diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-09-28 13:43:58 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-09-28 13:43:58 +0000 |
commit | ef61b085afd77976a2c7fc5dfa13bc4b293b4f95 (patch) | |
tree | 99c82e4ec0681c6d13ea68bfcecb76516c2a54b1 /src/Persistent_cohomology | |
parent | 82fdc7d643e6ad589e16bc25782e8dd068d033ae (diff) |
Remove python rips_complex construction from files as it can lead to errors with correlation matrix
Add examples for doxygen
Cythonization of rips correlation matrix
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2727 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 8aae33839fa27f9d26897e625904671b2c05e0e7
Diffstat (limited to 'src/Persistent_cohomology')
-rw-r--r-- | src/Persistent_cohomology/example/CMakeLists.txt | 2 | ||||
-rw-r--r-- | src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp | 92 |
2 files changed, 40 insertions, 54 deletions
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 8a21d038..926cef6b 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -40,7 +40,7 @@ add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<T add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence> "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence - ${CMAKE_SOURCE_DIR}/data/distance_matrix/full_correlation_matrix.csv.csv -r 1.0 -d 3 -p 3 -m 0) + ${CMAKE_SOURCE_DIR}/data/correlation_matrix/full_correlation_matrix.csv.csv -r 1.0 -d 3 -p 3 -m 0) add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step> diff --git a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp index 6f2891fe..41cf915a 100644 --- a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp @@ -1,5 +1,5 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ +/* 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 @@ -31,24 +31,18 @@ #include <vector> #include <limits> // infinity - // Types definition using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; using Filtration_value = Simplex_tree::Filtration_value; using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; using Correlation_matrix = std::vector<std::vector<Filtration_value>>; -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); +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[]) { +int main(int argc, char* argv[]) { std::string csv_matrix_file; std::string filediag; Filtration_value threshold; @@ -58,22 +52,20 @@ int main(int argc, char * argv[]) { program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); - Correlation_matrix correlations = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); - - //Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix: - for ( size_t i = 0 ; i != correlations.size() ; ++i ) - { - for ( size_t j = 0 ; j != correlations[i].size() ; ++j ) - { - correlations[i][j] = 1-correlations[i][j]; - if ( correlations[i][j] < 0 ) - { - std::cerr << "The input matrix is not a correlation matrix. \n"; - throw "The input matrix is not a correlation matrix. \n"; - } - } - } - + Correlation_matrix correlations = + Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); + + // Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix: + for (size_t i = 0; i != correlations.size(); ++i) { + for (size_t j = 0; j != correlations[i].size(); ++j) { + correlations[i][j] = 1 - correlations[i][j]; + if (correlations[i][j] < 0) { + std::cerr << "The input matrix is not a correlation matrix. \n"; + throw "The input matrix is not a correlation matrix. \n"; + } + } + } + Rips_complex rips_complex_from_file(correlations, threshold); // Construct the Rips complex in a Simplex Tree @@ -104,33 +96,28 @@ int main(int argc, char * argv[]) { 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) { +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<std::string>(&csv_matrix_file), - "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'."); + hidden.add_options()( + "input-file", po::value<std::string>(&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<std::string>(&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<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value<int>(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value<Filtration_value>(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value<std::string>(&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<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Rips complex construction.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.")( + "field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value<Filtration_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); @@ -139,8 +126,7 @@ void program_options(int argc, char * argv[] all.add(visible).add(hidden); po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); + po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); po::notify(vm); if (vm.count("help") || !vm.count("input-file")) { |