From ca6b3d72f2114cdd2d0899fd44dba19303dd3bb2 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 28 Sep 2016 11:15:34 +0000 Subject: Add rips complex module and first modification step git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1577 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fc949570c6cffa4756f84a15c41fadc8c45b2af2 --- src/Rips_complex/doc/Intro_rips_complex.h | 104 ++++++++++++++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 src/Rips_complex/doc/Intro_rips_complex.h (limited to 'src/Rips_complex/doc/Intro_rips_complex.h') diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h new file mode 100644 index 00000000..85108168 --- /dev/null +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -0,0 +1,104 @@ +/* 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): Clément Maria & Vincent Rouvreau + * + * Copyright (C) 2015 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#ifndef DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_ +#define DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_ + +namespace Gudhi { + +namespace rips_complex { + +/** \defgroup rips_complex Rips complex + * + * \author Clément Maria & Vincent Rouvreau + * + * @{ + * + * \section definition Definition + * + * Rips_complex + * (Wikipedia) is a + * simplicial complex + * constructed from a one skeleton graph. + * + * The filtration value of each edge is computed from a user-given distance function. + * + * All edges that have a filtration value strictly greater than a given threshold value are not inserted into + * the complex. + * + * When creating a simplicial complex from this one skeleton graph, rips inserts the one skeleton graph into the data + * structure, and then expands the simplicial when required. + * + * \image html "rips_complex_representation.png" "Rips-complex one skeleton graph representation" + * + * On this example, as edges (4,5), (4,6) and (5,6) are in the complex, simplex (4,5,6) is added with the filtration + * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$. + * And so on for simplex (0,1,2,3). + * + * \section ripspointsexample Example from points + * + * This example builds the one skeleton graph from the given points, threshold value, and distance function. + * Then it creates a `Simplex_tree` with it. + * + * Then, it is asked to display information about the simplicial complex. + * + * \include Rips_complex/example_rips_complex_from_points.cpp + * + * When launching: + * + * \code $> ./ripspoints + * \endcode + * + * the program output is: + * + * \include Rips_complex/rips_points_for_doc_12_2.txt + * + * \section offexample Example from OFF file + * + * This example builds the one skeleton graph from the given points in an OFF file, threshold value, and distance + * function. + * Then it creates a `Simplex_tree` with it. + * + * + * Then, it is asked to display information about the rips complex. + * + * \include Rips_complex/example_rips_complex_from_off_file.cpp + * + * When launching: + * + * \code $> ./ripsoffreader ../../data/points/alphacomplexdoc.off 12.0 3 + * \endcode + * + * the program output is: + * + * \include Rips_complex/rips_points_for_doc_12_3.txt + * + * \copyright GNU General Public License v3. + * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + */ +/** @} */ // end defgroup rips_complex + +} // namespace rips_complex + +} // namespace Gudhi + +#endif // DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_ -- cgit v1.2.3 From 1c1c3073e0612ee401a941008a6b13438b3429e2 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 29 Sep 2016 12:34:19 +0000 Subject: Fix doxygen Add tests git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1589 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3b03e969f43f4f41c7bca1b2de96a71688475742 --- CMakeLists.txt | 1 + src/CMakeLists.txt | 1 + src/Doxyfile | 3 +- src/Rips_complex/doc/Intro_rips_complex.h | 17 +- src/Rips_complex/example/CMakeLists.txt | 21 +- .../example_one_skeleton_rips_from_points.cpp | 64 ++++++ .../example/example_rips_complex_from_points.cpp | 69 ------ .../example/full_skeleton_rips_points_for_doc.txt | 26 +++ .../example/one_skeleton_rips_points_for_doc.txt | 20 ++ .../example/rips_points_for_doc_12_1.txt | 20 -- .../example/rips_points_for_doc_12_3.txt | 26 --- src/Rips_complex/test/CMakeLists.txt | 24 +++ src/Rips_complex/test/README | 12 ++ src/Rips_complex/test/test_rips_complex.cpp | 231 +++++++++++++++++++++ src/cmake/modules/GUDHI_user_version_target.txt | 2 +- src/common/doc/main_page.h | 23 ++ 16 files changed, 431 insertions(+), 129 deletions(-) create mode 100644 src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp delete mode 100644 src/Rips_complex/example/example_rips_complex_from_points.cpp create mode 100644 src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt create mode 100644 src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt delete mode 100644 src/Rips_complex/example/rips_points_for_doc_12_1.txt delete mode 100644 src/Rips_complex/example/rips_points_for_doc_12_3.txt create mode 100644 src/Rips_complex/test/CMakeLists.txt create mode 100644 src/Rips_complex/test/README create mode 100644 src/Rips_complex/test/test_rips_complex.cpp (limited to 'src/Rips_complex/doc/Intro_rips_complex.h') diff --git a/CMakeLists.txt b/CMakeLists.txt index 89e130f4..972df204 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -144,6 +144,7 @@ else() add_subdirectory(src/Alpha_complex/example) add_subdirectory(src/Alpha_complex/test) add_subdirectory(src/Rips_complex/example) + add_subdirectory(src/Rips_complex/test) # data points generator add_subdirectory(data/points/generator) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index c7744c49..7973ae39 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -108,6 +108,7 @@ else() add_subdirectory(example/Bitmap_cubical_complex) add_subdirectory(example/Witness_complex) add_subdirectory(example/Alpha_complex) + add_subdirectory(example/Rips_complex) # data points generator add_subdirectory(data/points/generator) diff --git a/src/Doxyfile b/src/Doxyfile index dd9a33fb..40d07049 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -845,7 +845,8 @@ IMAGE_PATH = doc/Skeleton_blocker/ \ doc/Simplex_tree/ \ doc/Persistent_cohomology/ \ doc/Witness_complex/ \ - doc/Bitmap_cubical_complex/ + doc/Bitmap_cubical_complex/ \ + doc/Rips_complex/ # 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 diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 85108168..bd9f5fad 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -29,11 +29,11 @@ namespace rips_complex { /** \defgroup rips_complex Rips complex * - * \author Clément Maria & Vincent Rouvreau + * \author Clément Maria and Vincent Rouvreau * * @{ * - * \section definition Definition + * \section ripsdefinition Definition * * Rips_complex * (Wikipedia) is a @@ -61,18 +61,19 @@ namespace rips_complex { * * Then, it is asked to display information about the simplicial complex. * - * \include Rips_complex/example_rips_complex_from_points.cpp + * \include Rips_complex/example_one_skeleton_rips_from_points.cpp * - * When launching: + * When launching (rips maximal distance between 2 points is 12.0, is expanded until dimension 1 - one skeleton graph + * with other words): * - * \code $> ./ripspoints + * \code $> ./oneskeletonripspoints 12.0 * \endcode * * the program output is: * - * \include Rips_complex/rips_points_for_doc_12_2.txt + * \include Rips_complex/one_skeleton_rips_points_for_doc.txt * - * \section offexample Example from OFF file + * \section ripsoffexample Example from OFF file * * This example builds the one skeleton graph from the given points in an OFF file, threshold value, and distance * function. @@ -90,7 +91,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/rips_points_for_doc_12_3.txt + * \include Rips_complex/full_skeleton_rips_points_for_doc.txt * * \copyright GNU General Public License v3. * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index f8dcf94d..3962b15e 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -3,12 +3,25 @@ project(Rips_complex_examples) add_executable ( ripsoffreader example_rips_complex_from_off_file.cpp ) target_link_libraries(ripsoffreader ${Boost_SYSTEM_LIBRARY}) + +add_executable ( oneskeletonripspoints example_one_skeleton_rips_from_points.cpp ) +target_link_libraries(oneskeletonripspoints ${Boost_SYSTEM_LIBRARY}) + if (TBB_FOUND) target_link_libraries(ripsoffreader ${TBB_LIBRARIES}) + target_link_libraries(oneskeletonripspoints ${TBB_LIBRARIES}) endif() -add_executable ( ripspoints example_rips_complex_from_points.cpp ) -target_link_libraries(ripspoints ${Boost_SYSTEM_LIBRARY}) -if (TBB_FOUND) - target_link_libraries(ripspoints ${TBB_LIBRARIES}) +add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 12.0) +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt) +add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt) +if (DIFF_PATH) + # Do not forget to copy test results files in current binary dir + file(COPY "one_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "full_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_points_for_doc.txt) + add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_points_for_doc.txt) endif() diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp new file mode 100644 index 00000000..db41b425 --- /dev/null +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp @@ -0,0 +1,64 @@ +#include +// to construct Rips_complex from a OFF file of points +#include +// to construct a simplex_tree from rips complex +#include +#include + +#include +#include +#include // for std::numeric_limits + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " threshold\n"; + std::cerr << " i.e.: " << progName << " 12.0\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if (argc != 2) usage(argc, argv[0]); + + double threshold = atof(argv[1]); + + // Type definitions + using Point = std::vector; + using Simplex_tree = Gudhi::Simplex_tree<>; + using Rips_complex = Gudhi::rips_complex::Rips_complex; + + std::vector points; + points.push_back({1.0, 1.0}); + points.push_back({7.0, 0.0}); + points.push_back({4.0, 6.0}); + points.push_back({9.0, 6.0}); + points.push_back({0.0, 14.0}); + points.push_back({2.0, 19.0}); + points.push_back({9.0, 17.0}); + + // ---------------------------------------------------------------------------- + // Init of a rips complex from points + // ---------------------------------------------------------------------------- + Rips_complex rips_complex_from_file(points, threshold, euclidean_distance); + + Simplex_tree simplex; + if (rips_complex_from_file.create_complex(simplex, 1)) { + // ---------------------------------------------------------------------------- + // Display information about the one skeleton rips complex + // ---------------------------------------------------------------------------- + std::cout << "Rips complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + } + return 0; +} diff --git a/src/Rips_complex/example/example_rips_complex_from_points.cpp b/src/Rips_complex/example/example_rips_complex_from_points.cpp deleted file mode 100644 index c241d137..00000000 --- a/src/Rips_complex/example/example_rips_complex_from_points.cpp +++ /dev/null @@ -1,69 +0,0 @@ -#include -// to construct Rips_complex from a OFF file of points -#include -// to construct a simplex_tree from rips complex -#include -#include - -#include -#include -#include // for std::numeric_limits - -void usage(int nbArgs, char * const progName) { - std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " dim_max [threshold]\n"; - std::cerr << " i.e.: " << progName << " 3 12.0\n"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if ((argc != 2) && (argc != 3)) usage(argc, argv[0]); - - double threshold = std::numeric_limits::infinity(); - int dim_max = atoi(argv[1]); - - if (argc == 3) { - threshold = atof(argv[2]); - } - - // Type definitions - using Point = std::vector; - using Simplex_tree = Gudhi::Simplex_tree<>; - using Rips_complex = Gudhi::rips_complex::Rips_complex; - - std::vector points; - points.push_back({1.0, 1.0}); - points.push_back({7.0, 0.0}); - points.push_back({4.0, 6.0}); - points.push_back({9.0, 6.0}); - points.push_back({0.0, 14.0}); - points.push_back({2.0, 19.0}); - points.push_back({9.0, 17.0}); - - // ---------------------------------------------------------------------------- - // Init of a rips complex from an OFF file - // ---------------------------------------------------------------------------- - Rips_complex rips_complex_from_file(points, threshold, euclidean_distance); - - Simplex_tree simplex; - if (rips_complex_from_file.create_complex(simplex, dim_max)) { - // ---------------------------------------------------------------------------- - // Display information about the rips complex - // ---------------------------------------------------------------------------- - std::cout << "Rips complex is of dimension " << simplex.dimension() << - " - " << simplex.num_simplices() << " simplices - " << - simplex.num_vertices() << " vertices." << std::endl; - - std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << - std::endl; - for (auto f_simplex : simplex.filtration_simplex_range()) { - std::cout << " ( "; - for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; - } - std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; - std::cout << std::endl; - } - } - return 0; -} diff --git a/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt new file mode 100644 index 00000000..319931e0 --- /dev/null +++ b/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt @@ -0,0 +1,26 @@ +Rips complex is of dimension 3 - 24 simplices - 7 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [5] + ( 5 4 ) -> [5.38516] + ( 2 0 ) -> [5.83095] + ( 1 0 ) -> [6.08276] + ( 3 1 ) -> [6.32456] + ( 2 1 ) -> [6.7082] + ( 2 1 0 ) -> [6.7082] + ( 3 2 1 ) -> [6.7082] + ( 6 5 ) -> [7.28011] + ( 4 2 ) -> [8.94427] + ( 3 0 ) -> [9.43398] + ( 3 1 0 ) -> [9.43398] + ( 3 2 0 ) -> [9.43398] + ( 3 2 1 0 ) -> [9.43398] + ( 6 4 ) -> [9.48683] + ( 6 5 4 ) -> [9.48683] + ( 6 3 ) -> [11] diff --git a/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt new file mode 100644 index 00000000..b0e25cc5 --- /dev/null +++ b/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt @@ -0,0 +1,20 @@ +Rips complex is of dimension 1 - 18 simplices - 7 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [5] + ( 5 4 ) -> [5.38516] + ( 2 0 ) -> [5.83095] + ( 1 0 ) -> [6.08276] + ( 3 1 ) -> [6.32456] + ( 2 1 ) -> [6.7082] + ( 6 5 ) -> [7.28011] + ( 4 2 ) -> [8.94427] + ( 3 0 ) -> [9.43398] + ( 6 4 ) -> [9.48683] + ( 6 3 ) -> [11] diff --git a/src/Rips_complex/example/rips_points_for_doc_12_1.txt b/src/Rips_complex/example/rips_points_for_doc_12_1.txt deleted file mode 100644 index b0e25cc5..00000000 --- a/src/Rips_complex/example/rips_points_for_doc_12_1.txt +++ /dev/null @@ -1,20 +0,0 @@ -Rips complex is of dimension 1 - 18 simplices - 7 vertices. -Iterator on rips complex simplices in the filtration order, with [filtration value]: - ( 0 ) -> [0] - ( 1 ) -> [0] - ( 2 ) -> [0] - ( 3 ) -> [0] - ( 4 ) -> [0] - ( 5 ) -> [0] - ( 6 ) -> [0] - ( 3 2 ) -> [5] - ( 5 4 ) -> [5.38516] - ( 2 0 ) -> [5.83095] - ( 1 0 ) -> [6.08276] - ( 3 1 ) -> [6.32456] - ( 2 1 ) -> [6.7082] - ( 6 5 ) -> [7.28011] - ( 4 2 ) -> [8.94427] - ( 3 0 ) -> [9.43398] - ( 6 4 ) -> [9.48683] - ( 6 3 ) -> [11] diff --git a/src/Rips_complex/example/rips_points_for_doc_12_3.txt b/src/Rips_complex/example/rips_points_for_doc_12_3.txt deleted file mode 100644 index 319931e0..00000000 --- a/src/Rips_complex/example/rips_points_for_doc_12_3.txt +++ /dev/null @@ -1,26 +0,0 @@ -Rips complex is of dimension 3 - 24 simplices - 7 vertices. -Iterator on rips complex simplices in the filtration order, with [filtration value]: - ( 0 ) -> [0] - ( 1 ) -> [0] - ( 2 ) -> [0] - ( 3 ) -> [0] - ( 4 ) -> [0] - ( 5 ) -> [0] - ( 6 ) -> [0] - ( 3 2 ) -> [5] - ( 5 4 ) -> [5.38516] - ( 2 0 ) -> [5.83095] - ( 1 0 ) -> [6.08276] - ( 3 1 ) -> [6.32456] - ( 2 1 ) -> [6.7082] - ( 2 1 0 ) -> [6.7082] - ( 3 2 1 ) -> [6.7082] - ( 6 5 ) -> [7.28011] - ( 4 2 ) -> [8.94427] - ( 3 0 ) -> [9.43398] - ( 3 1 0 ) -> [9.43398] - ( 3 2 0 ) -> [9.43398] - ( 3 2 1 0 ) -> [9.43398] - ( 6 4 ) -> [9.48683] - ( 6 5 4 ) -> [9.48683] - ( 6 3 ) -> [11] diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt new file mode 100644 index 00000000..3972e9fc --- /dev/null +++ b/src/Rips_complex/test/CMakeLists.txt @@ -0,0 +1,24 @@ +cmake_minimum_required(VERSION 2.6) +project(Rips_complex_tests) + +if (GCOVR_PATH) + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") +endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") +endif() + +add_executable ( rips_complex_UT test_rips_complex.cpp ) +target_link_libraries(rips_complex_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(rips_complex_UT ${TBB_LIBRARIES}) +endif() + +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + +add_test(rips_complex_UT ${CMAKE_CURRENT_BINARY_DIR}/rips_complex_UT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/rips_complex_UT.xml --log_level=test_suite --report_level=no) diff --git a/src/Rips_complex/test/README b/src/Rips_complex/test/README new file mode 100644 index 00000000..28236b52 --- /dev/null +++ b/src/Rips_complex/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./rips_complex_UT --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp new file mode 100644 index 00000000..5f129160 --- /dev/null +++ b/src/Rips_complex/test/test_rips_complex.cpp @@ -0,0 +1,231 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2016 INRIA 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 . + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "rips_complex" +#include + +#include // float comparison +#include +#include +#include +#include // std::max + +#include +// to construct Rips_complex from a OFF file of points +#include +// to construct a simplex_tree from rips complex +#include +#include + +// Type definitions +using Point = std::vector; +using Simplex_tree = Gudhi::Simplex_tree<>; +using Rips_complex = Gudhi::rips_complex::Rips_complex; + +bool are_almost_the_same(float a, float b) { + return std::fabs(a - b) < std::numeric_limits::epsilon(); +} + +BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) { + // ---------------------------------------------------------------------------- + // + // Init of a rips complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("alphacomplexdoc.off"); + double rips_threshold = 12.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - rips threshold=" << + rips_threshold << "==========" << std::endl; + + Gudhi::Points_off_reader off_reader(off_file_name); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, euclidean_distance); + + const int DIMENSION_1 = 1; + Simplex_tree st; + BOOST_CHECK(rips_complex_from_file.create_complex(st, DIMENSION_1)); + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION_1); + + const int NUMBER_OF_VERTICES = 7; + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 18); + + // Check filtration values of vertices is 0.0 + for (auto f_simplex : st.skeleton_simplex_range(0)) { + BOOST_CHECK(st.filtration(f_simplex) == 0.0); + } + + // Check filtration values of edges + for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) { + if (DIMENSION_1 == st.dimension(f_simplex)) { + std::vector vp; + std::cout << "vertex = ("; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << ","; + vp.push_back(off_reader.get_point_cloud().at(vertex)); + } + std::cout << ") - distance =" << euclidean_distance(vp.at(0), vp.at(1)) << + " - filtration =" << st.filtration(f_simplex) << std::endl; + BOOST_CHECK(vp.size() == 2); + BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), euclidean_distance(vp.at(0), vp.at(1)))); + } + } + + const int DIMENSION_2 = 2; + Simplex_tree st2; + BOOST_CHECK(rips_complex_from_file.create_complex(st2, DIMENSION_2)); + std::cout << "st2.dimension()=" << st2.dimension() << std::endl; + BOOST_CHECK(st2.dimension() == DIMENSION_2); + + std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl; + BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl; + BOOST_CHECK(st2.num_simplices() == 23); + + Simplex_tree::Filtration_value f01 = st2.filtration(st2.find({0, 1})); + Simplex_tree::Filtration_value f02 = st2.filtration(st2.find({0, 2})); + Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2})); + Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2})); + std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl; + BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12)))); + + Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5})); + Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6})); + Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6})); + Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6})); + std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl; + BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46)))); + + const int DIMENSION_3 = 3; + Simplex_tree st3; + BOOST_CHECK(rips_complex_from_file.create_complex(st3, DIMENSION_3)); + std::cout << "st3.dimension()=" << st3.dimension() << std::endl; + BOOST_CHECK(st3.dimension() == DIMENSION_3); + + std::cout << "st3.num_vertices()=" << st3.num_vertices() << std::endl; + BOOST_CHECK(st3.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st3.num_simplices()=" << st3.num_simplices() << std::endl; + BOOST_CHECK(st3.num_simplices() == 24); + + Simplex_tree::Filtration_value f123 = st3.filtration(st3.find({1, 2, 3})); + Simplex_tree::Filtration_value f013 = st3.filtration(st3.find({0, 1, 3})); + Simplex_tree::Filtration_value f023 = st3.filtration(st3.find({0, 2, 3})); + Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3})); + std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 << + " - f023= " << f023 << std::endl; + BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023))))); + +} + +using Vector_of_points = std::vector; + +bool is_point_in_list(Vector_of_points points_list, Point point) { + for (auto& point_in_list : points_list) { + if (point_in_list == point) { + return true; // point found + } + } + return false; // point not found +} + +/* Compute the square value of Euclidean distance between two Points given by a range of coordinates. + * The points are assumed to have the same dimension. */ +template< typename Point > +double custom_square_euclidean_distance(const Point &p1,const Point &p2) { + double dist = 0.; + auto it1 = p1.begin(); + auto it2 = p2.begin(); + for (; it1 != p1.end(); ++it1, ++it2) { + double tmp = *it1 - *it2; + dist += tmp*tmp; + } + return dist; +} + +BOOST_AUTO_TEST_CASE(Rips_complex_from_points) { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points points; + std::vector coords = { 0.0, 0.0, 0.0, 1.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 0.0, 0.0, 1.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 0.0, 1.0, 0.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 1.0, 0.0, 0.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + + // ---------------------------------------------------------------------------- + // Init of a rips complex from the list of points + // ---------------------------------------------------------------------------- + Rips_complex rips_complex_from_points(points, 2.0, custom_square_euclidean_distance); + + std::cout << "========== Rips_complex_from_points ==========" << std::endl; + Simplex_tree st; + const int DIMENSION = 3; + BOOST_CHECK(rips_complex_from_points.create_complex(st, DIMENSION)); + + // Another way to check num_simplices + std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << std::endl; + int num_simplices = 0; + for (auto f_simplex : st.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << st.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 15); + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 15); + + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION); + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == 4); + + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl; + switch (st.dimension(f_simplex)) { + case 0: + BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 0.0)); + break; + case 1: + case 2: + case 3: + BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 2.0)); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } +} diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index 805f0a83..78d3092f 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -48,7 +48,7 @@ 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;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex") + set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Contraction;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Witness_complex") foreach(GUDHI_MODULE ${GUDHI_MODULES}) # doc files diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 21cf6925..a38dbcdf 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -55,6 +55,23 @@ User manual: \ref cubical_complex - Reference manual: Gudhi::cubical_complex::Bitmap_cubical_complex + \subsection RipsComplexDataStructure Rips complex + \image html "rips_complex_representation.png" "Rips complex representation" + + + + + +
+ Author: Clément Maria
+ Introduced in: GUDHI 1.4.0
+ Copyright: GPL v3
+ 		+ Rips_complex is a simplicial complex constructed from a one skeleton graph.
+ The filtration value of each edge is computed from a user-given distance function and is inserted until a + user-given threshold value.
+ User manual: \ref rips_complex - Reference manual: Gudhi::rips_complex::Rips_complex +
\subsection SimplexTreeDataStructure Simplex tree \image html "Simplex_tree_representation.png" "Simplex tree representation" @@ -288,6 +305,10 @@ make \endverbatim * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp + * \li + * Rips_complex/example_one_skeleton_rips_from_points.cpp + * \li + * Rips_complex/example_rips_complex_from_off_file.cpp * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: @@ -330,6 +351,8 @@ make \endverbatim * @example Persistent_cohomology/rips_multifield_persistence.cpp * @example Persistent_cohomology/rips_persistence.cpp * @example Persistent_cohomology/custom_persistence_sort.cpp + * @example Rips_complex/example_one_skeleton_rips_from_points.cpp + * @example Rips_complex/example_rips_complex_from_off_file.cpp * @example Simplex_tree/mini_simplex_tree.cpp * @example Simplex_tree/simple_simplex_tree.cpp * @example Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp -- cgit v1.2.3 From ede6f875e8340fb72d114ad9db3b54862566594f Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 17 Nov 2016 09:52:03 +0000 Subject: Modify examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1757 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4b6f26947ad16f440ea4d4b7cb5e145a58f28dcb --- .../example/alpha_complex_3d_persistence.cpp | 2 +- .../example/alpha_complex_persistence.cpp | 7 +- .../periodic_alpha_complex_3d_persistence.cpp | 2 +- .../persistence_from_simple_simplex_tree.cpp | 4 +- .../example/rips_multifield_persistence.cpp | 2 +- .../example/rips_persistence.cpp | 2 +- .../rips_persistence_via_boundary_matrix.cpp | 3 +- src/Rips_complex/doc/Intro_rips_complex.h | 6 +- src/Rips_complex/include/gudhi/Rips_complex.h | 2 +- src/Simplex_tree/example/simple_simplex_tree.cpp | 2 +- .../example/simplex_tree_from_cliques_of_graph.cpp | 2 +- .../example/witness_complex_from_file.cpp | 6 +- .../example/witness_complex_sphere.cpp | 2 +- .../gudhi/Construct_closest_landmark_table.h | 2 +- .../gudhi/Landmark_choice_by_furthest_point.h | 105 --------------------- .../gudhi/Landmark_choice_by_random_point.h | 96 ------------------- .../include/gudhi/Witness_complex.h | 1 - .../test/simple_witness_complex.cpp | 2 +- .../test/witness_complex_points.cpp | 2 +- .../include/gudhi/graph_simplicial_complex.h | 57 ----------- 20 files changed, 24 insertions(+), 283 deletions(-) delete mode 100644 src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h delete mode 100644 src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h (limited to 'src/Rips_complex/doc/Intro_rips_complex.h') diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index f7e8f800..978dc942 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp index bca4b66c..9e84e91f 100644 --- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp @@ -11,7 +11,8 @@ #include #include // for numeric_limits -using Filtration_value = double; +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; void program_options(int argc, char * argv[] , std::string & off_file_points @@ -36,7 +37,7 @@ int main(int argc, char **argv) { using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; Gudhi::alpha_complex::Alpha_complex alpha_complex_from_file(off_file_points); - Gudhi::Simplex_tree<> simplex; + Simplex_tree simplex; if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { // ---------------------------------------------------------------------------- // Display information about the alpha complex @@ -50,7 +51,7 @@ int main(int argc, char **argv) { std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>, + Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree, Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex); // initializes the coefficient field for homology pcoh.init_coefficients(coeff_field_characteristic); diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp index 5184ef52..6c03afce 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp index 817aac4d..7ca9410a 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -30,7 +30,7 @@ #include // Types definition -using Simplex_tree = Gudhi::Simplex_tree; +using Simplex_tree = Gudhi::Simplex_tree<>; using Filtration_value = Simplex_tree::Filtration_value; using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp index 8e5c83a1..6db85d16 100644 --- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp index b74d0094..709c2eab 100644 --- a/src/Persistent_cohomology/example/rips_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp index ee6577f4..b7daf6ae 100644 --- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp @@ -4,8 +4,7 @@ * * Author(s): Clément Maria, Marc Glisse * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France), - * 2015 INRIA Saclay Île de France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index bd9f5fad..a71946b5 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clément Maria & Vincent Rouvreau + * Author(s): Clément Maria, Vincent Rouvreau * - * Copyright (C) 2015 INRIA + * Copyright (C) 2016 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -29,7 +29,7 @@ namespace rips_complex { /** \defgroup rips_complex Rips complex * - * \author Clément Maria and Vincent Rouvreau + * \author Clément Maria, Vincent Rouvreau * * @{ * diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h index aee6c969..da755b7c 100644 --- a/src/Rips_complex/include/gudhi/Rips_complex.h +++ b/src/Rips_complex/include/gudhi/Rips_complex.h @@ -2,7 +2,7 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clément Maria & Vincent Rouvreau + * Author(s): Clément Maria, Vincent Rouvreau * * Copyright (C) 2016 INRIA * diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index bf6dc470..60f9a35e 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 * * 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/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp index 8d729c56..13c700c6 100644 --- a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp +++ b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp index 59dd28e0..5dd18d0a 100644 --- a/src/Witness_complex/example/witness_complex_from_file.cpp +++ b/src/Witness_complex/example/witness_complex_from_file.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -36,9 +36,9 @@ #include #include -typedef std::vector< int > typeVectorVertex; -typedef std::vector< std::vector > Point_Vector; typedef Gudhi::Simplex_tree<> Simplex_tree; +typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; +typedef std::vector< std::vector > Point_Vector; int main(int argc, char * const argv[]) { if (argc != 3) { diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp index 7ab86cc0..60e02225 100644 --- a/src/Witness_complex/example/witness_complex_sphere.cpp +++ b/src/Witness_complex/example/witness_complex_sphere.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h b/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h index ec93ae71..1ae2e393 100644 --- a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h +++ b/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h deleted file mode 100644 index bcb89e00..00000000 --- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h +++ /dev/null @@ -1,105 +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): Siargey Kachanovich - * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (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 LANDMARK_CHOICE_BY_FURTHEST_POINT_H_ -#define LANDMARK_CHOICE_BY_FURTHEST_POINT_H_ - -#include - -#include // for numeric_limits<> -#include -#include // for sort -#include - -namespace Gudhi { - -namespace witness_complex { - - typedef std::vector typeVectorVertex; - - /** - * \ingroup witness_complex - * \brief Landmark choice strategy by iteratively adding the furthest witness from the - * current landmark set as the new landmark. - * \details It chooses nbL landmarks from a random access range `points` and - * writes {witness}*{closest landmarks} matrix in `knn`. - * - * The type KNearestNeighbors can be seen as - * Witness_range>, where - * Witness_range and Closest_landmark_range are random access ranges - * - */ - - template - void landmark_choice_by_furthest_point(Point_random_access_range const &points, - int nbL, - KNearestNeighbours &knn) { - int nb_points = boost::size(points); - assert(nb_points >= nbL); - // distance matrix witness x landmarks - std::vector> wit_land_dist(nb_points, std::vector()); - // landmark list - typeVectorVertex chosen_landmarks; - - knn = KNearestNeighbours(nb_points, std::vector()); - int current_number_of_landmarks = 0; // counter for landmarks - double curr_max_dist = 0; // used for defining the furhest point from L - const double infty = std::numeric_limits::infinity(); // infinity (see next entry) - std::vector< double > dist_to_L(nb_points, infty); // vector of current distances to L from points - - // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety - // or better yet std::uniform_int_distribution - int rand_int = rand() % nb_points; - int curr_max_w = rand_int; // For testing purposes a pseudo-random number is used here - - for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) { - // curr_max_w at this point is the next landmark - chosen_landmarks.push_back(curr_max_w); - unsigned i = 0; - for (auto& p : points) { - double curr_dist = euclidean_distance(p, *(std::begin(points) + chosen_landmarks[current_number_of_landmarks])); - wit_land_dist[i].push_back(curr_dist); - knn[i].push_back(current_number_of_landmarks); - if (curr_dist < dist_to_L[i]) - dist_to_L[i] = curr_dist; - ++i; - } - curr_max_dist = 0; - for (i = 0; i < dist_to_L.size(); i++) - if (dist_to_L[i] > curr_max_dist) { - curr_max_dist = dist_to_L[i]; - curr_max_w = i; - } - } - for (int i = 0; i < nb_points; ++i) - std::sort(std::begin(knn[i]), - std::end(knn[i]), - [&wit_land_dist, i](int a, int b) { - return wit_land_dist[i][a] < wit_land_dist[i][b]; }); - } - -} // namespace witness_complex - -} // namespace Gudhi - -#endif // LANDMARK_CHOICE_BY_FURTHEST_POINT_H_ diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h deleted file mode 100644 index b5aab9d5..00000000 --- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h +++ /dev/null @@ -1,96 +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): Siargey Kachanovich - * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (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 LANDMARK_CHOICE_BY_RANDOM_POINT_H_ -#define LANDMARK_CHOICE_BY_RANDOM_POINT_H_ - -#include - -#include // for priority_queue<> -#include // for pair<> -#include -#include -#include - -namespace Gudhi { - -namespace witness_complex { - - /** - * \ingroup witness_complex - * \brief Landmark choice strategy by taking random vertices for landmarks. - * \details It chooses nbL distinct landmarks from a random access range `points` - * and outputs a matrix {witness}*{closest landmarks} in knn. - * - * The type KNearestNeighbors can be seen as - * Witness_range>, where - * Witness_range and Closest_landmark_range are random access ranges and - * Vertex_handle is the label type of a vertex in a simplicial complex. - * Closest_landmark_range needs to have push_back operation. - */ - - template - void landmark_choice_by_random_point(Point_random_access_range const &points, - int nbL, - KNearestNeighbours &knn) { - int nbP = boost::size(points); - assert(nbP >= nbL); - std::set landmarks; - int current_number_of_landmarks = 0; // counter for landmarks - - // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety - int chosen_landmark = rand() % nbP; - for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) { - while (landmarks.find(chosen_landmark) != landmarks.end()) - chosen_landmark = rand() % nbP; - landmarks.insert(chosen_landmark); - } - - int dim = boost::size(*std::begin(points)); - typedef std::pair dist_i; - typedef bool (*comp)(dist_i, dist_i); - knn = KNearestNeighbours(nbP); - for (int points_i = 0; points_i < nbP; points_i++) { - std::priority_queue, comp> l_heap([](dist_i j1, dist_i j2) { - return j1.first > j2.first; - }); - std::set::iterator landmarks_it; - int landmarks_i = 0; - for (landmarks_it = landmarks.begin(), landmarks_i = 0; landmarks_it != landmarks.end(); - ++landmarks_it, landmarks_i++) { - dist_i dist = std::make_pair(euclidean_distance(points[points_i], points[*landmarks_it]), landmarks_i); - l_heap.push(dist); - } - for (int i = 0; i < dim + 1; i++) { - dist_i dist = l_heap.top(); - knn[points_i].push_back(dist.second); - l_heap.pop(); - } - } - } - -} // namespace witness_complex - -} // namespace Gudhi - -#endif // LANDMARK_CHOICE_BY_RANDOM_POINT_H_ diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 2cec921a..1eb126f1 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -72,7 +72,6 @@ class Witness_complex { typedef std::vector< Point_t > Point_Vector; typedef std::vector< Vertex_handle > typeVectorVertex; - //typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex; typedef std::pair< Simplex_handle, bool > typePairSimplexBool; typedef int Witness_id; diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp index adaadfb0..6be39f58 100644 --- a/src/Witness_complex/test/simple_witness_complex.cpp +++ b/src/Witness_complex/test/simple_witness_complex.cpp @@ -33,7 +33,7 @@ #include typedef Gudhi::Simplex_tree<> Simplex_tree; -typedef std::vector< int > typeVectorVertex; +typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; typedef Gudhi::witness_complex::Witness_complex WitnessComplex; BOOST_AUTO_TEST_CASE(simple_witness_complex) { diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp index b7067f87..92f53417 100644 --- a/src/Witness_complex/test/witness_complex_points.cpp +++ b/src/Witness_complex/test/witness_complex_points.cpp @@ -34,8 +34,8 @@ #include typedef std::vector Point; -typedef std::vector< int > typeVectorVertex; typedef Gudhi::Simplex_tree<> Simplex_tree; +typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; typedef Gudhi::witness_complex::Witness_complex WitnessComplex; BOOST_AUTO_TEST_CASE(witness_complex_points) { diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 773889d9..9dbcd891 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -39,61 +39,4 @@ struct vertex_filtration_t { typedef boost::vertex_property_tag kind; }; -/*typedef int Vertex_handle; -typedef double Filtration_value; -typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS -, boost::property < vertex_filtration_t, Filtration_value > -, boost::property < edge_filtration_t, Filtration_value > -> Graph_t; -typedef std::pair< Vertex_handle, Vertex_handle > Edge_t; -*/ -/** \brief Output the proximity graph of the points. - * - * If points contains n elements, the proximity graph is the graph - * with n vertices, and an edge [u,v] iff the distance function between - * points u and v is smaller than threshold. - * - * The type PointCloud furnishes .begin() and .end() methods, that return - * iterators with value_type Point. - */ -/*template< typename PointCloud -, typename Point > -Graph_t compute_proximity_graph(PointCloud &points - , Filtration_value threshold - , Filtration_value distance(Point p1, Point p2)) { - std::vector< Edge_t > edges; - std::vector< Filtration_value > edges_fil; - std::map< Vertex_handle, Filtration_value > vertices; - - Vertex_handle idx_u, idx_v; - Filtration_value fil; - idx_u = 0; - for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { - idx_v = idx_u + 1; - for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { - fil = distance(*it_u, *it_v); - if (fil <= threshold) { - edges.emplace_back(idx_u, idx_v); - edges_fil.push_back(fil); - } - } - ++idx_u; - } - - Graph_t skel_graph(edges.begin() - , edges.end() - , edges_fil.begin() - , idx_u); // number of points labeled from 0 to idx_u-1 - - auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); - - boost::graph_traits::vertex_iterator vi, vi_end; - for (std::tie(vi, vi_end) = boost::vertices(skel_graph); - vi != vi_end; ++vi) { - boost::put(vertex_prop, *vi, 0.); - } - - return skel_graph; -}*/ - #endif // GRAPH_SIMPLICIAL_COMPLEX_H_ -- cgit v1.2.3 From 1a728400187d89db914e865a979c85c7260b0b02 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 21 Nov 2016 16:24:15 +0000 Subject: Add distance matrix rips construction (doc, code, test) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1766 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6b9bdecbaf0aca12facb023e66bdea71e8e8cd38 --- biblio/how_to_cite_gudhi.bib | 9 +++ src/Doxyfile | 6 +- src/Rips_complex/doc/Intro_rips_complex.h | 52 ++++++++++++-- src/Rips_complex/example/CMakeLists.txt | 23 ++++++ ...mple_one_skeleton_rips_from_distance_matrix.cpp | 68 ++++++++++++++++++ .../example_one_skeleton_rips_from_points.cpp | 2 - ..._rips_complex_from_csv_distance_matrix_file.cpp | 72 +++++++++++++++++++ .../full_skeleton_rips_distance_for_doc.txt | 32 +++++++++ .../example/one_skeleton_rips_distance_for_doc.txt | 17 +++++ src/Rips_complex/include/gudhi/Rips_complex.h | 13 ++++ src/common/doc/main_page.h | 3 +- src/common/include/gudhi/distance_functions.h | 11 +-- .../include/gudhi/graph_simplicial_complex.h | 2 +- src/common/include/gudhi/reader_utils.h | 84 +++++++++++----------- src/common/test/test_distance_matrix_reader.cpp | 16 ++--- 15 files changed, 347 insertions(+), 63 deletions(-) create mode 100644 src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp create mode 100644 src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp create mode 100644 src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt create mode 100644 src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt (limited to 'src/Rips_complex/doc/Intro_rips_complex.h') diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib index 03c05728..77b6e284 100644 --- a/biblio/how_to_cite_gudhi.bib +++ b/biblio/how_to_cite_gudhi.bib @@ -94,4 +94,13 @@ , booktitle = "{GUDHI} User and Reference Manual" , url = "http://gudhi.gforge.inria.fr/doc/latest/group__tangential__complex.html" , year = 2016 +} + +@incollection{gudhi:RipsComplex +, author = "Cl\'ement Maria, Pawel Dlotko, Vincent Rouvreau" +, title = "Rips complex" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__rips__complex.html" +, year = 2016 } \ No newline at end of file diff --git a/src/Doxyfile b/src/Doxyfile index e7c1a0e1..cf79755f 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -500,7 +500,7 @@ HIDE_SCOPE_NAMES = NO # the files that are included by a file in the documentation of that file. # The default value is: YES. -SHOW_INCLUDE_FILES = YES +SHOW_INCLUDE_FILES = NO # If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each # grouped member an include statement to the documentation, telling the reader @@ -2151,7 +2151,7 @@ TEMPLATE_RELATIONS = YES # The default value is: YES. # This tag requires that the tag HAVE_DOT is set to YES. -INCLUDE_GRAPH = YES +INCLUDE_GRAPH = NO # If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are # set to YES then doxygen will generate a graph for each documented file showing @@ -2160,7 +2160,7 @@ INCLUDE_GRAPH = YES # The default value is: YES. # This tag requires that the tag HAVE_DOT is set to YES. -INCLUDED_BY_GRAPH = YES +INCLUDED_BY_GRAPH = NO # If the CALL_GRAPH tag is set to YES then doxygen will generate a call # dependency graph for every global function or class method. diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index a71946b5..d01b14bb 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -2,7 +2,7 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clément Maria, Vincent Rouvreau + * Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau * * Copyright (C) 2016 INRIA * @@ -29,7 +29,7 @@ namespace rips_complex { /** \defgroup rips_complex Rips complex * - * \author Clément Maria, Vincent Rouvreau + * \author Clément Maria, Pawel Dlotko, Vincent Rouvreau * * @{ * @@ -54,7 +54,9 @@ namespace rips_complex { * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$. * And so on for simplex (0,1,2,3). * - * \section ripspointsexample Example from points + * \section ripspointsdistance Point cloud and distance function + * + * \subsection ripspointscloudexample Example from a point cloud and a distance function * * This example builds the one skeleton graph from the given points, threshold value, and distance function. * Then it creates a `Simplex_tree` with it. @@ -73,7 +75,7 @@ namespace rips_complex { * * \include Rips_complex/one_skeleton_rips_points_for_doc.txt * - * \section ripsoffexample Example from OFF file + * \subsection ripsoffexample Example from OFF file * * This example builds the one skeleton graph from the given points in an OFF file, threshold value, and distance * function. @@ -93,6 +95,48 @@ namespace rips_complex { * * \include Rips_complex/full_skeleton_rips_points_for_doc.txt * + * + * + * \section ripsdistancematrix Distance matrix + * + * \subsection ripsdistancematrixexample Example from a distance matrix + * + * This example builds the one skeleton graph from the given distance matrix and threshold value. + * Then it creates a `Simplex_tree` with it. + * + * Then, it is asked to display information about the simplicial complex. + * + * \include Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp + * + * When launching (rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph + * with other words): + * + * \code $> ./oneskeletonripsdistance 1.0 + * \endcode + * + * the program output is: + * + * \include Rips_complex/one_skeleton_rips_distance_for_doc.txt + * + * \subsection ripscsvdistanceexample Example from a distance matrix read in a csv file + * + * This example builds the one skeleton graph from the given distance matrix read in a csv file and threshold value. + * Then it creates a `Simplex_tree` with it. + * + * + * Then, it is asked to display information about the rips complex. + * + * \include Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp + * + * When launching: + * + * \code $> ./ripscsvdistancereader ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3 + * \endcode + * + * the program output is: + * + * \include Rips_complex/full_skeleton_rips_distance_for_doc.txt + * * \copyright GNU General Public License v3. * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index 3962b15e..9ba9d941 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -1,27 +1,50 @@ cmake_minimum_required(VERSION 2.6) project(Rips_complex_examples) +# Point cloud add_executable ( ripsoffreader example_rips_complex_from_off_file.cpp ) target_link_libraries(ripsoffreader ${Boost_SYSTEM_LIBRARY}) add_executable ( oneskeletonripspoints example_one_skeleton_rips_from_points.cpp ) target_link_libraries(oneskeletonripspoints ${Boost_SYSTEM_LIBRARY}) +# Distance matrix +add_executable ( oneskeletonripsdistance example_one_skeleton_rips_from_distance_matrix.cpp ) +target_link_libraries(oneskeletonripsdistance ${Boost_SYSTEM_LIBRARY}) + +add_executable ( ripscsvdistancereader example_rips_complex_from_csv_distance_matrix_file.cpp ) +target_link_libraries(ripscsvdistancereader ${Boost_SYSTEM_LIBRARY}) + if (TBB_FOUND) target_link_libraries(ripsoffreader ${TBB_LIBRARIES}) target_link_libraries(oneskeletonripspoints ${TBB_LIBRARIES}) + target_link_libraries(oneskeletonripsdistance ${TBB_LIBRARIES}) + target_link_libraries(ripscsvdistancereader ${TBB_LIBRARIES}) endif() add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 12.0) + +add_test(oneskeletonripsdistance ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 1.0) + # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt) add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt) + +file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(ripscsvdistancereader_doc_1_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt) +add_test(ripscsvdistancereader_doc_1_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt) + + if (DIFF_PATH) # Do not forget to copy test results files in current binary dir file(COPY "one_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) file(COPY "full_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "one_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "full_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_points_for_doc.txt) add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_points_for_doc.txt) + add_test(ripscsvreader_doc_1_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_distance_for_doc.txt) + add_test(ripscsvreader_doc_1_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_distance_for_doc.txt) endif() diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp new file mode 100644 index 00000000..54fa3aa1 --- /dev/null +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp @@ -0,0 +1,68 @@ +#include +// to construct a simplex_tree from rips complex +#include +#include + +#include +#include +#include // for std::numeric_limits + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " threshold\n"; + std::cerr << " i.e.: " << progName << " 12.0\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if (argc != 2) usage(argc, argv[0]); + + double threshold = atof(argv[1]); + + // Type definitions + using Simplex_tree = Gudhi::Simplex_tree; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex; + using Distance_matrix = std::vector>; + + // User defined distance matrix is: + // | 0 0.94 0.77 0.99 0.11 | + // | 0.94 0 0.26 0.99 0.39 | + // | 0.77 0.26 0 0.28 0.97 | + // | 0.99 0.99 0.28 0 0.30 | + // | 0.11 0.39 0.97 0.30 0 | + + Distance_matrix distances; + distances.push_back({}); + distances.push_back({0.94}); + distances.push_back({0.77, 0.26}); + distances.push_back({0.99, 0.99, 0.28}); + distances.push_back({0.11, 0.39, 0.97, 0.30}); + + // ---------------------------------------------------------------------------- + // Init of a rips complex from points + // ---------------------------------------------------------------------------- + Rips_complex rips_complex_from_points(distances, threshold); + + Simplex_tree simplex; + if (rips_complex_from_points.create_complex(simplex, 1)) { + // ---------------------------------------------------------------------------- + // Display information about the one skeleton rips complex + // ---------------------------------------------------------------------------- + std::cout << "Rips complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + } + return 0; +} diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp index 2e63d9a6..26517876 100644 --- a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp @@ -1,6 +1,4 @@ #include -// to construct Rips_complex from a OFF file of points -#include // to construct a simplex_tree from rips complex #include #include diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp new file mode 100644 index 00000000..cfada84a --- /dev/null +++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp @@ -0,0 +1,72 @@ +#include +// to construct Rips_complex from a OFF file of points +#include +// to construct a simplex_tree from rips complex +#include +#include + +#include +#include + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " filename.csv threshold dim_max [ouput_file.txt]\n"; + std::cerr << " i.e.: " << progName << " ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1)); + + std::string csv_file_name(argv[1]); + double threshold = atof(argv[2]); + int dim_max = atoi(argv[3]); + + // Type definitions + using Simplex_tree = Gudhi::Simplex_tree<>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex; + using Distance_matrix = std::vector>; + + // ---------------------------------------------------------------------------- + // Init of a rips complex from a distance matrix in a csv file + // Default separator is ';' + // ---------------------------------------------------------------------------- + Distance_matrix distances = read_lower_triangular_matrix_from_csv_file(csv_file_name); + Rips_complex rips_complex_from_file(distances, threshold); + + std::streambuf* streambufffer; + std::ofstream ouput_file_stream; + + if (argc == 5) { + ouput_file_stream.open(std::string(argv[4])); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + Simplex_tree simplex; + if (rips_complex_from_file.create_complex(simplex, dim_max)) { + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the rips complex + // ---------------------------------------------------------------------------- + output_stream << "Rips complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + output_stream << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + output_stream << std::endl; + } + } + ouput_file_stream.close(); + return 0; +} diff --git a/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt new file mode 100644 index 00000000..6744532d --- /dev/null +++ b/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt @@ -0,0 +1,32 @@ +Rips complex is of dimension 3 - 30 simplices - 5 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 4 0 ) -> [0.11] + ( 2 1 ) -> [0.26] + ( 3 2 ) -> [0.28] + ( 4 3 ) -> [0.3] + ( 4 1 ) -> [0.39] + ( 2 0 ) -> [0.77] + ( 1 0 ) -> [0.94] + ( 2 1 0 ) -> [0.94] + ( 4 1 0 ) -> [0.94] + ( 4 2 ) -> [0.97] + ( 4 2 0 ) -> [0.97] + ( 4 2 1 ) -> [0.97] + ( 4 2 1 0 ) -> [0.97] + ( 4 3 2 ) -> [0.97] + ( 3 0 ) -> [0.99] + ( 3 1 ) -> [0.99] + ( 3 1 0 ) -> [0.99] + ( 3 2 0 ) -> [0.99] + ( 3 2 1 ) -> [0.99] + ( 3 2 1 0 ) -> [0.99] + ( 4 3 0 ) -> [0.99] + ( 4 3 1 ) -> [0.99] + ( 4 3 1 0 ) -> [0.99] + ( 4 3 2 0 ) -> [0.99] + ( 4 3 2 1 ) -> [0.99] diff --git a/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt new file mode 100644 index 00000000..9bb1a7ab --- /dev/null +++ b/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt @@ -0,0 +1,17 @@ +Rips complex is of dimension 1 - 15 simplices - 5 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 4 0 ) -> [0.11] + ( 2 1 ) -> [0.26] + ( 3 2 ) -> [0.28] + ( 4 3 ) -> [0.3] + ( 4 1 ) -> [0.39] + ( 2 0 ) -> [0.77] + ( 1 0 ) -> [0.94] + ( 4 2 ) -> [0.97] + ( 3 0 ) -> [0.99] + ( 3 1 ) -> [0.99] diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h index 6f947f41..63207892 100644 --- a/src/Rips_complex/include/gudhi/Rips_complex.h +++ b/src/Rips_complex/include/gudhi/Rips_complex.h @@ -78,6 +78,19 @@ class Rips_complex { compute_proximity_graph(points, threshold, distance); } + /** \brief Rips_complex constructor from a distance matrix. + * + * @param[in] distance_matrix Range of distances. + * @param[in] threshold rips value. + * + * The type InputDistanceRange must be a range for which std::begin and std::end return input iterators on a point. + */ + template + Rips_complex(const InputDistanceRange& distance_matrix, Filtration_value threshold) { + compute_proximity_graph(boost::irange((size_t)0,distance_matrix.size()), threshold, + [&](size_t i, size_t j){return distance_matrix[j][i];}); + } + /** \brief Initializes the simplicial complex from the 1-skeleton graph and expands it until a given maximal * dimension. * diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 85310f66..85ae8679 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -60,7 +60,7 @@ @@ -68,6 +68,7 @@ Rips_complex is a simplicial complex constructed from a one skeleton graph.
The filtration value of each edge is computed from a user-given distance function and is inserted until a user-given threshold value.
+ This complex can be built from a point cloud and a distance function, or from a distance matrix.
User manual: \ref rips_complex - Reference manual: Gudhi::rips_complex::Rips_complex diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index 006df275..ed2c1f5d 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -25,9 +25,12 @@ #include // for std::sqrt -/* Compute the Euclidean distance between two Points given - * by a range of coordinates. The points are assumed to have - * the same dimension. */ +/** @file + * @brief Global distance functions + */ + +/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to + * have the same dimension. */ template< typename Filtration_value, typename Point > Filtration_value euclidean_distance(const Point &p1,const Point &p2) { Filtration_value dist = 0.; diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 9dbcd891..5fe7c826 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 40d566d8..3799e583 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -34,14 +34,20 @@ #include #include +// Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented. +// It is required for global functions and variables. + +/** @file + * @brief This file includes common file reader for GUDHI + */ + /** - * \brief Read a set of points to turn it - * into a vector< vector > by filling points + * @brief Read a set of points to turn it into a vector< vector > by filling points. * - * File format: 1 point per line - * X11 X12 ... X1d - * X21 X22 ... X2d - * etc + * File format: 1 point per line
+ * X11 X12 ... X1d
+ * X21 X22 ... X2d
+ * etc
*/ inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) { std::ifstream in_file(file_name.c_str(), std::ios::in); @@ -66,12 +72,12 @@ inline void read_points(std::string file_name, std::vector< std::vector< double } /** - * \brief Read a graph from a file. + * @brief Read a graph from a file. * - * File format: 1 simplex per line - * Dim1 X11 X12 ... X1d Fil1 - * Dim2 X21 X22 ... X2d Fil2 - * etc + * File format: 1 simplex per line
+ * Dim1 X11 X12 ... X1d Fil1
+ * Dim2 X21 X22 ... X2d Fil2
+ * etc
* * The vertices must be labeled from 0 to n-1. * Every simplex must appear exactly once. @@ -141,12 +147,12 @@ inline Graph_t read_graph(std::string file_name) { } /** - * \brief Read a face from a file. + * @brief Read a face from a file. * - * File format: 1 simplex per line - * Dim1 X11 X12 ... X1d Fil1 - * Dim2 X21 X22 ... X2d Fil2 - * etc + * File format: 1 simplex per line
+ * Dim1 X11 X12 ... X1d Fil1
+ * Dim2 X21 X22 ... X2d Fil2
+ * etc
* * The vertices must be labeled from 0 to n-1. * Every simplex must appear exactly once. @@ -167,18 +173,16 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi } /** - * \brief Read a hasse simplex from a file. + * @brief Read a hasse simplex from a file. * - * File format: 1 simplex per line - * Dim1 k11 k12 ... k1Dim1 Fil1 - * Dim2 k21 k22 ... k2Dim2 Fil2 - * etc + * File format: 1 simplex per line
+ * Dim1 k11 k12 ... k1Dim1 Fil1
+ * Dim2 k21 k22 ... k2Dim2 Fil2
+ * etc
* - * The key of a simplex is its position in the filtration order - * and also the number of its row in the file. - * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the - * filtration has dimension Dimi, filtration value fil1 and simplices with - * key ki1 ... kiDimi in its boundary.*/ + * The key of a simplex is its position in the filtration order and also the number of its row in the file. + * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the filtration has dimension Dimi, filtration value + * fil1 and simplices with key ki1 ... kiDimi in its boundary.*/ template< typename Simplex_key, typename Filtration_value > bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) { int dim; @@ -197,27 +201,27 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar } /** - * \brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole + * @brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole * (square) matrix. * - * \author Pawel Dlotko + * @author Pawel Dlotko * - * Square matrix file format: - * 0;D12;...;D1j - * D21;0;...;D2j - * ... - * Dj1;Dj2;...;0 + * Square matrix file format:
+ * 0;D12;...;D1j
+ * D21;0;...;D2j
+ * ...
+ * Dj1;Dj2;...;0
* - * lower matrix file format: - * 0 - * D21; - * D31;D32; - * ... - * Dj1;Dj2;...;Dj(j-1); + * lower matrix file format:
+ * 0
+ * D21;
+ * D31;D32;
+ * ...
+ * Dj1;Dj2;...;Dj(j-1);
* **/ template< typename Filtration_value > -std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(std::string filename, +std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename, const char separator=';') { bool dbg = false; if (dbg) { diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp index 7eb7e846..a4c46bb1 100644 --- a/src/common/test/test_distance_matrix_reader.cpp +++ b/src/common/test/test_distance_matrix_reader.cpp @@ -47,21 +47,21 @@ BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix ) std::cout << "from_lower_triangular size = " << from_lower_triangular.size() << std::endl; BOOST_CHECK(from_lower_triangular.size() == 5); - for (int i = 0; i < from_lower_triangular.size(); i++) { + for (std::size_t i = 0; i < from_lower_triangular.size(); i++) { std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl; BOOST_CHECK(from_lower_triangular[i].size() == i); } std::vector expected = {1}; - BOOST_CHECK(from_lower_triangular[0] == expected); + BOOST_CHECK(from_lower_triangular[1] == expected); expected = {2,3}; - BOOST_CHECK(from_lower_triangular[0] == expected); + BOOST_CHECK(from_lower_triangular[2] == expected); expected = {4,5,6}; - BOOST_CHECK(from_lower_triangular[0] == expected); + BOOST_CHECK(from_lower_triangular[3] == expected); expected = {7,8,9,10}; - BOOST_CHECK(from_lower_triangular[0] == expected); + BOOST_CHECK(from_lower_triangular[4] == expected); } @@ -78,8 +78,8 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix ) } std::cout << "from_full_square size = " << from_full_square.size() << std::endl; BOOST_CHECK(from_full_square.size() == 5); - for (int i = 0; i < from_lower_triangular.size(); i++) { - std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl; - BOOST_CHECK(from_lower_triangular[i].size() == i); + for (std::size_t i = 0; i < from_full_square.size(); i++) { + std::cout << "from_full_square[" << i << "] size = " << from_full_square[i].size() << std::endl; + BOOST_CHECK(from_full_square[i].size() == i); } } -- cgit v1.2.3 From 71f9bed6df48dedc0d4e8ef620496af9c494eccc Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 22 Nov 2016 13:29:59 +0000 Subject: Fix examples and tests git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1767 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4a1c78aec05d443e0525bf24a0cc7f7b5c628629 --- .../full_square_distance_matrix.csv | 12 +- src/Persistent_cohomology/example/CMakeLists.txt | 9 +- src/Persistent_cohomology/example/README | 50 ++++--- .../example/rips_distance_matrix_persistence.cpp | 145 +++++++++++++++++++++ .../example/rips_persistence.cpp | 5 +- src/Rips_complex/doc/Intro_rips_complex.h | 8 +- src/Rips_complex/example/CMakeLists.txt | 20 ++- .../full_skeleton_rips_distance_for_doc.txt | 32 ----- .../example/full_skeleton_rips_for_doc.txt | 26 ++++ .../example/full_skeleton_rips_points_for_doc.txt | 26 ---- .../example/one_skeleton_rips_distance_for_doc.txt | 17 --- .../example/one_skeleton_rips_for_doc.txt | 20 +++ .../example/one_skeleton_rips_points_for_doc.txt | 20 --- src/common/include/gudhi/reader_utils.h | 21 ++- src/common/test/test_distance_matrix_reader.cpp | 2 +- 15 files changed, 264 insertions(+), 149 deletions(-) create mode 100644 src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp delete mode 100644 src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt create mode 100644 src/Rips_complex/example/full_skeleton_rips_for_doc.txt delete mode 100644 src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt delete mode 100644 src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt create mode 100644 src/Rips_complex/example/one_skeleton_rips_for_doc.txt delete mode 100644 src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt (limited to 'src/Rips_complex/doc/Intro_rips_complex.h') diff --git a/data/distance_matrix/full_square_distance_matrix.csv b/data/distance_matrix/full_square_distance_matrix.csv index 7225a5fd..51512b03 100644 --- a/data/distance_matrix/full_square_distance_matrix.csv +++ b/data/distance_matrix/full_square_distance_matrix.csv @@ -1,5 +1,7 @@ -0;0.94;0.77;0.99;0.11; -0.94;0;0.26;0.99;0.39; -0.77;0.26;0;0.28;0.97; -0.99;0.99;0.28;0;0.30; -0.11;0.39;0.97;0.30;0; +0;6.0827625303;5.8309518948;9.4339811321;13.0384048104;18.0277563773;17.88854382; +6.0827625303;0;6.7082039325;6.3245553203;15.6524758425;19.6468827044;17.1172427686; +5.8309518948;6.7082039325;0;5;8.94427191;13.152946438;12.0830459736; +9.4339811321;6.3245553203;5;0;12.0415945788;14.7648230602;11; +13.0384048104;15.6524758425;8.94427191;12.0415945788;0;5.3851648071;9.4868329805; +18.0277563773;19.6468827044;13.152946438;14.7648230602;5.3851648071;0;7.2801098893; +17.88854382;17.1172427686;12.0830459736;11;9.4868329805;7.2801098893;0; \ No newline at end of file diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index e50e8ca9..b2ac9736 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -11,6 +11,9 @@ target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY}) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY}) +add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) +target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_executable(rips_persistence rips_persistence.cpp) target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) @@ -23,6 +26,7 @@ target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROG if (TBB_FOUND) target_link_libraries(plain_homology ${TBB_LIBRARIES}) target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES}) + target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) target_link_libraries(rips_persistence ${TBB_LIBRARIES}) target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) @@ -30,7 +34,8 @@ endif() add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology) add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0) -add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100) +add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence ${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv -r 1.0 -d 3 -p 3 -m 0) +add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3) add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100) add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0) add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100) @@ -42,7 +47,7 @@ if(GMP_FOUND) if (TBB_FOUND) target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) - add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100) + add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71) endif(GMPXX_FOUND) endif(GMP_FOUND) diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README index 7803e5ab..1063ea41 100644 --- a/src/Persistent_cohomology/example/README +++ b/src/Persistent_cohomology/example/README @@ -10,13 +10,13 @@ Example of use of RIPS: Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points sampling a Klein bottle: -./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100 +./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 output: -210 0 0 inf -210 1 0.0702103 inf -2 1 0.0702103 inf -2 2 0.159992 inf +2 0 0 inf +2 1 0.0983494 inf +2 1 0.104347 inf +2 2 0.138335 inf Every line is of this format: p1*...*pr dim b d @@ -29,31 +29,45 @@ where with Z/3Z coefficients: -./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100 +./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 output: -3 0 0 inf -3 1 0.0702103 inf +3 0 0 inf +3 1 0.0983494 inf +3 1 0.104347 inf +3 2 0.138335 inf and the computation with Z/2Z and Z/3Z coefficients simultaneously: -./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100 +./rips_multifield_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.12 -d 3 -p 2 -q 3 output: -6 0 0 inf -6 1 0.0702103 inf -2 1 0.0702103 inf -2 2 0.159992 inf +6 0 0 inf +6 1 0.0983494 inf +6 1 0.104347 inf +6 2 0.138335 inf +6 0 0 0.122545 +6 0 0 0.121171 +6 0 0 0.120964 +6 0 0 0.12057 +6 0 0 0.12047 +6 0 0 0.120414 and finally the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers): - ./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100 + ./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -m 0.5 -d 3 -p 2 -q 71 output: -557940830126698960967415390 0 0 inf -557940830126698960967415390 1 0.0702103 inf -2 1 0.0702103 inf -2 2 0.159992 inf +557940830126698960967415390 0 0 inf +557940830126698960967415390 1 0.0983494 inf +557940830126698960967415390 1 0.104347 inf +557940830126698960967415390 2 0.138335 inf +557940830126698960967415390 0 0 0.122545 +557940830126698960967415390 0 0 0.121171 +557940830126698960967415390 0 0 0.120964 +557940830126698960967415390 0 0 0.12057 +557940830126698960967415390 0 0 0.12047 +557940830126698960967415390 0 0 0.120414 *********************************************************************************************************************** Example of use of ALPHA: diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp new file mode 100644 index 00000000..7a9e9c8b --- /dev/null +++ b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp @@ -0,0 +1,145 @@ +/* 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, Vincent Rouvreau + * + * Copyright (C) 2016 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include +#include +#include +#include + +#include + +#include +#include +#include // infinity + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; +using Distance_matrix = std::vector>; + +void program_options(int argc, char * argv[] + , std::string & csv_matrix_file + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string csv_matrix_file; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); + + Distance_matrix distances = read_lower_triangular_matrix_from_csv_file(csv_matrix_file); + Rips_complex rips_complex_from_file(distances, threshold); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree simplex_tree; + + if (rips_complex_from_file.create_complex(simplex_tree, dim_max)) { + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + } + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & csv_matrix_file + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&csv_matrix_file), + "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'."); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of distance matrix.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp index 709c2eab..3fa8aa30 100644 --- a/src/Persistent_cohomology/example/rips_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_persistence.cpp @@ -104,14 +104,15 @@ void program_options(int argc, char * argv[] po::options_description hidden("Hidden options"); hidden.add_options() ("input-file", po::value(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + "Name of an OFF file containing a point set.\n"); po::options_description visible("Allowed options", 100); visible.add_options() ("help,h", "produce help message") ("output-file,o", po::value(&filediag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-edge-length,r", po::value(&threshold)->default_value(std::numeric_limits::infinity()), + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), "Maximal length of an edge for the Rips complex construction.") ("cpx-dimension,d", po::value(&dim_max)->default_value(1), "Maximal dimension of the Rips complex we want to compute.") diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index d01b14bb..0ae89ffc 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -73,7 +73,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/one_skeleton_rips_points_for_doc.txt + * \include Rips_complex/one_skeleton_rips_for_doc.txt * * \subsection ripsoffexample Example from OFF file * @@ -93,7 +93,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/full_skeleton_rips_points_for_doc.txt + * \include Rips_complex/full_skeleton_rips_for_doc.txt * * * @@ -116,7 +116,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/one_skeleton_rips_distance_for_doc.txt + * \include Rips_complex/one_skeleton_rips_for_doc.txt * * \subsection ripscsvdistanceexample Example from a distance matrix read in a csv file * @@ -135,7 +135,7 @@ namespace rips_complex { * * the program output is: * - * \include Rips_complex/full_skeleton_rips_distance_for_doc.txt + * \include Rips_complex/full_skeleton_rips_for_doc.txt * * \copyright GNU General Public License v3. * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index 9ba9d941..c15a13d0 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -32,19 +32,17 @@ add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphac add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt) file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) -add_test(ripscsvdistancereader_doc_1_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt) -add_test(ripscsvdistancereader_doc_1_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 1.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt) +add_test(ripscsvdistancereader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt) +add_test(ripscsvdistancereader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt) if (DIFF_PATH) # Do not forget to copy test results files in current binary dir - file(COPY "one_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "full_skeleton_rips_points_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "one_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "full_skeleton_rips_distance_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - - add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_points_for_doc.txt) - add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_points_for_doc.txt) - add_test(ripscsvreader_doc_1_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_distance_for_doc.txt) - add_test(ripscsvreader_doc_1_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_1_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_distance_for_doc.txt) + file(COPY "one_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "full_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt) + add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt) + add_test(ripscsvreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt) + add_test(ripscsvreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt) endif() diff --git a/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt deleted file mode 100644 index 6744532d..00000000 --- a/src/Rips_complex/example/full_skeleton_rips_distance_for_doc.txt +++ /dev/null @@ -1,32 +0,0 @@ -Rips complex is of dimension 3 - 30 simplices - 5 vertices. -Iterator on rips complex simplices in the filtration order, with [filtration value]: - ( 0 ) -> [0] - ( 1 ) -> [0] - ( 2 ) -> [0] - ( 3 ) -> [0] - ( 4 ) -> [0] - ( 4 0 ) -> [0.11] - ( 2 1 ) -> [0.26] - ( 3 2 ) -> [0.28] - ( 4 3 ) -> [0.3] - ( 4 1 ) -> [0.39] - ( 2 0 ) -> [0.77] - ( 1 0 ) -> [0.94] - ( 2 1 0 ) -> [0.94] - ( 4 1 0 ) -> [0.94] - ( 4 2 ) -> [0.97] - ( 4 2 0 ) -> [0.97] - ( 4 2 1 ) -> [0.97] - ( 4 2 1 0 ) -> [0.97] - ( 4 3 2 ) -> [0.97] - ( 3 0 ) -> [0.99] - ( 3 1 ) -> [0.99] - ( 3 1 0 ) -> [0.99] - ( 3 2 0 ) -> [0.99] - ( 3 2 1 ) -> [0.99] - ( 3 2 1 0 ) -> [0.99] - ( 4 3 0 ) -> [0.99] - ( 4 3 1 ) -> [0.99] - ( 4 3 1 0 ) -> [0.99] - ( 4 3 2 0 ) -> [0.99] - ( 4 3 2 1 ) -> [0.99] diff --git a/src/Rips_complex/example/full_skeleton_rips_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt new file mode 100644 index 00000000..319931e0 --- /dev/null +++ b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt @@ -0,0 +1,26 @@ +Rips complex is of dimension 3 - 24 simplices - 7 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [5] + ( 5 4 ) -> [5.38516] + ( 2 0 ) -> [5.83095] + ( 1 0 ) -> [6.08276] + ( 3 1 ) -> [6.32456] + ( 2 1 ) -> [6.7082] + ( 2 1 0 ) -> [6.7082] + ( 3 2 1 ) -> [6.7082] + ( 6 5 ) -> [7.28011] + ( 4 2 ) -> [8.94427] + ( 3 0 ) -> [9.43398] + ( 3 1 0 ) -> [9.43398] + ( 3 2 0 ) -> [9.43398] + ( 3 2 1 0 ) -> [9.43398] + ( 6 4 ) -> [9.48683] + ( 6 5 4 ) -> [9.48683] + ( 6 3 ) -> [11] diff --git a/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt deleted file mode 100644 index 319931e0..00000000 --- a/src/Rips_complex/example/full_skeleton_rips_points_for_doc.txt +++ /dev/null @@ -1,26 +0,0 @@ -Rips complex is of dimension 3 - 24 simplices - 7 vertices. -Iterator on rips complex simplices in the filtration order, with [filtration value]: - ( 0 ) -> [0] - ( 1 ) -> [0] - ( 2 ) -> [0] - ( 3 ) -> [0] - ( 4 ) -> [0] - ( 5 ) -> [0] - ( 6 ) -> [0] - ( 3 2 ) -> [5] - ( 5 4 ) -> [5.38516] - ( 2 0 ) -> [5.83095] - ( 1 0 ) -> [6.08276] - ( 3 1 ) -> [6.32456] - ( 2 1 ) -> [6.7082] - ( 2 1 0 ) -> [6.7082] - ( 3 2 1 ) -> [6.7082] - ( 6 5 ) -> [7.28011] - ( 4 2 ) -> [8.94427] - ( 3 0 ) -> [9.43398] - ( 3 1 0 ) -> [9.43398] - ( 3 2 0 ) -> [9.43398] - ( 3 2 1 0 ) -> [9.43398] - ( 6 4 ) -> [9.48683] - ( 6 5 4 ) -> [9.48683] - ( 6 3 ) -> [11] diff --git a/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt deleted file mode 100644 index 9bb1a7ab..00000000 --- a/src/Rips_complex/example/one_skeleton_rips_distance_for_doc.txt +++ /dev/null @@ -1,17 +0,0 @@ -Rips complex is of dimension 1 - 15 simplices - 5 vertices. -Iterator on rips complex simplices in the filtration order, with [filtration value]: - ( 0 ) -> [0] - ( 1 ) -> [0] - ( 2 ) -> [0] - ( 3 ) -> [0] - ( 4 ) -> [0] - ( 4 0 ) -> [0.11] - ( 2 1 ) -> [0.26] - ( 3 2 ) -> [0.28] - ( 4 3 ) -> [0.3] - ( 4 1 ) -> [0.39] - ( 2 0 ) -> [0.77] - ( 1 0 ) -> [0.94] - ( 4 2 ) -> [0.97] - ( 3 0 ) -> [0.99] - ( 3 1 ) -> [0.99] diff --git a/src/Rips_complex/example/one_skeleton_rips_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt new file mode 100644 index 00000000..b0e25cc5 --- /dev/null +++ b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt @@ -0,0 +1,20 @@ +Rips complex is of dimension 1 - 18 simplices - 7 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [5] + ( 5 4 ) -> [5.38516] + ( 2 0 ) -> [5.83095] + ( 1 0 ) -> [6.08276] + ( 3 1 ) -> [6.32456] + ( 2 1 ) -> [6.7082] + ( 6 5 ) -> [7.28011] + ( 4 2 ) -> [8.94427] + ( 3 0 ) -> [9.43398] + ( 6 4 ) -> [9.48683] + ( 6 3 ) -> [11] diff --git a/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt deleted file mode 100644 index b0e25cc5..00000000 --- a/src/Rips_complex/example/one_skeleton_rips_points_for_doc.txt +++ /dev/null @@ -1,20 +0,0 @@ -Rips complex is of dimension 1 - 18 simplices - 7 vertices. -Iterator on rips complex simplices in the filtration order, with [filtration value]: - ( 0 ) -> [0] - ( 1 ) -> [0] - ( 2 ) -> [0] - ( 3 ) -> [0] - ( 4 ) -> [0] - ( 5 ) -> [0] - ( 6 ) -> [0] - ( 3 2 ) -> [5] - ( 5 4 ) -> [5.38516] - ( 2 0 ) -> [5.83095] - ( 1 0 ) -> [6.08276] - ( 3 1 ) -> [6.32456] - ( 2 1 ) -> [6.7082] - ( 6 5 ) -> [7.28011] - ( 4 2 ) -> [8.94427] - ( 3 0 ) -> [9.43398] - ( 6 4 ) -> [9.48683] - ( 6 3 ) -> [11] diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 3799e583..ddec5ba7 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -223,10 +223,9 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar template< typename Filtration_value > std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename, const char separator=';') { - bool dbg = false; - if (dbg) { - std::cerr << "Using procedure read_lower_triangular_matrix_from_csv_file \n"; - } +#ifdef DEBUG_TRACES + std::cout << "Using procedure read_lower_triangular_matrix_from_csv_file \n"; +#endif // DEBUG_TRACES std::vector< std::vector< Filtration_value > > result; std::ifstream in; in.open(filename.c_str()); @@ -278,15 +277,15 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from } in.close(); - if (dbg) { - std::cerr << "Here is the matrix we read : \n"; - for (size_t i = 0; i != result.size(); ++i) { - for (size_t j = 0; j != result[i].size(); ++j) { - std::cerr << result[i][j] << " "; - } - std::cerr << std::endl; +#ifdef DEBUG_TRACES + std::cerr << "Here is the matrix we read : \n"; + for (size_t i = 0; i != result.size(); ++i) { + for (size_t j = 0; j != result[i].size(); ++j) { + std::cerr << result[i][j] << " "; } + std::cerr << std::endl; } +#endif // DEBUG_TRACES return result; } // read_lower_triangular_matrix_from_csv_file diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp index a4c46bb1..95a73bd9 100644 --- a/src/common/test/test_distance_matrix_reader.cpp +++ b/src/common/test/test_distance_matrix_reader.cpp @@ -77,7 +77,7 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix ) std::cout << std::endl; } std::cout << "from_full_square size = " << from_full_square.size() << std::endl; - BOOST_CHECK(from_full_square.size() == 5); + BOOST_CHECK(from_full_square.size() == 7); for (std::size_t i = 0; i < from_full_square.size(); i++) { std::cout << "from_full_square[" << i << "] size = " << from_full_square[i].size() << std::endl; BOOST_CHECK(from_full_square[i].size() == i); -- cgit v1.2.3 From 04e1b011959f93de8a7a252cdc9fa1f4aed0c12e Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 12 Dec 2016 16:52:02 +0000 Subject: Doc fix from review git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1857 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 88619abff993bd776310f18034d2ab5fa0b41944 --- src/Rips_complex/doc/Intro_rips_complex.h | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'src/Rips_complex/doc/Intro_rips_complex.h') diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 0ae89ffc..5b424a26 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -37,10 +37,13 @@ namespace rips_complex { * * Rips_complex * (Wikipedia) is a + * one skeleton graph that allows to construct a * simplicial complex - * constructed from a one skeleton graph. + * from it. + * The input can be a point cloud with a given distance function, or a distance matrix. * - * The filtration value of each edge is computed from a user-given distance function. + * The filtration value of each edge is computed from a user-given distance function, or directly from the distance + * matrix. * * All edges that have a filtration value strictly greater than a given threshold value are not inserted into * the complex. @@ -77,7 +80,7 @@ namespace rips_complex { * * \subsection ripsoffexample Example from OFF file * - * This example builds the one skeleton graph from the given points in an OFF file, threshold value, and distance + * This example builds the Rips_complex from the given points in an OFF file, threshold value, and distance * function. * Then it creates a `Simplex_tree` with it. * -- cgit v1.2.3 From 8340ca1acd568c93d115fcd46a996749a8cc295d Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Dec 2016 10:22:49 +0000 Subject: Modify documentatin after review git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1894 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4bd2b575d6f58aab2ea1d03b20d3e06693bec182 --- src/Rips_complex/concept/Simplicial_complex_for_rips.h | 6 ++++-- src/Rips_complex/doc/Intro_rips_complex.h | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) (limited to 'src/Rips_complex/doc/Intro_rips_complex.h') diff --git a/src/Rips_complex/concept/Simplicial_complex_for_rips.h b/src/Rips_complex/concept/Simplicial_complex_for_rips.h index ba9a2f5e..08173289 100644 --- a/src/Rips_complex/concept/Simplicial_complex_for_rips.h +++ b/src/Rips_complex/concept/Simplicial_complex_for_rips.h @@ -34,11 +34,13 @@ struct SimplicialComplexForRips { /** \brief Handle to specify the simplex filtration value. */ typedef unspecified Filtration_value; - /** \brief Inserts a given range `Gudhi::rips_complex::Rips_complex::OneSkeletonGraph` in the simplicial complex. */ + /** \brief Inserts a given range `Gudhi::rips_complex::Rips_complex::OneSkeletonGraph` in the simplicial + * complex. */ template void insert_graph(const OneSkeletonGraph& skel_graph); - /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension. */ + /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension as + * defined in \ref ripsdefinition. */ void expansion(int max_dim); /** \brief Returns the number of vertices in the simplicial complex. */ diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 5b424a26..8bacd0e7 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -33,7 +33,7 @@ namespace rips_complex { * * @{ * - * \section ripsdefinition Definition + * \section ripsdefinition Rips complex definition * * Rips_complex * (Wikipedia) is a -- cgit v1.2.3 From b987fc9acca83d8a0dca40647cfe804edfcee2a7 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 16 Jan 2017 09:43:21 +0000 Subject: Remove the usage functions and modified the doc for oneskeletonripspoints and oneskeletonripsdistance. No added value as distance matrix and points set is hard defined. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1939 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 13142245f95995a13c5bf484a6f8bf5d4bf53b58 --- src/Rips_complex/doc/Intro_rips_complex.h | 6 +++--- src/Rips_complex/example/CMakeLists.txt | 5 ++--- .../example_one_skeleton_rips_from_distance_matrix.cpp | 14 ++------------ .../example/example_one_skeleton_rips_from_points.cpp | 14 ++------------ 4 files changed, 9 insertions(+), 30 deletions(-) (limited to 'src/Rips_complex/doc/Intro_rips_complex.h') diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 8bacd0e7..64fd34bc 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -69,9 +69,9 @@ namespace rips_complex { * \include Rips_complex/example_one_skeleton_rips_from_points.cpp * * When launching (rips maximal distance between 2 points is 12.0, is expanded until dimension 1 - one skeleton graph - * with other words): + * in other words): * - * \code $> ./oneskeletonripspoints 12.0 + * \code $> ./oneskeletonripspoints * \endcode * * the program output is: @@ -114,7 +114,7 @@ namespace rips_complex { * When launching (rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph * with other words): * - * \code $> ./oneskeletonripsdistance 1.0 + * \code $> ./oneskeletonripsdistance * \endcode * * the program output is: diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index c15a13d0..070ac710 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -22,9 +22,8 @@ if (TBB_FOUND) target_link_libraries(ripscsvdistancereader ${TBB_LIBRARIES}) endif() -add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 12.0) - -add_test(oneskeletonripsdistance ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints 1.0) +add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints) +add_test(oneskeletonripsdistance ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripsdistance) # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp index 326ad52f..765d65ea 100644 --- a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp @@ -7,18 +7,7 @@ #include #include // for std::numeric_limits -void usage(int nbArgs, char * const progName) { - std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " threshold\n"; - std::cerr << " i.e.: " << progName << " 12.0\n"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if (argc != 2) usage(argc, argv[0]); - - double threshold = atof(argv[1]); - +int main() { // Type definitions using Simplex_tree = Gudhi::Simplex_tree; using Filtration_value = Simplex_tree::Filtration_value; @@ -42,6 +31,7 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Init of a rips complex from points // ---------------------------------------------------------------------------- + double threshold = 1.0; Rips_complex rips_complex_from_points(distances, threshold); Simplex_tree stree; diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp index 6e8dee27..5d1216a0 100644 --- a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp @@ -7,18 +7,7 @@ #include #include // for std::numeric_limits -void usage(int nbArgs, char * const progName) { - std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " threshold\n"; - std::cerr << " i.e.: " << progName << " 12.0\n"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if (argc != 2) usage(argc, argv[0]); - - double threshold = atof(argv[1]); - +int main() { // Type definitions using Point = std::vector; using Simplex_tree = Gudhi::Simplex_tree; @@ -37,6 +26,7 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Init of a rips complex from points // ---------------------------------------------------------------------------- + double threshold = 12.0; Rips_complex rips_complex_from_points(points, threshold, Euclidean_distance()); Simplex_tree stree; -- cgit v1.2.3
- Author: Clément Maria
+ Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau
Introduced in: GUDHI 1.4.0
Copyright: GPL v3