maps/compute_distance_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp ) -target_link_libraries(persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_heat_maps/create_pssk persistence_heat_maps/create_pssk.cpp ) -target_link_libraries(persistence_heat_maps/create_pssk ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp ) -target_link_libraries(persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp ) -target_link_libraries(persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp ) -target_link_libraries(persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence ${Boost_SYSTEM_LIBRARY}) - - -#persitence vectors -add_executable ( persistence_vectors/average_persistence_vectors persistence_vectors/average_persistence_vectors.cpp ) -target_link_libraries(persistence_vectors/average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_vectors/create_persistence_vectors persistence_vectors/create_persistence_vectors.cpp ) -target_link_libraries(persistence_vectors/create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_vectors/compute_distance_of_persistence_vectors persistence_vectors/compute_distance_of_persistence_vectors.cpp ) -target_link_libraries(persistence_vectors/compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_vectors/compute_scalar_product_of_persistence_vectors persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp ) -target_link_libraries(persistence_vectors/compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_executable ( persistence_vectors/plot_persistence_vectors persistence_vectors/plot_persistence_vectors.cpp ) -target_link_libraries(persistence_vectors/plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - - #some stat libraries: add_executable ( permutation_test permutation_test.cpp ) target_link_libraries(permutation_test ${Boost_SYSTEM_LIBRARY}) @@ -110,11 +13,11 @@ target_link_libraries(permutation_test ${Boost_SYSTEM_LIBRARY}) #add_executable ( topological_process_2 topological_process_2.cpp ) #target_link_libraries(topological_process_2 ${Boost_SYSTEM_LIBRARY}) -add_executable ( Hausdorff_bootstrap Hausdorff_bootstrap.cpp ) +add_executable ( Hausdorff_subsampling Hausdorff_subsampling.cpp ) if (TBB_FOUND) -target_link_libraries(Hausdorff_bootstrap ${TBB_LIBRARIES}) +target_link_libraries(Hausdorff_subsampling ${TBB_LIBRARIES}) endif(TBB_FOUND) -target_link_libraries(Hausdorff_bootstrap ${Boost_SYSTEM_LIBRARY}) +target_link_libraries(Hausdorff_subsampling ${Boost_SYSTEM_LIBRARY}) add_executable ( Landscape_bootstrap Landscape_bootstrap.cpp ) diff --git a/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp b/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp deleted file mode 100644 index 7fd665c3..00000000 --- a/src/Gudhi_stat/utilities/Hausdorff_bootstrap.cpp +++ /dev/null @@ -1,81 +0,0 @@ -/* 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): Pawel Dlotko - * - * Copyright (C) 2015 INRIA (France) - * - * 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 - - -using namespace Gudhi; -using namespace Gudhi::Gudhi_stat; - - - -int main( int argc , char** argv ) -{ - std::cout << "The parameters of this program are : " << std::endl; - std::cout << "(a) a name of a file with points," << std:: endl; - std::cout << "(b) a number of repetitions of bootstrap (integer)," << std::endl; - std::cout << "(c) a size of subsample (integer, smaller than the number of points," << std::endl; - std::cout << "(d) a quantile (real number between 0 and 1. If you do not know what to set, set it to 0.95." << std::endl; - if ( argc != 5 ) - { - std::cerr << "Wrong number of parameters, the program will now terminate.\n"; - return 1; - } - - const char* filename = argv[1]; - size_t number_of_repetitions_of_bootstrap = (size_t)atoi( argv[2] ); - size_t size_of_subsample = (size_t)atoi( argv[3] ); - double quantile = atof( argv[4] ); - - std::cout << "Now we will read points from the file : " << filename << " and then perform " << number_of_repetitions_of_bootstrap << " times the bootstrap on it by choosing subsample of a size " << size_of_subsample << std::endl; - - std::vector< std::vector< double > > points = read_numbers_from_file_line_by_line( filename ); - - std::cout << "Read : " << points.size() << " points.\n"; - - //comute all-to-all distance matrix: - std::vector< std::vector > all_to_all_distance_matrix_between_points = compute_all_to_all_distance_matrix_between_points< std::vector , Euclidean_distance >( points ); - Hausdorff_distance_between_subspace_and_the_whole_metric_space distance( all_to_all_distance_matrix_between_points ); - identity< std::vector > identity_char; - - //and now we can run the real bootstrap. - //template < typename PointCloudCharacteristics , typename CharacteristicFunction , typename DistanceBetweenPointsCharacteristics > - //In this case, the PointCloudCharacteristics is just a vector of numbers of points (in a order fixed on points vector). - //CharacteristicFunction is just identity, transforming std::vector< size_t > to itself. - //DistanceBetweenPointsCharacteristics is the place were all happens. This class have the information about the coordinates of the points, and allows to compute a Hausdorff distance between - //the collection of all points, and the subsample. - double result = bootstrap< - std::vector< size_t > , //PointCloudCharacteristics - identity< std::vector > , //CharacteristicFunction - Hausdorff_distance_between_subspace_and_the_whole_metric_space //DistanceBetweenPointsCharacteristics. This function have the information about point's coordinates. - > - ( points.size() , identity_char , distance , number_of_repetitions_of_bootstrap , size_of_subsample , quantile ); - - std::cout << "result of bootstrap : " << result << std::endl; - - - return 0; -} diff --git a/src/Gudhi_stat/utilities/Hausdorff_subsampling.cpp b/src/Gudhi_stat/utilities/Hausdorff_subsampling.cpp new file mode 100644 index 00000000..5556a8ee --- /dev/null +++ b/src/Gudhi_stat/utilities/Hausdorff_subsampling.cpp @@ -0,0 +1,114 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * 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 + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + + + +int main( int argc , char** argv ) +{ + std::cout << "The parameters of this program are : " << std::endl; + std::cout << "(a) a name of a file with points," << std:: endl; + std::cout << "(b) a number of repetitions of bootstrap (integer)," << std::endl; + std::cout << "(c) a size of subsample (integer, smaller than the number of points," << std::endl; + std::cout << "(d) a quantile (real number between 0 and 1. If you do not know what to set, set it to 0.95." << std::endl; + if ( argc != 5 ) + { + std::cerr << "Wrong number of parameters, the program will now terminate.\n"; + return 1; + } + + const char* filename = argv[1]; + size_t number_of_repetitions_of_subsampling = (size_t)atoi( argv[2] ); + size_t size_of_subsample = (size_t)atoi( argv[3] ); + double quantile = atof( argv[4] ); + + std::cout << "Now we will read points from the file : " << filename << " and then perform " << number_of_repetitions_of_subsampling << " times the subsampling on it by choosing subsample of a size " << size_of_subsample << std::endl; + + std::vector< std::vector< double > > points = read_numbers_from_file_line_by_line( filename ); + /* + std::vector< std::vector< double > > points; + std::vector< double > point1(2); + point1[0] = -1; + point1[1] = 0; + std::vector< double > point2(2); + point2[0] = 1; + point2[1] = 0; + std::vector< double > point3(2); + point3[0] = -1; + point3[1] = 3; + std::vector< double > point4(2); + point4[0] = 1; + point4[1] = 3; + points.push_back( point1 ); + points.push_back( point2 ); + points.push_back( point3 ); + points.push_back( point4 ); + + + std::vector< std::vector > all_to_all_distance_matrix_between_points = compute_all_to_all_distance_matrix_between_points< std::vector , Euclidean_distance >( points ); + Hausdorff_distance_between_subspace_and_the_whole_metric_space distance( all_to_all_distance_matrix_between_points ); + + std::vector characteristic_of_all_points = {0,1,2,3}; + std::vector characteristic_of_subsampled_points = {2,3}; + std::cerr << "DISTANCE BETWEEN SAMPLE AND SUBSAMPLE: " << distance( characteristic_of_subsampled_points , characteristic_of_all_points ) << std::endl; + */ + + + std::cout << "Read : " << points.size() << " points.\n"; + + //comute all-to-all distance matrix: + std::vector< std::vector > all_to_all_distance_matrix_between_points = compute_all_to_all_distance_matrix_between_points< std::vector , Euclidean_distance >( points ); + Hausdorff_distance_between_subspace_and_the_whole_metric_space distance( all_to_all_distance_matrix_between_points ); + identity< std::vector > identity_char; + + + + + + + //and now we can run the real bootstrap. + //template < typename PointCloudCharacteristics , typename CharacteristicFunction , typename DistanceBetweenPointsCharacteristics > + //In this case, the PointCloudCharacteristics is just a vector of numbers of points (in a order fixed on points vector). + //CharacteristicFunction is just identity, transforming std::vector< size_t > to itself. + //DistanceBetweenPointsCharacteristics is the place were all happens. This class have the information about the coordinates of the points, and allows to compute a Hausdorff distance between + //the collection of all points, and the subsample. + double result = bootstrap< + std::vector< size_t > , //PointCloudCharacteristics + identity< std::vector > , //CharacteristicFunction + Hausdorff_distance_between_subspace_and_the_whole_metric_space //DistanceBetweenPointsCharacteristics. This function have the information about point's coordinates. + > + ( points.size() , identity_char , distance , number_of_repetitions_of_subsampling , size_of_subsample , quantile ); + + std::cout << "result of the subsampling : " << result << std::endl; + + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/CMakeLists.txt b/src/Gudhi_stat/utilities/persistence_heat_maps/CMakeLists.txt new file mode 100644 index 00000000..39240db2 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + +#persitence heat maps +add_executable ( average_persistence_heat_maps average_persistence_heat_maps.cpp ) +target_link_libraries(average_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_persistence_heat_maps create_persistence_heat_maps.cpp ) +target_link_libraries(create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_executable ( plot_persistence_heat_map plot_persistence_heat_map.cpp ) +target_link_libraries(plot_persistence_heat_map ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_distance_of_persistence_heat_maps compute_distance_of_persistence_heat_maps.cpp ) +target_link_libraries(compute_distance_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_scalar_product_of_persistence_heat_maps compute_scalar_product_of_persistence_heat_maps.cpp ) +target_link_libraries(compute_scalar_product_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_pssk create_pssk.cpp ) +target_link_libraries(create_pssk ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_persistence_heat_maps_weighted_by_distance_from_diagonal create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp ) +target_link_libraries(create_persistence_heat_maps_weighted_by_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp ) +target_link_libraries(create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_persistence_heat_maps_weighted_by_arctan_of_their_persistence create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp ) +target_link_libraries(create_persistence_heat_maps_weighted_by_arctan_of_their_persistence ${Boost_SYSTEM_LIBRARY}) + diff --git a/src/Gudhi_stat/utilities/persistence_intervals/CMakeLists.txt b/src/Gudhi_stat/utilities/persistence_intervals/CMakeLists.txt new file mode 100644 index 00000000..96cb1a5e --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_intervals/CMakeLists.txt @@ -0,0 +1,22 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + + + +#persitence diagrams +add_executable ( plot_persistence_intervals plot_persistence_intervals.cpp ) +target_link_libraries( plot_persistence_intervals ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_birth_death_range_in_persistence_diagram compute_birth_death_range_in_persistence_diagram.cpp ) +target_link_libraries( compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) +target_link_libraries( compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY}) + +add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) +target_link_libraries( plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY}) + +add_executable ( plot_persistence_Betti_numebrs plot_persistence_Betti_numebrs.cpp ) +target_link_libraries( plot_persistence_Betti_numebrs ${Boost_SYSTEM_LIBRARY}) + +#when we have bottleneck and wasserstein distance computations, add suitable programs here. diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp index 40f6fbaf..04a05caa 100644 --- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp +++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -44,8 +44,8 @@ int main( int argc , char** argv ) std::cout << "To run this program, please provide the name of a file with persistence diagram \n"; return 1; } - - Persistence_intervals b( argv[1] ); + std::vector< std::pair< double , double > > intervals = read_gudhi_file( argv[1] , 2 ); + Persistence_intervals b( intervals ); b.plot( argv[1] ); return 0; } diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/CMakeLists.txt b/src/Gudhi_stat/utilities/persistence_landscapes/CMakeLists.txt new file mode 100644 index 00000000..9caf73f6 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes/CMakeLists.txt @@ -0,0 +1,21 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + + + +#persitence landscapes +add_executable ( average_landscapes average_landscapes.cpp ) +target_link_libraries(average_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_landscapes create_landscapes.cpp ) +target_link_libraries(create_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_executable ( plot_landscapes plot_landscapes.cpp ) +target_link_libraries(plot_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_distance_of_landscapes compute_distance_of_landscapes.cpp ) +target_link_libraries(compute_distance_of_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_scalar_product_of_landscapes compute_scalar_product_of_landscapes.cpp ) +target_link_libraries(compute_scalar_product_of_landscapes ${Boost_SYSTEM_LIBRARY}) + diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/CMakeLists.txt new file mode 100644 index 00000000..bb7c3987 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/CMakeLists.txt @@ -0,0 +1,22 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + + + + +#persitence landscapes on a grid +add_executable ( average_landscapes_on_grid average_landscapes_on_grid.cpp ) +target_link_libraries(average_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_landscapes_on_grid create_landscapes_on_grid.cpp ) +target_link_libraries(create_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( plot_landscapes_on_grid plot_landscapes_on_grid.cpp ) +target_link_libraries(plot_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_distance_of_landscapes_on_grid compute_distance_of_landscapes_on_grid.cpp ) +target_link_libraries(compute_distance_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_scalar_product_of_landscapes_on_grid compute_scalar_product_of_landscapes_on_grid.cpp ) +target_link_libraries(compute_scalar_product_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + diff --git a/src/Gudhi_stat/utilities/persistence_vectors/CMakeLists.txt b/src/Gudhi_stat/utilities/persistence_vectors/CMakeLists.txt new file mode 100644 index 00000000..ebf4898e --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/CMakeLists.txt @@ -0,0 +1,20 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + +#persitence vectors +add_executable ( average_persistence_vectors average_persistence_vectors.cpp ) +target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_persistence_vectors create_persistence_vectors.cpp ) +target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_distance_of_persistence_vectors compute_distance_of_persistence_vectors.cpp ) +target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_scalar_product_of_persistence_vectors compute_scalar_product_of_persistence_vectors.cpp ) +target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( plot_persistence_vectors plot_persistence_vectors.cpp ) +target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + + -- cgit v1.2.3 From 0654bfbab17fe16edf90445f0a351454b460028f Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 30 May 2017 15:20:29 +0000 Subject: Fix spell checker errors git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2475 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 94422e6f356532b2db4dc5a55cbb851210b3c36d --- CMakeLists.txt | 16 +- src/CMakeLists.txt | 12 +- src/Doxyfile | 4 +- .../concept/Real_valued_topological_data.h | 21 ++- .../concept/Topological_data_with_averages.h | 11 +- .../concept/Topological_data_with_distances.h | 22 ++- .../concept/Topological_data_with_scalar_product.h | 15 +- .../concept/Vectorized_topological_data.h | 15 +- .../doc/Persistence_representations_doc.h | 52 +++--- .../example/persistence_heat_maps.cpp | 4 +- .../example/persistence_intervals.cpp | 4 +- .../example/persistence_landscape.cpp | 4 +- .../example/persistence_landscape_on_grid.cpp | 2 +- .../include/gudhi/PSSK.h | 15 +- .../include/gudhi/Persistence_heat_maps.h | 85 +++++---- .../include/gudhi/Persistence_intervals.h | 106 +++--------- .../gudhi/Persistence_intervals_with_distances.h | 12 +- .../include/gudhi/Persistence_landscape.h | 116 +++++-------- .../include/gudhi/Persistence_landscape_on_grid.h | 192 ++++++--------------- .../include/gudhi/Persistence_vectors.h | 105 ++++------- .../gudhi/common_persistence_representations.h | 28 ++- .../include/gudhi/read_persistence_from_file.h | 104 ++--------- .../compute_distance_of_persistence_heat_maps.cpp | 9 +- ...h_m_weighted_by_arctan_of_their_persistence.cpp | 4 +- ...te_p_h_m_weighted_by_distance_from_diagonal.cpp | 4 +- ...ate_p_h_m_weighted_by_squared_diag_distance.cpp | 2 +- .../create_persistence_heat_maps.cpp | 2 +- .../persistence_heat_maps/create_pssk.cpp | 2 +- .../plot_persistence_heat_map.cpp | 2 +- .../compute_bottleneck_distance.cpp | 2 +- .../plot_histogram_of_intervals_lengths.cpp | 2 +- .../plot_persistence_Betti_numbers.cpp | 7 +- .../compute_distance_of_landscapes.cpp | 2 +- .../persistence_landscapes/plot_landscapes.cpp | 2 +- .../compute_distance_of_landscapes_on_grid.cpp | 6 +- .../plot_landscapes_on_grid.cpp | 2 +- .../compute_distance_of_persistence_vectors.cpp | 3 +- .../create_persistence_vectors.cpp | 3 +- src/cmake/modules/GUDHI_user_version_target.txt | 2 +- src/common/doc/main_page.h | 13 +- src/common/include/gudhi/distance_functions.h | 5 + 41 files changed, 384 insertions(+), 635 deletions(-) (limited to 'CMakeLists.txt') diff --git a/CMakeLists.txt b/CMakeLists.txt index 4c772506..30306885 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -52,7 +52,7 @@ include_directories(src/Spatial_searching/include/) include_directories(src/Subsampling/include/) include_directories(src/Tangential_complex/include/) include_directories(src/Witness_complex/include/) -include_directories(src/Gudhi_stat/include/) +include_directories(src/Persistence_representations/include/) add_subdirectory(src/common/example) add_subdirectory(src/common/test) @@ -82,13 +82,13 @@ add_subdirectory(src/Bottleneck_distance/test) add_subdirectory(src/Bottleneck_distance/benchmark) add_subdirectory(src/Rips_complex/example) add_subdirectory(src/Rips_complex/test) -add_subdirectory(src/Gudhi_stat/test) -add_subdirectory(src/Gudhi_stat/example) -add_subdirectory(src/Gudhi_stat/utilities/persistence_heat_maps) -add_subdirectory(src/Gudhi_stat/utilities/persistence_intervals) -add_subdirectory(src/Gudhi_stat/utilities/persistence_landscapes) -add_subdirectory(src/Gudhi_stat/utilities/persistence_landscapes_on_grid) -add_subdirectory(src/Gudhi_stat/utilities/persistence_vectors) +add_subdirectory(src/Persistence_representations/test) +add_subdirectory(src/Persistence_representations/example) +add_subdirectory(src/Persistence_representations/utilities/persistence_heat_maps) +add_subdirectory(src/Persistence_representations/utilities/persistence_intervals) +add_subdirectory(src/Persistence_representations/utilities/persistence_landscapes) +add_subdirectory(src/Persistence_representations/utilities/persistence_landscapes_on_grid) +add_subdirectory(src/Persistence_representations/utilities/persistence_vectors) # data points generator add_subdirectory(data/points/generator) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index fe4eb677..06e479be 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -52,12 +52,12 @@ add_subdirectory(example/Spatial_searching) add_subdirectory(example/Subsampling) add_subdirectory(example/Tangential_complex) add_subdirectory(example/Bottleneck_distance) -add_subdirectory(example/Gudhi_stat) -add_subdirectory(utilities/Gudhi_stat/persistence_heat_maps) -add_subdirectory(utilities/Gudhi_stat/persistence_intervals) -add_subdirectory(utilities/Gudhi_stat/persistence_landscapes) -add_subdirectory(utilities/Gudhi_stat/persistence_landscapes_on_grid) -add_subdirectory(utilities/Gudhi_stat/persistence_vectors) +add_subdirectory(example/Persistence_representations) +add_subdirectory(utilities/Persistence_representations/persistence_heat_maps) +add_subdirectory(utilities/Persistence_representations/persistence_intervals) +add_subdirectory(utilities/Persistence_representations/persistence_landscapes) +add_subdirectory(utilities/Persistence_representations/persistence_landscapes_on_grid) +add_subdirectory(utilities/Persistence_representations/persistence_vectors) # data points generator add_subdirectory(data/points/generator) diff --git a/src/Doxyfile b/src/Doxyfile index f4df4e84..eb0b3e9e 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -852,7 +852,7 @@ IMAGE_PATH = doc/Skeleton_blocker/ \ doc/Spatial_searching/ \ doc/Tangential_complex/ \ doc/Bottleneck_distance/ \ - doc/Gudhi_stat/ + doc/Persistence_representations/ # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program @@ -2116,7 +2116,7 @@ COLLABORATION_GRAPH = NO # The default value is: YES. # This tag requires that the tag HAVE_DOT is set to YES. -GROUP_GRAPHS = YES +GROUP_GRAPHS = NO # If the UML_LOOK tag is set to YES doxygen will generate inheritance and # collaboration diagrams in a style similar to the OMG's Unified Modeling diff --git a/src/Persistence_representations/concept/Real_valued_topological_data.h b/src/Persistence_representations/concept/Real_valued_topological_data.h index 4d4ee8d3..5a15c769 100644 --- a/src/Persistence_representations/concept/Real_valued_topological_data.h +++ b/src/Persistence_representations/concept/Real_valued_topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -20,6 +20,14 @@ * along with this program. If not, see . */ +#ifndef CONCEPT_REAL_VALUED_TOPOLOGICAL_DATA_H_ +#define CONCEPT_REAL_VALUED_TOPOLOGICAL_DATA_H_ + +namespace Gudhi { + +namespace Persistence_representations { + + /** \brief The concept Real_valued_topological_data describes the requirements * for a type to implement a container that allows computations of its projections to R. */ @@ -27,12 +35,19 @@ class Real_valued_topological_data { public: /** - * Typically there are various ways data can be projected to R. This function give us the number of functions for vectorization provided by a given class. + * Typically there are various ways data can be projected to R. This function gives us the number of functions for + * vectorization provided by a given class. **/ size_t number_of_projections_to_R(); /** - * This is a function to compute the projection from this container to reals. The parameter of a function have to be between 0 and the value returned by number_of_projections_to_R(). + * This is a function to compute the projection from this container to reals. The parameter of a function have to + * be between 0 and the value returned by number_of_projections_to_R(). **/ double project_to_R( size_t number_of_projection ); }; +} // namespace Persistence_representations + +} // namespace Gudhi + +#endif // CONCEPT_REAL_VALUED_TOPOLOGICAL_DATA_H_ diff --git a/src/Persistence_representations/concept/Topological_data_with_averages.h b/src/Persistence_representations/concept/Topological_data_with_averages.h index aeeb94f0..0501c306 100644 --- a/src/Persistence_representations/concept/Topological_data_with_averages.h +++ b/src/Persistence_representations/concept/Topological_data_with_averages.h @@ -5,7 +5,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -21,7 +21,12 @@ * along with this program. If not, see . */ +#ifndef CONCEPT_TOPOLOGICAL_DATA_WITH_AVERAGES_H_ +#define CONCEPT_TOPOLOGICAL_DATA_WITH_AVERAGES_H_ +namespace Gudhi { + +namespace Persistence_representations { /** \brief The concept Topological_data_with_averages describes the requirements * for a type to implement a container that allows computations of averages. @@ -33,4 +38,8 @@ public: void compute_average( const std::vector< Topological_data_with_averages* >& to_average ); }; +} // namespace Persistence_representations + +} // namespace Gudhi +#endif // CONCEPT_TOPOLOGICAL_DATA_WITH_AVERAGES_H_ diff --git a/src/Persistence_representations/concept/Topological_data_with_distances.h b/src/Persistence_representations/concept/Topological_data_with_distances.h index 1318b9d1..2e6de729 100644 --- a/src/Persistence_representations/concept/Topological_data_with_distances.h +++ b/src/Persistence_representations/concept/Topological_data_with_distances.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -20,11 +20,22 @@ * along with this program. If not, see . */ +#ifndef CONCEPT_TOPOLOGICAL_DATA_WITH_DISTANCES_H_ +#define CONCEPT_TOPOLOGICAL_DATA_WITH_DISTANCES_H_ + +namespace Gudhi { + +namespace Persistence_representations { + + /** \brief The concept Topological_data_with_distances describes the requirements - * for a type to implement a container that allows computations of distance to another contained of that type. + * for a type to implement a container that allows computations of distance to another contained of that type. + * \details * The second parameter of the distance function allow to declare power of a distance. The exact meaning of that * number will be different for different distances. A few examples are given below: - * In case of p-Wasserstein distance, the power is equal to p. power = std::limit::max() for bottleneck distance. + * In case of p-Wasserstein distance, the power is equal to p. power = std::limit::max() for bottleneck + * distance. + * * In case of L^p landscape distance, the power is equal to p. s */ class Topological_data_with_distances @@ -33,3 +44,8 @@ public: double distance( const Topological_data_with_distances& second , double power = 1); }; +} // namespace Persistence_representations + +} // namespace Gudhi + +#endif // CONCEPT_TOPOLOGICAL_DATA_WITH_DISTANCES_H_ diff --git a/src/Persistence_representations/concept/Topological_data_with_scalar_product.h b/src/Persistence_representations/concept/Topological_data_with_scalar_product.h index f32271c7..203a1d91 100644 --- a/src/Persistence_representations/concept/Topological_data_with_scalar_product.h +++ b/src/Persistence_representations/concept/Topological_data_with_scalar_product.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -20,6 +20,13 @@ * along with this program. If not, see . */ +#ifndef CONCEPT_TOPOLOGICAL_DATA_WITH_SCALAR_PRODUCT_H_ +#define CONCEPT_TOPOLOGICAL_DATA_WITH_SCALAR_PRODUCT_H_ + +namespace Gudhi { + +namespace Persistence_representations { + /** \brief The concept Topological_data_with_scalar_product describes the requirements * for a type to implement a container that allows computations of scalar products. @@ -29,3 +36,9 @@ class Topological_data_with_scalar_product public: double compute_scalar_product( const Topological_data_with_scalar_product& second ); }; + +} // namespace Persistence_representations + +} // namespace Gudhi + +#endif // CONCEPT_TOPOLOGICAL_DATA_WITH_SCALAR_PRODUCT_H_ diff --git a/src/Persistence_representations/concept/Vectorized_topological_data.h b/src/Persistence_representations/concept/Vectorized_topological_data.h index 2dd966fd..8d4105a2 100644 --- a/src/Persistence_representations/concept/Vectorized_topological_data.h +++ b/src/Persistence_representations/concept/Vectorized_topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -20,6 +20,12 @@ * along with this program. If not, see . */ +#ifndef CONCEPT_VECTORIZED_TOPOLOGICAL_DATA_H_ +#define CONCEPT_VECTORIZED_TOPOLOGICAL_DATA_H_ + +namespace Gudhi { + +namespace Persistence_representations { /** \brief The concept Vectorized_topological_data describes the requirements * for a type to implement a container that allows vectorization. @@ -28,7 +34,7 @@ class Vectorized_topological_data { public: /** - * There are various ways data can be verctorized. This function give us the number of functions for vectorization provided by a given class. + * There are various ways data can be vectorized. This function give us the number of functions for vectorization provided by a given class. **/ size_t number_of_vectorize_functions(); /** @@ -37,3 +43,8 @@ public: std::vector vectorize( int number_of_function ); }; +} // namespace Persistence_representations + +} // namespace Gudhi + +#endif // CONCEPT_VECTORIZED_TOPOLOGICAL_DATA_H_ diff --git a/src/Persistence_representations/doc/Persistence_representations_doc.h b/src/Persistence_representations/doc/Persistence_representations_doc.h index 215616a0..bc11d2c4 100644 --- a/src/Persistence_representations/doc/Persistence_representations_doc.h +++ b/src/Persistence_representations/doc/Persistence_representations_doc.h @@ -28,12 +28,12 @@ namespace Gudhi { namespace Persistence_representations { -/** \defgroup Persistence_representations Persistence_representations +/** \defgroup Persistence_representations Persistence representations * * \author Pawel Dlotko * * @{ - *\section idea Idea + *\section Persistence_representations_idea Idea *In order to perform most of the statistical tests and machine learning algorithms on a data one need to be able to perform only a very limited number of operations on them. Let us fix a representation of * data of a type A. To perform most of the statistical and machine learning operations one need to be able to compute average of objects of type A (so that the averaged object is also of a type A), to @@ -71,24 +71,24 @@ namespace Persistence_representations { *\li Persistence diagrams / barcodes (allow computation of distances, vectorizations and real value characteristics). * * - *Note that at the while functionalities like averaging, distances and scalar products are fixed, there is no canonical way of vectorizing and computing real valued characteristics of objects. Therefore the + * Note that at the while functionalities like averaging, distances and scalar products are fixed, there is no canonical way of vectorizing and computing real valued characteristics of objects. Therefore the * vectorizations and computation of real value characteristics procedures are quite likely to evolve in the furthering versions of the library. * - *The main aim of this implementation is to be able to implement various statistical methods, both on the level of C++ and on the level of python. The methods will operate on the functionalities offered + * The main aim of this implementation is to be able to implement various statistical methods, both on the level of C++ and on the level of python. The methods will operate on the functionalities offered * by concepts. That means that the statistical and ML methods will be able to operate on any representation that implement the required concept (including the ones that are not in the library at the moment). * That gives provides a framework, that is very easy to extend, for topological statistics. * - *Below we are discussing the representations which are currently implemented in Persistence\_representations package: + * Below we are discussing the representations which are currently implemented in Persistence\_representations package: * - *\section sec_persistence_landscapes Persistence Landscapes - * Reference manual: \ref Gudhi::Persistence_representations::Persistence_landscape - *Persistence landscapes were originally proposed by Bubenik in \cite bubenik_landscapes_2015. Efficient algorithms to compute them rigorously were proposed by Bubenik and Dlotko in \cite bubenik_dlotko_landscapes_2016. The idea of + * \section sec_persistence_landscapes Persistence Landscapes + * Reference manual: \ref Gudhi::Persistence_representations::Persistence_landscape
+ * Persistence landscapes were originally proposed by Bubenik in \cite bubenik_landscapes_2015. Efficient algorithms to compute them rigorously were proposed by Bubenik and Dlotko in \cite bubenik_dlotko_landscapes_2016. The idea of * persistence landscapes is shortly summarized in below. * - *To begin with, suppose we are given a point \f$(b,d) \in \mathbb{R}^2\f$ in a - *persistence diagram. With this point, we associate a piecewise - *linear function \f$f_{(b,d)} : \mathbb{R} \rightarrow [0,\infty)\f$, which is - *defined as + * To begin with, suppose we are given a point \f$(b,d) \in \mathbb{R}^2\f$ in a + * persistence diagram. With this point, we associate a piecewise + * linear function \f$f_{(b,d)} : \mathbb{R} \rightarrow [0,\infty)\f$, which is + * defined as * * \f[f_{(b,d)}(x) = * \left\{ \begin{array}{ccl} @@ -100,16 +100,16 @@ namespace Persistence_representations { * \end{array} \right. *\f] * - *A persistence landscape of the birth-death - *pairs \f$(b_i , d_i)\f$, where \f$i = 1,\ldots,m\f$, which constitute the given - *persistence diagram is the sequence of functions \f$\lambda_k : \mathbb{R} \rightarrow [0,\infty)\f$ for \f$k \in \mathbb{N}\f$, where \f$\lambda_k(x)\f$ - *denotes the \f$k^{\rm th}\f$ largest value of the numbers \f$f_{(b_i,d_i)}(x)\f$, - *for \f$i = 1, \ldots, m\f$, and we define \f$\lambda_k(x) = 0\f$ if \f$k > m\f$. - *Equivalently, this sequence of functions can be combined into a single - *function \f$L : \mathbb{N} \times \mathbb{R} \to [0,\infty)\f$ of two - *variables, if we define \f$L(k,t) = \lambda_k(t)\f$. + * A persistence landscape of the birth-death + * pairs \f$(b_i , d_i)\f$, where \f$i = 1,\ldots,m\f$, which constitute the given + * persistence diagram is the sequence of functions \f$\lambda_k : \mathbb{R} \rightarrow [0,\infty)\f$ for \f$k \in \mathbb{N}\f$, where \f$\lambda_k(x)\f$ + * denotes the \f$k^{\rm th}\f$ largest value of the numbers \f$f_{(b_i,d_i)}(x)\f$, + * for \f$i = 1, \ldots, m\f$, and we define \f$\lambda_k(x) = 0\f$ if \f$k > m\f$. + * Equivalently, this sequence of functions can be combined into a single + * function \f$L : \mathbb{N} \times \mathbb{R} \to [0,\infty)\f$ of two + * variables, if we define \f$L(k,t) = \lambda_k(t)\f$. * - *The detailed description of algorithms used to compute persistence landscapes can be found in \cite bubenik_dlotko_landscapes_2016. + * The detailed description of algorithms used to compute persistence landscapes can be found in \cite bubenik_dlotko_landscapes_2016. * Note that this implementation provides exact representation of landscapes. That have many advantages, but also a few drawbacks. For instance, as discussed * in \cite bubenik_dlotko_landscapes_2016, the exact representation of landscape may be of quadratic size with respect to the input persistence diagram. It may therefore happen * that, for very large diagrams, using this representation may be memory--prohibitive. In such a case, there are two possible ways to proceed: @@ -120,13 +120,13 @@ namespace Persistence_representations { * * *\section sec_landscapes_on_grid Persistence Landscapes on a grid - * Reference manual: \ref Gudhi::Persistence_representations::Persistence_landscape_on_grid - *This is an alternative, not--exact, representation of persistence landscapes defined in the Section \ref sec_persistence_landscapes. Unlike in the Section \ref sec_persistence_landscapes we build a + * Reference manual: \ref Gudhi::Persistence_representations::Persistence_landscape_on_grid
+ * This is an alternative, not--exact, representation of persistence landscapes defined in the Section \ref sec_persistence_landscapes. Unlike in the Section \ref sec_persistence_landscapes we build a * representation of persistence landscape by sampling its values on a finite, equally distributed grid of points. * Since, the persistence landscapes that originate from persistence diagrams have slope \f$1\f$ or \f$-1\f$, we have an estimate of a region between the grid points where the landscape cab be located. * That allows to estimate an error make when performing various operations on landscape. Note that for average landscapes the slope is in range \f$[-1,1]\f$ and similar estimate can be used. * - *Due to a lack of rigorous description of the algorithms to deal with this non--rigorous representaion of persistence landscapes in the literature, we are providing a short discussion of them in below. + * Due to a lack of rigorous description of the algorithms to deal with this non--rigorous representation of persistence landscapes in the literature, we are providing a short discussion of them in below. * *Let us assume that we want to compute persistence landscape on a interval \f$[x,y]\f$. Let us assume that we want to use \f$N\f$ grid points for that purpose. * Then we will sample the persistence landscape on points \f$x_1 = x , x_2 = x + \frac{y-x}{N}, \ldots , x_{N} = y\f$. Persistence landscapes are represented as a vector of @@ -153,7 +153,7 @@ namespace Persistence_representations { *Note that the same representation is used in TDA R-package \cite Fasy_Kim_Lecci_Maria_tda. * *\section sec_persistence_heat_maps Persistence heat maps - * Reference manual: \ref Gudhi::Persistence_representations::Persistence heat maps + * Reference manual: \ref Gudhi::Persistence_representations::Persistence_heat_maps
*This is a general class of discrete structures which are based on idea of placing a kernel in the points of persistence diagrams. *This idea appeared in work by many authors over the last 15 years. As far as we know this idea was firstly described in the work of Bologna group in \cite Ferri_Frosini_comparision_sheme_1 and \cite Ferri_Frosini_comparision_sheme_2. *Later it has been described by Colorado State University group in \cite Persistence_Images_2017. The presented paper in the first time provide a discussion of stability of the representation. @@ -177,7 +177,7 @@ namespace Persistence_representations { * * *\section sec_persistence_vectors Persistence vectors - * Reference manual: \ref Gudhi::Persistence_representations::Persistence vectors + * Reference manual: \ref Gudhi::Persistence_representations::Vector_distances_in_diagram
*This is a representation of persistent homology in a form of a vector which was designed for an application in 3d graphic in \cite Carriere_Oudot_Ovsjanikov_top_signatures_3d. Below we provide a short description of this representation. * *Given a persistence diagram \f$D = \{ (b_i,d_i) \}\f$, for every pair of birth--death points \f$(b_1,d_1)\f$ and \f$(b_2,d_2)\f$ we compute the following three distances: diff --git a/src/Persistence_representations/example/persistence_heat_maps.cpp b/src/Persistence_representations/example/persistence_heat_maps.cpp index da87486d..c75e2731 100644 --- a/src/Persistence_representations/example/persistence_heat_maps.cpp +++ b/src/Persistence_representations/example/persistence_heat_maps.cpp @@ -55,7 +55,7 @@ int main( int argc , char** argv ) persistence2.push_back( std::make_pair(3,5) ); persistence2.push_back( std::make_pair(6,10) ); - //over here we define a function we sill put on a top on every birth--death pair in the persistence interval. It can be anything. Over here we will use standarg Gaussian + //over here we define a function we sill put on a top on every birth--death pair in the persistence interval. It can be anything. Over here we will use standard Gaussian std::vector< std::vector > filter = create_Gaussian_filter(5,1); //creating two heat maps. @@ -72,7 +72,7 @@ int main( int argc , char** argv ) Persistence_heat_maps median; median.compute_median( vector_of_maps ); - //to compute L^1 disance between hm1 and hm2: + //to compute L^1 distance between hm1 and hm2: std::cout << "The L^1 distance is : " << hm1.distance( hm2 , 1 ) << std::endl; //to average of hm1 and hm2: diff --git a/src/Persistence_representations/example/persistence_intervals.cpp b/src/Persistence_representations/example/persistence_intervals.cpp index ed5b4e34..947c9627 100644 --- a/src/Persistence_representations/example/persistence_intervals.cpp +++ b/src/Persistence_representations/example/persistence_intervals.cpp @@ -47,7 +47,7 @@ int main( int argc , char** argv ) std::vector dominant_ten_intervals_length = p.length_of_dominant_intervals(10); - std::cout << "Lendth of ten dominant intervals : " < cumulative_histogram = p.cumulative_histogram_of_lengths( 10 ); - std::cout<< "Cumuative histogram : " <. */ -#pragma once -#ifndef PSSK_H -#define PSSK_H +#ifndef PSSK_H_ +#define PSSK_H_ //gudhi include #include @@ -138,7 +137,7 @@ void PSSK::construct( const std::vector< std::pair >& intervals_ std::cerr << "y_grid : " << y_grid << std::endl; } - //x_grid and y_grid gives a center of the kernel. We want to have its lower left cordner. To get this, we need to shift x_grid and y_grid by a grid diameter. + //x_grid and y_grid gives a center of the kernel. We want to have its lower left corner. To get this, we need to shift x_grid and y_grid by a grid diameter. x_grid -= filter.size()/2; y_grid -= filter.size()/2; //note that the numbers x_grid and y_grid may be negative. @@ -174,8 +173,8 @@ void PSSK::construct( const std::vector< std::pair >& intervals_ } }//construct +} //namespace Persistence_representations +} //namespace Gudhi -#endif -}//namespace Gudhi_stat -}//namespace Gudhi +#endif // PSSK_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h index 59e58e41..a20702ff 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h +++ b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -20,8 +20,8 @@ * along with this program. If not, see . */ -#ifndef Persistence_heat_maps_H -#define Persistence_heat_maps_H +#ifndef PERSISTENCE_HEAT_MAPS_H_ +#define PERSISTENCE_HEAT_MAPS_H_ //standard include #include @@ -69,7 +69,7 @@ std::vector< std::vector > create_Gaussian_filter( size_t pixel_radius , if ( dbg ) { - std::cerr << "Kernel initalize \n"; + std::cerr << "Kernel initialize \n"; std::cerr << "pixel_radius : " << pixel_radius << std::endl; std::cerr << "kernel.size() : " << kernel.size() << std::endl; getchar(); @@ -114,7 +114,7 @@ std::vector< std::vector > create_Gaussian_filter( size_t pixel_radius , /* -* There are various options to scale the poits depending on their location. One can for instance: +* There are various options to scale the points depending on their location. One can for instance: * (1) do nothing (scale all of them with the weight 1), as in the function constant_function * (2) Scale them by the distance to the diagonal. This is implemented in function * (3) Scale them with the square of their distance to diagonal. This is implemented in function @@ -123,8 +123,8 @@ std::vector< std::vector > create_Gaussian_filter( size_t pixel_radius , /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. - * This particular functiona is a finction which always assign value 1 to a point in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. + * This particular functionality is a function which always assign value 1 to a point in the diagram. **/ class constant_scaling_function { @@ -137,7 +137,7 @@ public: /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. * The scaling given by this function to a point (b,d) is Euclidean distance of (b,d) from diagonal. **/ class distance_from_diagonal_scaling @@ -151,7 +151,7 @@ public: }; /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. * The scaling given by this function to a point (b,d) is a square of Euclidean distance of (b,d) from diagonal. **/ class squared_distance_from_diagonal_scaling @@ -164,7 +164,7 @@ public: }; /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. * The scaling given by this function to a point (b,d) is an arctan of a persistence of a point (i.e. arctan( b-d ). **/ class arc_tan_of_persistence_of_point @@ -177,7 +177,7 @@ public: }; /** - * This is one of a scaling functions used to weight poits depending on their persistence and/or location in the diagram. + * This is one of a scaling functions used to weight points depending on their persistence and/or location in the diagram. * This scaling function do not only depend on a point (p,d) in the diagram, but it depends on the whole diagram. * The longest persistence pair get a scaling 1. Any other pair get a scaling belong to [0,1], which is proportional * to the persistence of that pair. @@ -196,14 +196,19 @@ private: /** - * This class implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product -**/ + * \class Persistence_heat_maps Persistence_heat_maps.h gudhi/Persistence_heat_maps.h + * \brief A class implementing persistence heat maps. + * + * \ingroup Persistence_representations +**/ + +// This class implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product template class Persistence_heat_maps { public: /** - * The default constructor. A scaling function from the diagonal is set up to a constant function. The image is not erased below the diagonal. The gaussian have diameter 5. + * The default constructor. A scaling function from the diagonal is set up to a constant function. The image is not erased below the diagonal. The Gaussian have diameter 5. **/ Persistence_heat_maps() { @@ -217,7 +222,7 @@ public: /** * Construction that takes at the input the following parameters: * (1) A vector of pairs of doubles (representing persistence intervals). All other parameters are optional. They are: - * (2) a Gausian filter generated by create_Gaussian_filter filter (the default value of this vaiable is a Gaussian filter of a radius 5), + * (2) a Gaussian filter generated by create_Gaussian_filter filter (the default value of this variable is a Gaussian filter of a radius 5), * (3) a boolean value which determines if the area of image below diagonal should, or should not be erased (it will be erased by default). * (4) a number of pixels in each direction (set to 1000 by default). * (5) a min x and y value of points that are to be taken into account. By default it is set to std::numeric_limits::max(), in which case the program compute the values based on the data, @@ -226,12 +231,12 @@ public: Persistence_heat_maps( const std::vector< std::pair< double,double > > & interval , std::vector< std::vector > filter = create_Gaussian_filter(5,1) , bool erase_below_diagonal = false , size_t number_of_pixels = 1000 , double min_ = std::numeric_limits::max() , double max_ = std::numeric_limits::max() ); /** - * Construction that takes at the input a name of a file with persistence intervals, a filter (radius 5 by default), a scaling function (constant by default), a boolean value which determines if the area of image below diagonal should, or should not be erased (should by default). The next parameter is the number of pixels in each direction (set to 1000 by default). and min and max values of images (both set to std::numeric_limits::max() by defaulet. If this is the case, the program will pick the right values based on the data). + * Construction that takes at the input a name of a file with persistence intervals, a filter (radius 5 by default), a scaling function (constant by default), a boolean value which determines if the area of image below diagonal should, or should not be erased (should by default). The next parameter is the number of pixels in each direction (set to 1000 by default) and min and max values of images (both set to std::numeric_limits::max() by default. If this is the case, the program will pick the right values based on the data). **/ /** * Construction that takes at the input the following parameters: - * (1) A a name of a file with persistence intervals. The file shold be readable by the function read_persistence_intervals_in_one_dimension_from_file. All other parameters are optional. They are: - * (2) a Gausian filter generated by create_Gaussian_filter filter (the default value of this vaiable is a Gaussian filter of a radius 5), + * (1) A name of a file with persistence intervals. The file should be readable by the function read_persistence_intervals_in_one_dimension_from_file. All other parameters are optional. They are: + * (2) a Gaussian filter generated by create_Gaussian_filter filter (the default value of this variable is a Gaussian filter of a radius 5), * (3) a boolean value which determines if the area of image below diagonal should, or should not be erased (it will be erased by default). * (4) a number of pixels in each direction (set to 1000 by default). * (5) a min x and y value of points that are to be taken into account. By default it is set to std::numeric_limits::max(), in which case the program compute the values based on the data, @@ -259,14 +264,14 @@ public: //put to file subroutine /** - * The function outputs the perssitence image to a text file. The format as follow: + * The function outputs the persistence image to a text file. The format as follow: * In the first line, the values min and max of the image are stored * In the next lines, we have the persistence images in a form of a bitmap image. **/ void print_to_file( const char* filename )const; /** - * A function that load a heat map from file to the current object (and arase qhatever was stored in the current object before). + * A function that load a heat map from file to the current object (and erase whatever was stored in the current object before). **/ void load_from_file( const char* filename ); @@ -347,7 +352,7 @@ public: /** - * A function to generate a gnuplot script to vizualize the persistent image. + * A function to generate a gnuplot script to visualize the persistent image. **/ void plot( const char* filename )const; @@ -474,7 +479,7 @@ public: //Implementations of functions for various concepts. /** - * This function produce a vector of doubles based on a persisence heat map. It is required in a concept Vectorized_topological_data + * This function produce a vector of doubles based on a persistence heat map. It is required in a concept Vectorized_topological_data */ std::vector vectorize( int number_of_function )const; /** @@ -486,9 +491,9 @@ public: } /** - * This function is required by the Real_valued_topological_data concept. It returns various projections od the persistence heat map to a real line. - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * This function is required by the Real_valued_topological_data concept. It returns various projections on the persistence heat map to a real line. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const; /** @@ -515,7 +520,7 @@ public: /** * A function to compute scalar product of persistence heat maps. - * The parameter of this functionis a const reference to an object of a class Persistence_heat_maps. + * The parameter of this function is a const reference to an object of a class Persistence_heat_maps. * This function is required in Topological_data_with_scalar_product concept. **/ double compute_scalar_product( const Persistence_heat_maps& second_ )const; @@ -559,7 +564,6 @@ protected: } //data - //double (*scalling_function_with_respect_to_distance_from_diagonal)( const std::pair< double , double >& point_in_diagram ); Scalling_of_kernels f; bool erase_below_diagonal; double min_; @@ -583,7 +587,7 @@ void Persistence_heat_maps::construct( const std::vector< s if ( min_ == max_ ) { - if (dbg)std::cerr << "min and max parameters will be etermined based on intervals \n"; + if (dbg)std::cerr << "min and max parameters will be determined based on intervals \n"; //in this case, we want the program to set up the min_ and max_ values by itself. min_ = std::numeric_limits::max(); max_ = -std::numeric_limits::max(); @@ -636,7 +640,7 @@ void Persistence_heat_maps::construct( const std::vector< s std::cerr << "y_grid : " << y_grid << std::endl; } - //x_grid and y_grid gives a center of the kernel. We want to have its lower left cordner. To get this, we need to shift x_grid and y_grid by a grid diameter. + //x_grid and y_grid gives a center of the kernel. We want to have its lower left corner. To get this, we need to shift x_grid and y_grid by a grid diameter. x_grid -= filter.size()/2; y_grid -= filter.size()/2; //note that the numbers x_grid and y_grid may be negative. @@ -711,11 +715,6 @@ Persistence_heat_maps::Persistence_heat_maps( const char* f { intervals_ = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); } - //std::cerr << "intervals_.size() : " << intervals_.size() << std::endl; - //for ( size_t i = 0 ; i != intervals_.size() ; ++i ) - //{ - // std::cerr << intervals_[i].first << " " << intervals_[i].second << std::endl; - //} this->construct( intervals_ , filter, erase_below_diagonal , number_of_pixels , min_ , max_ ); this->set_up_parameters_for_basic_classes(); } @@ -956,11 +955,11 @@ double Persistence_heat_maps::distance( const Persistence_h //first we need to check if (*this) and second are defined on the same domain and have the same dimensions: if ( !this->check_if_the_same(second) ) { - std::cerr << "The persistence images are of noncompatible sizes. We cannot therefore compute distance between them. The program will now terminate"; - throw "The persistence images are of noncompatible sizes. We cannot therefore compute distance between them. The program will now terminate"; + std::cerr << "The persistence images are of non compatible sizes. We cannot therefore compute distance between them. The program will now terminate"; + throw "The persistence images are of non compatible sizes. We cannot therefore compute distance between them. The program will now terminate"; } - //if we are here, we know that the two persistence iomages are defined on the same domain, so we can start computing their distances: + //if we are here, we know that the two persistence images are defined on the same domain, so we can start computing their distances: double distance = 0; if ( power < std::numeric_limits::max() ) @@ -1016,11 +1015,11 @@ double Persistence_heat_maps::compute_scalar_product( const //first we need to check if (*this) and second are defined on the same domain and have the same dimensions: if ( !this->check_if_the_same(second) ) { - std::cerr << "The persistence images are of noncompatible sizes. We cannot therefore compute distance between them. The program will now terminate"; - throw "The persistence images are of noncompatible sizes. We cannot therefore compute distance between them. The program will now terminate"; + std::cerr << "The persistence images are of non compatible sizes. We cannot therefore compute distance between them. The program will now terminate"; + throw "The persistence images are of non compatible sizes. We cannot therefore compute distance between them. The program will now terminate"; } - //if we are here, we know that the two persistence iomages are defined on the same domain, so we can start computing their scalar product: + //if we are here, we know that the two persistence images are defined on the same domain, so we can start computing their scalar product: double scalar_prod = 0; for ( size_t i = 0 ; i != this->heat_map.size() ; ++i ) { @@ -1035,8 +1034,8 @@ double Persistence_heat_maps::compute_scalar_product( const -}//namespace Gudhi_stat -}//namespace Gudhi +} // namespace Persistence_representations +} // namespace Gudhi -#endif +#endif // PERSISTENCE_HEAT_MAPS_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals.h b/src/Persistence_representations/include/gudhi/Persistence_intervals.h index 792c0a28..40c24670 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -20,8 +20,8 @@ * along with this program. If not, see . */ -#ifndef Persistence_intervals_H_ -#define Persistence_intervals_H_ +#ifndef PERSISTENCE_INTERVALS_H_ +#define PERSISTENCE_INTERVALS_H_ //gudhi include #include @@ -48,14 +48,14 @@ class Persistence_intervals { public: /** - * This is a constructor of a class Persistence_intervals from a text file. Each line of the input file is supposed to contain two numbers of a type doube (or convertable to double) + * This is a constructor of a class Persistence_intervals from a text file. Each line of the input file is supposed to contain two numbers of a type double (or convertible to double) * representing the birth and the death of the persistence interval. If the pairs are not sorted so that birth <= death, then the constructor will sort then that way. - * * The second parameter of a constructor is a dimension of intervals to be read from a file. If your file contains only birt-death pairs, use the default value. + * * The second parameter of a constructor is a dimension of intervals to be read from a file. If your file contains only birth-death pairs, use the default value. **/ Persistence_intervals( const char* filename , unsigned dimension = std::numeric_limits::max() ); /** - * This is a constructor of a class Persistence_intervals from a vector of pairs. Each pair is assumed to represent a persistence interval. We assume that the first elemnets of pairs + * This is a constructor of a class Persistence_intervals from a vector of pairs. Each pair is assumed to represent a persistence interval. We assume that the first elements of pairs * are smaller or equal the second elements of pairs. **/ Persistence_intervals( const std::vector< std::pair< double,double > >& intervals ); @@ -102,15 +102,15 @@ public: std::vector< std::pair > dominant_intervals( size_t where_to_cut = 100 )const; /** - * Procedure to compute a histogram of interva's length. A histogram is a block plot. The number of blocks is determined by the first parameter of the function (set by default to 10). + * Procedure to compute a histogram of interval's length. A histogram is a block plot. The number of blocks is determined by the first parameter of the function (set by default to 10). * For the sake of argument let us assume that the length of the longest interval is 1 and the number of bins is 10. In this case the i-th block correspond to a range between i-1/10 and i10. * The vale of a block supported at the interval is the number of persistence intervals of a length between x_0 and x_1. **/ std::vector< size_t > histogram_of_lengths( size_t number_of_bins = 10 )const; /** - * Based on a histogram of intervals lengts computed by the function histogram_of_lengths H the procedure below computes the cumulative histogram. The i-th position of the resulting histogram - * is the sume of values of H for the positions from 0 to i. + * Based on a histogram of intervals lengths computed by the function histogram_of_lengths H the procedure below computes the cumulative histogram. The i-th position of the resulting histogram + * is the sum of values of H for the positions from 0 to i. **/ std::vector< size_t > cumulative_histogram_of_lengths( size_t number_of_bins = 10 )const; @@ -127,13 +127,13 @@ public: std::vector< double > cumulative_characteristic_function_of_diagram( double x_min , double x_max , size_t number_of_bins = 10 )const; /** - * Compute the funtion of persistence Betti numbers. The returned value is a vector of pair. First element of each pair is a place where persistence Betti numbers change. + * Compute the function of persistence Betti numbers. The returned value is a vector of pair. First element of each pair is a place where persistence Betti numbers change. * Second element of each pair is the value of Persistence Betti numbers at that point. **/ std::vector< std::pair< double , size_t > > compute_persistent_betti_numbers()const; /** - *This is a non optimal procedure that compute vector of distances from each point of diagram to its k-th nearest neighbor (k is a parameted of the program). The resulting vector is by default truncated to 10 + *This is a non optimal procedure that compute vector of distances from each point of diagram to its k-th nearest neighbor (k is a parameter of the program). The resulting vector is by default truncated to 10 *elements (this value can be changed by using the second parameter of the program). The points are returned in order from the ones which are farthest away from their k-th nearest neighbors. **/ std::vector< double > k_n_n( size_t k , size_t where_to_cut = 10 )const; @@ -188,12 +188,9 @@ public: std::cout << "Gnuplot script to visualize persistence diagram written to the file: " << nameStr << ". Type load '" << nameStr << "' in gnuplot to visualize." << std::endl; } - - - /** - * Retun numbr of points in the diagram. + * Return number of points in the diagram. **/ size_t size()const{return this->intervals.size();} @@ -207,25 +204,12 @@ public: } - - - - - - - - - - - - - //Implementations of functions for various concepts. /** - * This is a simple function projectig the persistence intervals to a real number. The function we use here is a sum of squared lendgths of intervals. It can be naturally interpreted as + * This is a simple function projecting the persistence intervals to a real number. The function we use here is a sum of squared lengths of intervals. It can be naturally interpreted as * sum of step function, where the step hight it equal to the length of the interval. - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const; /** @@ -237,14 +221,14 @@ public: } /** - * Return a familly of vectors obtained from the persistence diagram. The i-th vector consist of the lenfth of i dominant persistence intervals. + * Return a family of vectors obtained from the persistence diagram. The i-th vector consist of the length of i dominant persistence intervals. **/ std::vector vectorize( int number_of_function )const { return this->length_of_dominant_intervals( number_of_function ); } /** - * This function return the number of functions that allows vectorization of a persisence diagram. It is required in a concept Vectorized_topological_data. + * This function return the number of functions that allows vectorization of a persistence diagram. It is required in a concept Vectorized_topological_data. **/ size_t number_of_vectorize_functions()const { @@ -252,19 +236,7 @@ public: } //end of implementation of functions needed for concepts. - //end of implementation of functions needed for concepts. - - - - - - - - - - - - + //For visualization use output from vectorize and build histograms. std::vector< std::pair< double,double > > output_for_visualization() @@ -289,37 +261,6 @@ protected: Persistence_intervals::Persistence_intervals( const char* filename , unsigned dimension ) { - //bool dbg = false; - //ifstream in; - //in.open( filename ); - - //if ( !in.good() ) - //{ - // throw("File with the persistence diagram do not exist, the program will now terminate.\n"); - //} - - //while ( true ) - //{ - // double first; - // double second; - // in >> first >> second; - - // if ( first > second ) - // { - // double buf = first; - // first = second; - // second = buf; - // } - - // if ( in.eof() )break; - // this->intervals.push_back( std::make_pair( first,second ) ); - // if ( dbg ) - // { - // std::cerr << "Adding interval [ " << first << " , " << second << " ]\n"; - // getchar(); - // } - //} - //in.close(); if ( dimension == std::numeric_limits::max() ) { this->intervals = read_persistence_intervals_in_one_dimension_from_file( filename ); @@ -490,7 +431,6 @@ std::vector< double > Persistence_intervals::characteristic_function_of_diagram( { result[pos] += ( (x_max - x_min)/(double)number_of_bins ) * ( this->intervals[i].second - this->intervals[i].first ); } - //cerr << "x_max : " << x_max << " x_min : " << x_min << " , number_of_bins : " << number_of_bins << " this->intervals[i].second : " << this->intervals[i].second << " this->intervals[i].first : " << this->intervals[i].first << endl; if ( dbg ) { std::cerr << "Result at this stage \n"; @@ -499,7 +439,6 @@ std::vector< double > Persistence_intervals::characteristic_function_of_diagram( std::cerr << result[aa] << " "; } std::cerr << std::endl; - //getchar(); } } return result; @@ -599,8 +538,7 @@ std::vector< double > Persistence_intervals::k_n_n( size_t k , size_t where_to_c { distancesFromI.push_back( compute_euclidean_distance( this->intervals[i] , this->intervals[j] ) ); } - //distances.push_back( distancesFromI ); - //also add a distance from this guy to daigonal: + //also add a distance from this guy to diagonal: double distanceToDiagonal = compute_euclidean_distance( this->intervals[i] , std::make_pair( 0.5*(this->intervals[i].first + this->intervals[i].second) , 0.5*(this->intervals[i].first + this->intervals[i].second) ) ); distances_from_diagonal[i] = distanceToDiagonal; @@ -694,7 +632,7 @@ double Persistence_intervals::project_to_R( int number_of_function )const } -}//namespace gudhi stat -}//namespace gudhi +} // namespace Persistence_representations +} // namespace gudhi -#endif +#endif // PERSISTENCE_INTERVALS_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h index 7ef711e9..0da58399 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -20,8 +20,8 @@ * along with this program. If not, see . */ -#ifndef Persistence_intervals_WITH_DISTANCES_H_ -#define Persistence_intervals_WITH_DISTANCES_H_ +#ifndef PERSISTENCE_INTERVALS_WITH_DISTANCES_H_ +#define PERSISTENCE_INTERVALS_WITH_DISTANCES_H_ #include @@ -59,7 +59,7 @@ public: }; -}//namespace gudhi stat -}//namespace gudhi +} // namespace Persistence_representations +} // namespace gudhi -#endif +#endif // PERSISTENCE_INTERVALS_WITH_DISTANCES_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape.h b/src/Persistence_representations/include/gudhi/Persistence_landscape.h index 9a177b60..642bba84 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -21,8 +21,8 @@ */ -#ifndef Persistence_landscapes_H -#define Persistence_landscapes_H +#ifndef PERSISTENCE_LANDSCAPE_H_ +#define PERSISTENCE_LANDSCAPE_H_ //standard include #include @@ -48,7 +48,7 @@ namespace Persistence_representations -//predeclaration +// pre declaration class Persistence_landscape; template < typename operation > Persistence_landscape operation_on_pair_of_landscapes( const Persistence_landscape& land1 , const Persistence_landscape& land2 ); @@ -56,12 +56,25 @@ Persistence_landscape operation_on_pair_of_landscapes( const Persistence_landsca /** - * A clas implementing persistence landascpes data structures. For theroretical desciritpion, please consult a paper ''Statistical topological data analysis using persistence landscapes'' by Peter Bubenik. - * For details of algorithms, please consult ''A persistence landscapes toolbox for topological statistics'' by Peter Bubenik and Pawel Dlotko. - * Persistence landscapes allow vertorization, computations of distances, computations of projections to Real, computations of averages and scalar products. Therefore they implement suitable interfaces. - * It implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product - * Note that at the moment, due to roundoff errors during the construction of persistence landscapes, elements which are different by 0.000005 are considered the same. If the scale in your persistence diagrams - * is comparable to this value, please rescale them before use this code. + * \class Persistence_landscape Persistence_landscape.h gudhi/Persistence_landscape.h + * \brief A class implementing persistence landscapes data structures. + * + * \ingroup Persistence_representations + * + * \details + * For theoretical description, please consult Statistical topological data analysis using persistence + * landscapes\cite bubenik_landscapes_2015 , and for details of algorithms, + * A persistence landscapes toolbox for topological statistics\cite bubenik_dlotko_landscapes_2016. + * + * Persistence landscapes allow vectorization, computations of distances, computations of projections to Real, + * computations of averages and scalar products. Therefore they implement suitable interfaces. + * It implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, + * Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product + * + * Note that at the moment, due to rounding errors during the construction of persistence landscapes, elements which + * are different by 0.000005 are considered the same. If the scale in your persistence diagrams is comparable to this + * value, please rescale them before use this code. + * **/ class Persistence_landscape { @@ -169,7 +182,7 @@ public: } /** - * An operator * that allows multipilication of a landscape by a real number. + * An operator * that allows multiplication of a landscape by a real number. **/ friend Persistence_landscape operator*( const Persistence_landscape& first , double con ) { @@ -177,7 +190,7 @@ public: } /** - * An operator * that allows multipilication of a landscape by a real number (order of parameters swapped). + * An operator * that allows multiplication of a landscape by a real number (order of parameters swapped). **/ friend Persistence_landscape operator*( double con , const Persistence_landscape& first ) { @@ -297,7 +310,6 @@ public: *\private Computations of \f$L^{\infty}\f$ distance between two landscapes. **/ friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape& first, const Persistence_landscape& second ); - //friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape& first, const Persistence_landscape& second , unsigned& nrOfLand , double&x , double& y1, double& y2 ); /** @@ -308,7 +320,7 @@ public: /** - * Function to compute absolute value of a PL function. The representation of persistence landscapes allow to store general PL-function. When computing distance betwen two landscapes, we compute difference between + * Function to compute absolute value of a PL function. The representation of persistence landscapes allow to store general PL-function. When computing distance between two landscapes, we compute difference between * them. In this case, a general PL-function with negative value can appear as a result. Then in order to compute distance, we need to take its absolute value. This is the purpose of this procedure. **/ Persistence_landscape abs(); @@ -319,7 +331,7 @@ public: size_t size()const{return this->land.size(); } /** - * Computate maximal value of lambda-level landscape. + * Compute maximal value of lambda-level landscape. **/ double find_max( unsigned lambda )const; @@ -328,27 +340,13 @@ public: **/ friend double compute_inner_product( const Persistence_landscape& l1 , const Persistence_landscape& l2 ); - - - - - - - - - - - - - - //Implementations of functions for various concepts. /** * The number of projections to R is defined to the number of nonzero landscape functions. I-th projection is an integral of i-th landscape function over whole R. * This function is required by the Real_valued_topological_data concept. - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const { @@ -382,7 +380,7 @@ public: return v; } /** - * This function return the number of functions that allows vectorization of persistence laandscape. It is required in a concept Vectorized_topological_data. + * This function return the number of functions that allows vectorization of persistence landscape. It is required in a concept Vectorized_topological_data. **/ size_t number_of_vectorize_functions()const { @@ -404,8 +402,8 @@ public: { nextLevelMerge[i] = to_average[i]; } - bool is_this_first_level = true;//in the loop, we will create dynamically a unmber of intermediate complexes. We have to clean that up, but we cannot erase the initial andscapes we have - //to average. In this case, we simply check if the nextLevelMerge are the input landscapes or the ones created in that loop by usig this extra variable. + bool is_this_first_level = true;//in the loop, we will create dynamically a number of intermediate complexes. We have to clean that up, but we cannot erase the initial landscapes we have + //to average. In this case, we simply check if the nextLevelMerge are the input landscapes or the ones created in that loop by using this extra variable. while ( nextLevelMerge.size() != 1 ) { @@ -446,7 +444,7 @@ public: /** * A function to compute distance between persistence landscape. - * The parameter of this functionis a Persistence_landscape. + * The parameter of this function is a Persistence_landscape. * This function is required in Topological_data_with_distances concept. * For max norm distance, set power to std::numeric_limits::max() **/ @@ -465,7 +463,7 @@ public: /** * A function to compute scalar product of persistence landscapes. - * The parameter of this functionis a Persistence_landscape. + * The parameter of this function is a Persistence_landscape. * This function is required in Topological_data_with_scalar_product concept. **/ double compute_scalar_product( const Persistence_landscape& second )const @@ -473,25 +471,6 @@ public: return compute_inner_product( (*this) , second ); } //end of implementation of functions needed for concepts. - - - // - // This procedure returns x-range of a given level persistence landscape. If a default value is used, the x-range - //of 0th level landscape is given (and this range contains the ranges of all other landscapes). - // - //std::pair< double , double > get_x_range( size_t level = 0 )const - //{ - // std::pair< double , double > result; - // if ( level < this->land.size() ) - // { - // result = std::make_pair( this->land[level][1].first , this->land[level][ this->land[level].size() - 2 ].first ); - // } - // else - // { - // result = std::make_pair( 0,0 ); - // } - // return result; - //} /** * This procedure returns y-range of a given level persistence landscape. If a default value is used, the y-range @@ -582,7 +561,6 @@ bool Persistence_landscape::operator == ( const Persistence_landscape& rhs )con { if ( !( almost_equal(this->land[level][i].first , rhs.land[level][i].first) && almost_equal(this->land[level][i].second , rhs.land[level][i].second) ) ) { - //std::cerr<< this->land[level][i].first << " , " << rhs.land[level][i].first << " and " << this->land[level][i].second << " , " << rhs.land[level][i].second << std::endl; if (operatorEqualDbg)std::cerr << "this->land[level][i] : " << this->land[level][i].first << " " << this->land[level][i].second << "\n"; if (operatorEqualDbg)std::cerr << "rhs.land[level][i] : " << rhs.land[level][i].first << " " << rhs.land[level][i].second << "\n"; if (operatorEqualDbg)std::cerr << "3\n"; @@ -768,7 +746,7 @@ double Persistence_landscape::compute_integral_of_landscape()const { for ( size_t nr = 2 ; nr != this->land[i].size()-1 ; ++nr ) { - //it suffices to compute every planar integral and then sum them ap for each lambda_n + //it suffices to compute every planar integral and then sum them up for each lambda_n result += 0.5*( this->land[i][nr].first - this->land[i][nr-1].first )*(this->land[i][nr].second + this->land[i][nr-1].second); } } @@ -780,7 +758,7 @@ double Persistence_landscape::compute_integral_of_a_level_of_a_landscape( size_t double result = 0; if ( level >= this->land.size() ) { - //this landscape function is constantly equal 0, so is the intergral. + //this landscape function is constantly equal 0, so is the integral. return result; } //also negative landscapes are assumed to be zero. @@ -788,7 +766,7 @@ double Persistence_landscape::compute_integral_of_a_level_of_a_landscape( size_t for ( size_t nr = 2 ; nr != this->land[ level ].size()-1 ; ++nr ) { - //it suffices to compute every planar integral and then sum them ap for each lambda_n + //it suffices to compute every planar integral and then sum them up for each lambda_n result += 0.5*( this->land[ level ][nr].first - this->land[ level ][nr-1].first )*(this->land[ level ][nr].second + this->land[ level ][nr-1].second); } @@ -826,7 +804,6 @@ double Persistence_landscape::compute_integral_of_landscape( double p )const std::cout << "result : " << result << std::endl; } } - //if (compute_integral_of_landscapeDbg) std::cin.ignore(); } return result; } @@ -953,7 +930,7 @@ Persistence_landscape Persistence_landscape::abs() for ( size_t i = 1 ; i != this->land[level].size() ; ++i ) { if ( AbsDbg ){std::cout << "this->land[" << level << "][" << i << "] : " << this->land[level][i].first << " " << this->land[level][i].second << std::endl;} - //if a line segment between this->land[level][i-1] and this->land[level][i] crosses the x-axis, then we have to add one landscape point t oresult + //if a line segment between this->land[level][i-1] and this->land[level][i] crosses the x-axis, then we have to add one landscape point t o result if ( (this->land[level][i-1].second)*(this->land[level][i].second) < 0 ) { double zero = find_zero_of_a_line_segment_between_those_two_points( this->land[level][i-1] , this->land[level][i] ); @@ -1025,7 +1002,7 @@ void Persistence_landscape::load_landscape_from_file( const char* filename ) this->land.clear(); - //this constructor reads persistence landscape form a file. This file have to be created by this software beforehead + //this constructor reads persistence landscape form a file. This file have to be created by this software before head std::ifstream in; in.open( filename ); if ( !in.good() ) @@ -1049,7 +1026,7 @@ void Persistence_landscape::load_landscape_from_file( const char* filename ) lineSS >> beginn; lineSS >> endd; landscapeAtThisLevel.push_back( std::make_pair( beginn , endd ) ); - if (dbg){std::cerr << "Reading a pont : " << beginn << " , " << endd << std::endl;} + if (dbg){std::cerr << "Reading a point : " << beginn << " , " << endd << std::endl;} } else { @@ -1117,7 +1094,6 @@ Persistence_landscape operation_on_pair_of_landscapes ( const Persistence_landsc std::cerr << "land2.land[" << i << "].size() : " << land2.land[i].size() << std::endl; std::cout << "land1.land[i][p].first : " << land1.land[i][p].first << "\n"; std::cout << "land2.land[i][q].first : " << land2.land[i][q].first << "\n"; - //getchar(); } if ( land1.land[i][p].first < land2.land[i][q].first ) @@ -1126,7 +1102,6 @@ Persistence_landscape operation_on_pair_of_landscapes ( const Persistence_landsc { std::cout << "first \n"; std::cout << " function_value(land2.land[i][q-1],land2.land[i][q],land1.land[i][p].first) : "<< function_value(land2.land[i][q-1],land2.land[i][q],land1.land[i][p].first) << "\n"; - //std::cout << "oper( " << land1.land[i][p].second <<"," << function_value(land2.land[i][q-1],land2.land[i][q],land1.land[i][p].first) << " : " << oper( land1.land[i][p].second , function_value(land2.land[i][q-1],land2.land[i][q],land1.land[i][p].first) ) << "\n"; } lambda_n.push_back( std::make_pair( @@ -1242,7 +1217,7 @@ double compute_maximal_distance_non_symmetric( const Persistence_landscape& pl1, } int p2Count = 0; - for ( size_t i = 1 ; i != pl1.land[level].size()-1 ; ++i ) //w tym przypadku nie rozwarzam punktow w nieskocznosci + for ( size_t i = 1 ; i != pl1.land[level].size()-1 ; ++i ) // In this case, I consider points at the infinity { while ( true ) { @@ -1488,11 +1463,8 @@ void Persistence_landscape::plot( const char* filename, double xRangeBegin , do std::cout << "Gnuplot script to visualize persistence diagram written to the file: " << nameStr << ". Type load '" << nameStr << "' in gnuplot to visualize." << std::endl; } +} // namespace Persistence_representations +} // namespace gudhi - -}//namespace gudhi stat -}//namespace gudhi - - -#endif +#endif // PERSISTENCE_LANDSCAPE_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h index 5703163a..d663b543 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -21,8 +21,8 @@ * along with this program. If not, see . **/ -#ifndef Persistence_landscape_on_grid_H_ -#define Persistence_landscape_on_grid_H_ +#ifndef PERSISTENCE_LANDSCAPE_ON_GRID_H_ +#define PERSISTENCE_LANDSCAPE_ON_GRID_H_ //standard include @@ -50,16 +50,25 @@ namespace Gudhi namespace Persistence_representations { -//predeclaration +// pre declaration class Persistence_landscape_on_grid; template < typename operation > Persistence_landscape_on_grid operation_on_pair_of_landscapes_on_grid( const Persistence_landscape_on_grid& land1 , const Persistence_landscape_on_grid& land2 ); /** - * A clas implementing persistence landascpes by approximating them on a collection of grid points. * Persistence landscapes on grid allow vertorization, computations of distances, computations - * of projections to Real, computations of averages and scalar products. Therefore they implement suitable interfaces. - * It implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product - * Note that at the moment, due to roundoff errors during the construction of persistence landscapes on a grid, elements which are different by 0.000005 are considered the same. If the scale in your persistence diagrams + * \class Persistence_landscape_on_grid Persistence_landscape_on_grid.h gudhi/Persistence_landscape_on_grid.h + * \brief A class implementing persistence landscapes by approximating them on a collection of grid points. + * + * \ingroup Persistence_representations + * + * \details + * Persistence landscapes on grid allows vectorization, computations of distances, computations of projections to Real, + * computations of averages and scalar products. Therefore they implement suitable interfaces. + * It implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, + * Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product + * + * Note that at the moment, due to rounding errors during the construction of persistence landscapes on a grid, + * elements which are different by 0.000005 are considered the same. If the scale in your persistence diagrams * is comparable to this value, please rescale them before use this code. **/ @@ -89,14 +98,14 @@ public: /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resoltion of a grid + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resolution of a grid * number of landscape functions to be created and the dimension of intervals that are need to be read from a file (in case of Gudhi format files). **/ Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , unsigned number_of_levels_of_landscape , unsigned short dimension_ = std::numeric_limits::max() ); /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resoltion of a grid + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resolution of a grid * and the dimension of intervals that are need to be read from a file (in case of Gudhi format files). **/ Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , unsigned short dimension_ = std::numeric_limits::max() ); @@ -104,16 +113,16 @@ public: /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resoution of a grid and the number of landscape - * functions to be created. The remaning parameters are calculated based on data. + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resolution of a grid and the number of landscape + * functions to be created. The remaining parameters are calculated based on data. **/ Persistence_landscape_on_grid(const char* filename , size_t number_of_points , unsigned number_of_levels_of_landscape , unsigned short dimension = std::numeric_limits::max() ); /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resoution of a grid. The last parameter is the dimension + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resolution of a grid. The last parameter is the dimension * of a persistence to read from the file. If your file contains only persistence pair in a single dimension, please set it up to std::numeric_limits::max(). - * The remaning parameters are calculated based on data. + * The remaining parameters are calculated based on data. **/ Persistence_landscape_on_grid(const char* filename , size_t number_of_points , unsigned short dimension = std::numeric_limits::max() ); @@ -258,7 +267,7 @@ public: if ( dbg ) { std::cerr << "Increasing result by : " << value_to_add << std::endl; - std::cerr << "restult : " << result << std::endl; + std::cerr << "result : " << result << std::endl; getchar(); } previous_x = current_x; @@ -311,9 +320,9 @@ public: std::cerr << "This is a procedure compute_value_at_a_given_point \n"; std::cerr << "level : " << level << std::endl; std::cerr << "x : " << x << std::endl; - std::cerr << "psoition : " << position << std::endl; + std::cerr << "position : " << position << std::endl; } - //check if we are not exacly in the grid point: + //check if we are not exactly in the grid point: if ( almost_equal( position*dx+ this->grid_min , x) ) { if ( this->values_of_landscapes[position].size() < level ) @@ -389,7 +398,7 @@ public: } /** - * An operator * that allows multipilication of a landscape by a real number. + * An operator * that allows multiplication of a landscape by a real number. **/ friend Persistence_landscape_on_grid operator*( const Persistence_landscape_on_grid& first , double con ) { @@ -397,7 +406,7 @@ public: } /** - * An operator * that allows multipilication of a landscape by a real number (order of parameters swapped). + * An operator * that allows multiplication of a landscape by a real number (order of parameters swapped). **/ friend Persistence_landscape_on_grid operator*( double con , const Persistence_landscape_on_grid& first ) { @@ -413,7 +422,7 @@ public: } /** - * Operator +=. The second parameter is persistnece landwscape. + * Operator +=. The second parameter is persistence landscape. **/ Persistence_landscape_on_grid operator += ( const Persistence_landscape_on_grid& rhs ) { @@ -422,7 +431,7 @@ public: } /** - * Operator -=. The second parameter is persistnece landwscape. + * Operator -=. The second parameter is persistence landscape. **/ Persistence_landscape_on_grid operator -= ( const Persistence_landscape_on_grid& rhs ) { @@ -458,7 +467,7 @@ public: bool dbg = true; if ( this->values_of_landscapes.size() != rhs.values_of_landscapes.size() ) { - if (dbg) std::cerr << "values_of_landscapes of incompatable sizes\n"; + if (dbg) std::cerr << "values_of_landscapes of incompatible sizes\n"; return false; } if ( !almost_equal( this->grid_min , rhs.grid_min ) ) @@ -546,28 +555,6 @@ public: std::pair< double , double > get_x_range( size_t level = 0 )const { return std::make_pair( this->grid_min , this->grid_max ); - //std::pair< double , double > result; - //if ( level < this->land.size() ) - //{ - // double dx = (this->grid_max - this->grid_min)/(double)this->values_of_landscapes.size(); - // size_t first_nonzero = 0; - // while ( (first_nonzero != this->values_of_landscapes.size()) && (this->values_of_landscapes[level][first_nonzero] == 0) )++first_nonzero; - // - // if ( first_nonzero == 0 ) - // { - // return std::make_pair( 0,0 );//this landscape is empty. - // } - // - // size_t last_nonzero = 0; - // while ( (last_nonzero != 0) && (this->values_of_landscapes[level][last_nonzero] == 0) )--last_nonzero; - // - // result = std::make_pair( this->grid_min +first_nonzero*dx , this->grid_max - last_nonzero*dx ); - //} - //else - //{ - // result = std::make_pair( 0,0 ); - //} - //return result; } /** @@ -577,16 +564,6 @@ public: std::pair< double , double > get_y_range( size_t level = 0 )const { return this->compute_minimum_maximum(); - //std::pair< double , double > result; - //if ( level < this->land.size() ) - //{ - // result = this->compute_minimum_maximum() - //} - //else - //{ - // result = std::make_pair( 0,0 ); - //} - //return result; } /** @@ -629,13 +606,11 @@ public: * Computations of \f$L^{\infty}\f$ distance between two landscapes. **/ friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape_on_grid& first, const Persistence_landscape_on_grid& second ); - //friend double compute_max_norm_distance_of_landscapes( const Persistence_landscape_on_grid& first, const Persistence_landscape_on_grid& second , unsigned& nrOfLand , double&x , double& y1, double& y2 ); - /** - * Function to compute absolute value of a PL function. The representation of persistence landscapes allow to store general PL-function. When computing distance betwen two landscapes, we compute difference between + * Function to compute absolute value of a PL function. The representation of persistence landscapes allow to store general PL-function. When computing distance between two landscapes, we compute difference between * them. In this case, a general PL-function with negative value can appear as a result. Then in order to compute distance, we need to take its absolute value. This is the purpose of this procedure. **/ void abs() @@ -655,7 +630,7 @@ public: size_t size()const{return this->number_of_nonzero_levels(); } /** - * Computate maximal value of lambda-level landscape. + * Compute maximal value of lambda-level landscape. **/ double find_max( unsigned lambda )const { @@ -742,14 +717,14 @@ public: } //now, to compute the inner product in this interval we need to compute the integral of (ax+b)(cx+d) = acx^2 + (ad+bc)x + bd in the interval from previous_x to current_x: - //The integal is ac/3*x^3 + (ac+bd)/2*x^2 + bd*x + //The integral is ac/3*x^3 + (ac+bd)/2*x^2 + bd*x double added_value = (a*c/3*current_x*current_x*current_x + (a*d+b*c)/2*current_x*current_x + b*d*current_x)- (a*c/3*previous_x*previous_x*previous_x + (a*d+b*c)/2*previous_x*previous_x + b*d*previous_x); if ( dbg ) { - std::cerr << "Value of the integral on the left end ie : " << previous_x << " is : " << a*c/3*previous_x*previous_x*previous_x + (a*d+b*c)/2*previous_x*previous_x + b*d*previous_x << std::endl; + std::cerr << "Value of the integral on the left end i.e. : " << previous_x << " is : " << a*c/3*previous_x*previous_x*previous_x + (a*d+b*c)/2*previous_x*previous_x + b*d*previous_x << std::endl; std::cerr << "Value of the integral on the right end i.e. : " << current_x << " is " << a*c/3*current_x*current_x*current_x + (a*d+b*c)/2*current_x*current_x + b*d*current_x << std::endl; } @@ -775,7 +750,7 @@ public: /** * Computations of \f$L^{p}\f$ distance between two landscapes on a grid. p is the parameter of the procedure. * FIXME: Note that, due to the grid representation, the method below may give non--accurate results in case when the landscape P and Q the difference of which we want to compute - * are interxsecting. This is a consequence of a general way they are computed. In the future, an integral of absolute value of a difference of P and Q will be given as a separated + * are intersecting. This is a consequence of a general way they are computed. In the future, an integral of absolute value of a difference of P and Q will be given as a separated * function to fix that inaccuracy. **/ friend double compute_distance_of_landscapes_on_grid( const Persistence_landscape_on_grid& first, const Persistence_landscape_on_grid& second , double p ) @@ -819,7 +794,7 @@ public: else { result = lan.compute_integral_of_landscape(); - if (dbg){std::cerr << "integral, wihtout power : " << result << std::endl;getchar();} + if (dbg){std::cerr << "integral, without power : " << result << std::endl;getchar();} } //(\int_{- \infty}^{+\infty}| first-second |^p)^(1/p) return pow( result , 1/(double)p ); @@ -830,45 +805,14 @@ public: return lan.compute_maximum(); } } - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //Functions that are needed for that class to implement the concept. /** * The number of projections to R is defined to the number of nonzero landscape functions. I-th projection is an integral of i-th landscape function over whole R. * This function is required by the Real_valued_topological_data concept. - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const { @@ -884,8 +828,6 @@ public: } - - /** * This function produce a vector of doubles based on a landscape. It is required in a concept Vectorized_topological_data */ @@ -909,16 +851,13 @@ public: } /** - * This function return the number of functions that allows vectorization of persistence laandscape. It is required in a concept Vectorized_topological_data. + * This function return the number of functions that allows vectorization of persistence landscape. It is required in a concept Vectorized_topological_data. **/ size_t number_of_vectorize_functions()const { return number_of_functions_for_vectorization; } - - - /** * A function to compute averaged persistence landscape on a grid, based on vector of persistence landscapes on grid. @@ -932,7 +871,7 @@ public: this->values_of_landscapes .clear(); this->grid_min = this->grid_max = 0; - //if there is nothing to averate, then the average is a zero landscape. + //if there is nothing to average, then the average is a zero landscape. if ( to_average.size() == 0 )return; //now we need to check if the grids in all objects of to_average are the same: @@ -968,7 +907,7 @@ public: std::cerr << "We are considering the point : " << grid_point << " of the grid. In this point, there are at most : " << maximal_size_of_vector << " nonzero landscape functions \n"; } - //and compute an arythmetic average: + //and compute an arithmetic average: for ( size_t land_no = 0 ; land_no != to_average.size() ; ++land_no ) { //summing: @@ -989,7 +928,7 @@ public: /** * A function to compute distance between persistence landscape on a grid. - * The parameter of this functionis a Persistence_landscape_on_grid. + * The parameter of this function is a Persistence_landscape_on_grid. * This function is required in Topological_data_with_distances concept. * For max norm distance, set power to std::numeric_limits::max() **/ @@ -1007,7 +946,7 @@ public: /** * A function to compute scalar product of persistence landscape on a grid. - * The parameter of this functionis a Persistence_landscape_on_grid. + * The parameter of this function is a Persistence_landscape_on_grid. * This function is required in Topological_data_with_scalar_product concept. **/ double compute_scalar_product( const Persistence_landscape_on_grid& second ) @@ -1016,28 +955,9 @@ public: } //end of implementation of functions needed for concepts. - - - - - - - - - - - - - - - - - - - /** - * A function that returns values of landsapes. It can be used for vizualization + * A function that returns values of landscapes. It can be used for visualization **/ std::vector< std::vector< double > > output_for_visualization()const { @@ -1046,7 +966,7 @@ public: /** * function used to create a gnuplot script for visualization of landscapes. Over here we need to specify which landscapes do we want to plot. - * In addition, the user may specify the range (min and max) where landscape is plot. The fefault values for min and max are std::numeric_limits::max(). If the procedure detect those + * In addition, the user may specify the range (min and max) where landscape is plot. The default values for min and max are std::numeric_limits::max(). If the procedure detect those * values, it will determine the range so that the whole landscape is supported there. If at least one min or max value is different from std::numeric_limits::max(), then the values * provided by the user will be used. **/ @@ -1123,7 +1043,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( grid_max_ <= grid_min_ ) { - throw "Wrong parameters of grid_min and grid_max given to the procedure. THe grid have negative, or zero size. The program will now terminate.\n"; + throw "Wrong parameters of grid_min and grid_max given to the procedure. The grid have negative, or zero size. The program will now terminate.\n"; } double dx = ( grid_max_ - grid_min_ )/(double)(number_of_points_); @@ -1174,7 +1094,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( this->values_of_landscapes[i].size() == number_of_levels-1 ) { //this->values_of_landscapes[i].size() == number_of_levels - //in this case we need to create the heep. + //in this case we need to create the heap. std::make_heap (this->values_of_landscapes[i].begin(),this->values_of_landscapes[i].end()); } } @@ -1212,7 +1132,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( this->values_of_landscapes[i].size() == number_of_levels-1 ) { //this->values_of_landscapes[i].size() == number_of_levels - //in this case we need to create the heep. + //in this case we need to create the heap. std::make_heap (this->values_of_landscapes[i].begin(),this->values_of_landscapes[i].end()); } } @@ -1225,7 +1145,7 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( dbg ) { - std::cerr << "AAdding landscape value (going down) for a point : " << i << " equal : " << landscape_value << std::endl; + std::cerr << "Adding landscape value (going down) for a point : " << i << " equal : " << landscape_value << std::endl; } } landscape_value -= dx; @@ -1235,11 +1155,10 @@ void Persistence_landscape_on_grid::set_up_values_of_landscapes( const std::vect if ( number_of_levels != std::numeric_limits< unsigned >::max() ) { //in this case, vectors are used as heaps. And, since we want to have the smallest element at the top of - //each heap, we store mminus distances. To get if right at the end, we need to multiply each value + //each heap, we store minus distances. To get if right at the end, we need to multiply each value //in the heap by -1 to get real vector of distances. for ( size_t pt = 0 ; pt != this->values_of_landscapes.size() ; ++pt ) { - //std::cerr << this->values_of_landscapes[pt].size() <values_of_landscapes[pt].size() ; ++j ) { this->values_of_landscapes[pt][j] *= -1; @@ -1362,7 +1281,6 @@ void Persistence_landscape_on_grid::load_landscape_from_file( const char* filena //read a line of a file and convert it to a vector. std::vector< double > vv; std::getline(in, line); - //std::cerr << "Reading line : " << line << std::endl;getchar(); std::istringstream stream(line); while (stream >> number) { @@ -1485,7 +1403,7 @@ Persistence_landscape_on_grid operation_on_pair_of_landscapes_on_grid ( const Pe result.grid_min = land1.grid_min; result.grid_max = land1.grid_max; - //now we perorm the operations: + //now we perform the operations: for ( size_t grid_point = 0 ; grid_point != land1.values_of_landscapes.size() ; ++grid_point ) { result.values_of_landscapes[grid_point] = std::vector< double >( std::max( land1.values_of_landscapes[grid_point].size() , land2.values_of_landscapes[grid_point].size() ) ); @@ -1555,9 +1473,7 @@ double compute_max_norm_distance_of_landscapes( const Persistence_landscape_on_g return result; } - - -}//namespace Gudhi_stat +}//namespace Persistence_representations }//namespace Gudhi -#endif +#endif // PERSISTENCE_LANDSCAPE_ON_GRID_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_vectors.h b/src/Persistence_representations/include/gudhi/Persistence_vectors.h index 7fde3413..616ec50f 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_vectors.h +++ b/src/Persistence_representations/include/gudhi/Persistence_vectors.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -21,8 +21,8 @@ */ -#ifndef Vector_distances_in_diagram_H -#define Vector_distances_in_diagram_H +#ifndef PERSISTENCE_VECTORS_H_ +#define PERSISTENCE_VECTORS_H_ #include #include @@ -42,32 +42,6 @@ namespace Gudhi namespace Persistence_representations { -/* -template -struct Euclidean_distance -{ - double operator() ( const std::pair< T,T >& f , const std::pair& s ) - { - return sqrt( (f.first-s.first)*(f.first-s.first) + (f.second-s.second)*(f.second-s.second) ); - } - double operator() ( const std::vector< T >& f , const std::vector < T >& s ) - { - if ( f.size() != s.size() ) - { - std::cerr << "Not compatible points dimensions in the procedure to compute Euclidean distance. The program will now terminate. \n"; - std::cout << f.size() << " , " << s.size() << std::endl; - throw "Not compatible points dimensions in the procedure to compute Euclidean distance. The program will now terminate. \n"; - } - double result = 0; - for ( size_t i = 0 ; i != f.size() ; ++i ) - { - result += ( f[i]-s[i] )*( f[i]-s[i] ); - } - return sqrt( result ); - } -}; -* */ - template struct Maximum_distance { @@ -79,16 +53,21 @@ struct Maximum_distance - /** -* This is an implementation of idea presented in the paper 'Stable Topological Signatures for Points on 3D Shapes' by -* M. Carriere, S. Y. Oudot and M. Ovsjanikov published in Computer Graphics Forum (proc. SGP 2015). -* The parameter of the class is the class that computes distance used to construct the vectors. The typical function is -* either Eucludean of maximum (Manhattan) distance. -* This class implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product -* -**/ - + * \class Vector_distances_in_diagram Vector_distances_in_diagram.h gudhi/Vector_distances_in_diagram.h + * \brief A class implementing persistence vectors. + * + * \ingroup Persistence_representations + * + * \details + * This is an implementation of idea presented in the paper Stable Topological Signatures for Points on 3D + * Shapes \cite Carriere_Oudot_Ovsjanikov_top_signatures_3d .
+ * The parameter of the class is the class that computes distance used to construct the vectors. The typical function + * is either Euclidean of maximum (Manhattan) distance. + * + * This class implements the following concepts: Vectorized_topological_data, Topological_data_with_distances, + * Real_valued_topological_data, Topological_data_with_averages, Topological_data_with_scalar_product + **/ template class Vector_distances_in_diagram { @@ -99,12 +78,12 @@ public: Vector_distances_in_diagram(){}; /** - * The constructor that takes as an input a multiset of persistence intervals (given as vector of birth-death pairs). The second parameter is the desiered length of the output vectors. + * The constructor that takes as an input a multiset of persistence intervals (given as vector of birth-death pairs). The second parameter is the desired length of the output vectors. **/ Vector_distances_in_diagram( const std::vector< std::pair< double , double > >& intervals , size_t where_to_cut ); /** - * The constructor taking as an input a file with birth-death pairs. The second parameter is the desiered length of the output vectors. + * The constructor taking as an input a file with birth-death pairs. The second parameter is the desired length of the output vectors. **/ Vector_distances_in_diagram( const char* filename , size_t where_to_cut , unsigned dimension = std::numeric_limits::max() ); @@ -155,7 +134,7 @@ public: void load_from_file( const char* filename ); /** - * Comparision operators: + * Comparison operators: **/ bool operator == ( const Vector_distances_in_diagram& second )const { @@ -172,14 +151,11 @@ public: return !( *this == second ); } - - - - //Implementations of functions for various concepts. + //Implementations of functions for various concepts. /** * Compute projection to real numbers of persistence vector. This function is required by the Real_valued_topological_data concept - * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it - * will be most likelly changed in the next versions. + * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when using it, keep in mind that it + * will be most likely changed in the next versions. **/ double project_to_R( int number_of_function )const; /** @@ -195,7 +171,7 @@ public: **/ std::vector vectorize( int number_of_function )const; /** - * This function return the number of functions that allows vectorization of a persisence vector. It is required in a concept Vectorized_topological_data. + * This function return the number of functions that allows vectorization of a persistence vector. It is required in a concept Vectorized_topological_data. **/ size_t number_of_vectorize_functions()const { @@ -220,22 +196,6 @@ public: //end of implementation of functions needed for concepts. - - - - - - - - - - - - - - - - /** * For visualization use output from vectorize and build histograms. **/ @@ -246,7 +206,7 @@ public: /** - * Create a gnuplot script to vizualize the data structure. + * Create a gnuplot script to visualize the data structure. **/ void plot( const char* filename )const { @@ -264,7 +224,7 @@ public: } out <sorted_vector_of_distances[0] , 0); } - //arythmetic operations: + //arithmetic operations: template < typename Operation_type > friend Vector_distances_in_diagram operation_on_pair_of_vectors( const Vector_distances_in_diagram& first , const Vector_distances_in_diagram& second , Operation_type opertion ) { @@ -511,7 +471,6 @@ void Vector_distances_in_diagram::compute_sorted_vector_of_distances_via_heap double value = f( this->intervals[i] , std::make_pair( 0.5*(this->intervals[i].first+this->intervals[i].second) , 0.5*(this->intervals[i].first+this->intervals[i].second) ) ); if ( -value < heap.front() ) { - //std::cerr << "Replacing : " << heap.front() << " with : " << -value <::distance( const Vector_distances_in_diagr } else { - //nax morm + // max norm if ( result < fabs( this->sorted_vector_of_distances[i] - second_.sorted_vector_of_distances[i] ) )result = fabs( this->sorted_vector_of_distances[i] - second_.sorted_vector_of_distances[i] ); } if ( dbg ) @@ -767,12 +726,8 @@ double Vector_distances_in_diagram::compute_scalar_product( const Vector_dist return result; } - - - - -}//namespace Gudhi_stat +}//namespace Persistence_representations }//namespace Gudhi -#endif // Vector_distances_in_diagram_H +#endif // PERSISTENCE_VECTORS_H_ diff --git a/src/Persistence_representations/include/gudhi/common_persistence_representations.h b/src/Persistence_representations/include/gudhi/common_persistence_representations.h index f223079a..f571ca4f 100644 --- a/src/Persistence_representations/include/gudhi/common_persistence_representations.h +++ b/src/Persistence_representations/include/gudhi/common_persistence_representations.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -20,15 +20,15 @@ * along with this program. If not, see . */ -#ifndef common_gudhi_stat_H -#define common_gudhi_stat_H +#ifndef COMMON_PERSISTENCE_REPRESENTATIONS_H_ +#define COMMON_PERSISTENCE_REPRESENTATIONS_H_ namespace Gudhi { namespace Persistence_representations { - //this file contain an implementation of some common procedures used in Gudhi_stat. + //this file contain an implementation of some common procedures used in Persistence_representations. //double epsi = std::numeric_limits::epsilon(); double epsi = 0.000005; @@ -38,8 +38,8 @@ double epsi = 0.000005; /** - * A procedure used to compare doubles. Typically gien two doubles A and B, comparing A == B is not good idea. In this case, we use the procedure almostEqual with the epsi defined at - * the top of the file. Setting up the epsi give the user a tolerance on what should be consider equal. + * A procedure used to compare doubles. Typically given two doubles A and B, comparing A == B is not good idea. In this case, we use the procedure almostEqual with the epsi defined at + * the top of the file. Setting up the epsi gives the user a tolerance on what should be consider equal. **/ inline bool almost_equal( double a , double b ) { @@ -78,7 +78,7 @@ std::pair compute_parameters_of_a_line( std::pair //landscapes /** - * This procedure given two points which lies on the opposide sides of x axis, compute x for which the line connecting those two points crosses x axis. + * This procedure given two points which lies on the opposite sides of x axis, compute x for which the line connecting those two points crosses x axis. **/ double find_zero_of_a_line_segment_between_those_two_points ( std::pair p1, std::pair p2 ) { @@ -86,7 +86,7 @@ double find_zero_of_a_line_segment_between_those_two_points ( std::pair 0 ) { std::ostringstream errMessage; - errMessage <<"In function find_zero_of_a_line_segment_between_those_two_points the agguments are: (" << p1.first << "," << p1.second << ") and (" << p2.first << "," << p2.second << "). There is no zero in line between those two points. Program terminated."; + errMessage <<"In function find_zero_of_a_line_segment_between_those_two_points the arguments are: (" << p1.first << "," << p1.second << ") and (" << p2.first << "," << p2.second << "). There is no zero in line between those two points. Program terminated."; std::string errMessageStr = errMessage.str(); const char* err = errMessageStr.c_str(); throw(err); @@ -94,8 +94,6 @@ double find_zero_of_a_line_segment_between_those_two_points ( std::pair f, std::pair s ) @@ -135,7 +133,7 @@ bool compare_points_sorting( std::pair f, std::pair p1, std::pair p2 , double x ) { @@ -148,7 +146,7 @@ double function_value ( std::pair p1, std::pair p2 -}//namespace Gudhi_stat -}//namespace Gudhi +} // namespace Persistence_representations +} // namespace Gudhi -#endif +#endif // COMMON_PERSISTENCE_REPRESENTATIONS_H_ diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h index 058c77a4..a4884314 100644 --- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h +++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2017 INRIA (France) * * 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 @@ -21,8 +21,8 @@ */ -#ifndef Read_Persitence_From_File_H -#define Read_Persitence_From_File_H +#ifndef READ_PERSISTENCE_FROM_FILE_H_ +#define READ_PERSISTENCE_FROM_FILE_H_ #include #include @@ -36,86 +36,6 @@ namespace Gudhi { namespace Persistence_representations { - - - -/** - * This procedure reads names of files which are stored in a file. -**/ -std::vector< std::string > readFileNames( const char* filenameWithFilenames ) -{ - bool dbg = false; - - std::ifstream in(filenameWithFilenames); - if ( !in.good() ) - { - std::cerr << "The file : " << filenameWithFilenames << " do not exist. The program will now terminate \n"; - throw "The file from which you are trying to read do not exist. The program will now terminate \n"; - } - - std::vector< std::string > result; - std::string line; - while (!in.eof()) - { - getline(in,line); - line.erase( std::remove_if( line.begin(), line.end(), ::isspace) , line.end() ); - - if (dbg){std::cerr << "line : " << line << std::endl;} - - if ( (line.length() == 0) || (line[0] == '#') ) - { - //in this case we have a file name. First we should remove all the white spaces. - if ( dbg ){std::cerr << "This is a line with comment, it will be ignored n";} - } - else - { - result.push_back( line ); - if (dbg){std::cerr << "Line after removing white spaces : " << line << std::endl;} - } - } - in.close(); - - return result; -}//readFileNames - - - -std::vector< std::vector< double > > read_numbers_from_file_line_by_line( const char* filename ) -{ - bool dbg = false; - std::ifstream in(filename); - if ( !in.good() ) - { - std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n"; - throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n"; - } - - std::vector< std::vector< double > > result; - double number; - - - std::string line; - while ( in.good() ) - { - std::getline(in,line); - std::stringstream ss(line); - - if ( dbg )std::cerr << "\n Reading line : " << line << std::endl; - - std::vector< double > this_line; - while ( ss.good() ) - { - ss >> number; - this_line.push_back( number ); - if ( dbg )std::cerr << number << " "; - } - if ( this_line.size() && in.good() ) result.push_back( this_line ); - } - in.close(); - - return result; -}//read_numbers_from_file_line_by_line - /** * Universal procedure to read files with persistence. It ignores the lines starting from # (treat them as comments). @@ -123,7 +43,7 @@ std::vector< std::vector< double > > read_numbers_from_file_line_by_line( const * that each other line in the file, which is not a comment, have the same number of numerical entries (2, 3 or 4). * If there are two numerical entries per line, then the function assume that they are birth/death coordinates. * If there are three numerical entries per line, then the function assume that they are: dimension and birth/death coordinates. - * If there are four numerical entries per line, then the function assume that they are: thc characteristic of a filed over which + * If there are four numerical entries per line, then the function assume that they are: the characteristic of a filed over which * persistence was computed, dimension and birth/death coordinates. * The 'inf' string can appear only as a last element of a line. * The procedure returns vector of persistence pairs. @@ -162,7 +82,7 @@ std::vector > read_persistence_intervals_in_one_dimensi if ( line_copy.find("inf") != std::string::npos ) { size_t np = line_copy.find("inf"); - //replace symbols 'inf' in line_copy with whilespaces: + //replace symbols 'inf' in line_copy with white spaces: line_copy[np] = ' '; line_copy[np+1] = ' '; line_copy[np+2] = ' '; @@ -194,7 +114,7 @@ std::vector > read_persistence_intervals_in_one_dimensi { std::cerr << "This line: " << line << " contains infinite interval. \n"; } - //first we substitute inf by whitespaces: + //first we substitute inf by white spaces: size_t np = line.find("inf"); line[np] = ' '; line[np+1] = ' '; @@ -288,13 +208,9 @@ std::vector > read_persistence_intervals_in_one_dimensi if ( dbg )std::cerr << "End of reading \n"; return barcode; -}//read_persistence_intervals_in_one_dimension_from_file +} // read_persistence_intervals_in_one_dimension_from_file -}//namespace Gudhi_stat -}//namespace Gudhi +} // namespace Persistence_representations +} // namespace Gudhi - - - -#endif - +#endif // READ_PERSISTENCE_FROM_FILE_H_ diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp index d3e6f322..27a7836f 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp @@ -34,8 +34,8 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { - std::cout << "This program compute dsitance of persistence heat maps stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the two heat maps. For L^infty distance choose p = -1. \n"; + std::cout << "This program compute distance of persistence heat maps stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat maps. For L^infty distance choose p = -1. \n"; std::cout << "The remaining parameters of this programs are names of files with persistence heat maps.\n"; if ( argc < 3 ) @@ -76,7 +76,7 @@ int main( int argc , char** argv ) distance[i] = v; } - //and now we can compute the distnaces: + //and now we can compute the distances: for ( size_t i = 0 ; i != filenames.size() ; ++i ) { for ( size_t j = i ; j != filenames.size() ; ++j ) @@ -106,6 +106,3 @@ int main( int argc , char** argv ) - - - diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp index aa887c9c..f755e9a6 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp @@ -36,10 +36,10 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the arcus tangens of their persistence.\n"; + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the arc tangential of their persistence.\n"; std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n"; std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl; diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp index aa13d786..732b3768 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp @@ -38,7 +38,7 @@ int main( int argc , char** argv ) std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the distance of a center from the diagonal.\n"; std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n"; std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl; @@ -62,8 +62,6 @@ int main( int argc , char** argv ) dimension = (unsigned)dim; } - //std::cout << "Parameters of the program : size_of_grid : " << size_of_grid << ", min_ : " << min_ << ", max_ : " << max_ << ", stdiv: " << stdiv << ", dim : " << dim << std::endl; - std::vector< const char* > filenames; for ( int i = 6 ; i != argc ; ++i ) { diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp index 46258329..58406d08 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp @@ -38,7 +38,7 @@ int main( int argc , char** argv ) std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are weighted by the square of distance of a center from the diagonal.\n"; std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n"; std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl; diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp index cac81495..90b50b0b 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -39,7 +39,7 @@ int main( int argc , char** argv ) std::cout << "This program creates persistence heat map of diagrams provided as an input.\n"; std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n"; std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp index 6aab42f7..6a07bf19 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp @@ -37,7 +37,7 @@ int main( int argc , char** argv ) std::cout << "This program creates PSSK of diagrams provided as an input.\n"; std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number of pixels \n"; std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl; diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp index 5a4776ff..7aedfbb1 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -34,7 +34,7 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { - std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape file \n"; + std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landscape file \n"; Persistence_heat_maps l; l.load_from_file( argv[1] ); l.plot( argv[1] ); diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp index 19e49bbb..fe4e709f 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -34,7 +34,7 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { - std::cout << "This program compute the bottleneck distance of persistence diarams stored in a files. \n"; + std::cout << "This program compute the bottleneck distance of persistence diagrams stored in a files. \n"; std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence landscapes. If your file contains "; std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence pairs you want to use. If your input files consist only "; std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp index b2cbac70..6e2598fa 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -71,7 +71,7 @@ int main( int argc , char** argv ) out << histogram[i] << std::endl; } out << std::endl; - std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; out.close(); return 0; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp index e20f85c0..5b36e0ce 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -89,12 +89,7 @@ int main( int argc , char** argv ) out << std::endl; out.close(); - //for ( size_t i = 0 ; i != pbns.size() ; ++i ) - //{ - // std::cout << pbns[i].first << " " << pbns[i].second << std::endl; - //} - - std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp index 85954cb2..ef969ed0 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -34,7 +34,7 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { std::cout << "This program compute distance of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the given landscapes. For L^infty distance choose p = -1. \n"; + std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the given landscapes. For L^infty distance choose p = -1. \n"; std::cout << "The remaining parameters of this programs are names of files with persistence landscapes."; if ( argc < 3 ) diff --git a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp index b79a689d..670f0364 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp @@ -33,7 +33,7 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { - std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape file \n"; + std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landscape file \n"; Persistence_landscape l; l.load_landscape_from_file( argv[1] ); diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp index 4ecbd548..3065b52c 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp @@ -33,8 +33,8 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { - std::cout << "This program compute dsitance of persistence landscapes on grid stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the the landscapes on grid. For L^infty distance choose p = -1. \n"; + std::cout << "This program compute distance of persistence landscapes on grid stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the landscapes on grid. For L^infty distance choose p = -1. \n"; std::cout << "The remaining parameters of this programs are names of files with persistence landscapes on grid.\n"; if ( argc < 3 ) @@ -106,5 +106,3 @@ int main( int argc , char** argv ) - - diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp index 700b2f1f..b4fa3046 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp @@ -33,7 +33,7 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { - std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape on grid file \n"; + std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created beforehand). Please call the code with the name of a landscape on grid file \n"; if ( argc == 1 ) { std::cout << "Wrong parameters of a program call, the program will now terminate \n"; diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp index 39e24cd7..5c0d3328 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -34,7 +34,7 @@ using namespace Gudhi::Persistence_representations; int main( int argc , char** argv ) { std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an interger p. The program compute l^p distance of the vectors. For l^infty distance choose p = -1. \n"; + std::cout << "The first parameter of a program is an integer p. The program compute l^p distance of the vectors. For l^infty distance choose p = -1. \n"; std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n"; if ( argc < 3 ) @@ -60,7 +60,6 @@ int main( int argc , char** argv ) vectors.reserve( filenames.size() ); for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) { - //cerr << filenames[file_no] << endl; Vector_distances_in_diagram< Euclidean_distance > l; l.load_from_file( filenames[file_no] ); vectors.push_back( l ); diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp index 634bcb13..d7a22e58 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -52,8 +52,7 @@ int main( int argc , char** argv ) for ( size_t i = 0 ; i != filenames.size() ; ++i ) { - std::cerr << "Creatign persistence vectors based on a file : " << filenames[i] << std::endl; - //std::vector< std::pair< double , double > > persistence_pairs = read_gudhi_persistence_file_in_one_dimension( filenames[i] , size_t dimension = 0 ) + std::cerr << "Creating persistence vectors based on a file : " << filenames[i] << std::endl; Vector_distances_in_diagram< Euclidean_distance > l( filenames[i] , dimension ); std::stringstream ss; ss << filenames[i] << ".vect"; diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index 8b7cf0e2..3172f6b1 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -47,7 +47,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) - set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Gudhi_stat;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex") + set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistence_representations;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex") set(GUDHI_DIRECTORIES "doc;example;concept;utilities") set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches") diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index d1cb691c..6986a6b5 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -212,19 +212,20 @@ - \subsection Gudhi_stat_sublibrary Gudhi statistical sublibrary - \image html "average_landscape.png" "Gudhi statistical sublibrary" + \subsection PersistenceRepresentationsToolbox Persistence representations + \image html "average_landscape.png" "Persistence representations" diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index f6e2ab5a..f683136b 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -48,6 +48,11 @@ class Euclidean_distance { } return std::sqrt(dist); } + template< typename T > + T operator() ( const std::pair< T,T >& f , const std::pair< T,T >& s ) + { + return sqrt( (f.first-s.first)*(f.first-s.first) + (f.second-s.second)*(f.second-s.second) ); + } }; } // namespace Gudhi -- cgit v1.2.3
Author: Pawel Dlotko
- Introduced in: GUDHI 2.0.0
+ Introduced in: GUDHI 2.1.0
Copyright: GPL v3
 - This is a statistical library for gudhi. It contain implementation of various representations of persistence diagrams; diagrams themselves, persistence landscapes (rigorous and grid version), - persistence heath maps, vectors and others. It implements basic functionalities which are neccessary to use persistence in statistics and machine learning. - User manual: \ref Gudhi_stat + It contain implementation of various representations of persistence diagrams; diagrams themselves, persistence + landscapes (rigorous and grid version), persistence heath maps, vectors and others. It implements basic + functionalities which are neccessary to use persistence in statistics and machine learning.
+ User manual: \ref Persistence_representations