diff options
Diffstat (limited to 'src/Persistence_representations/utilities')
40 files changed, 401 insertions, 604 deletions
diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt index 66524666..137eb0c1 100644 --- a/src/Persistence_representations/utilities/CMakeLists.txt +++ b/src/Persistence_representations/utilities/CMakeLists.txt @@ -1,6 +1,53 @@ +# Copy files, otherwise result files are created in sources +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") + +function(add_persistence_representation_creation_utility creation_utility) + add_executable ( ${creation_utility} ${creation_utility}.cpp ) + + # as the function is called in a subdirectory level, need to '../' to find persistence files + # ARGN will add all the other arguments (except creation_utility) sent to the CMake functions + add_test(NAME Persistence_representation_utilities_${creation_utility} COMMAND $<TARGET_FILE:${creation_utility}> + ${ARGN} "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") +endfunction(add_persistence_representation_creation_utility) + +function(add_persistence_representation_plot_utility plot_utility tool_extension) + add_executable ( ${plot_utility} ${plot_utility}.cpp ) + + # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files + add_test(NAME Persistence_representation_utilities_${plot_utility}_first COMMAND $<TARGET_FILE:${plot_utility}> + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}") + #add_test(NAME Persistence_representation_utilities_${plot_utility}_second COMMAND $<TARGET_FILE:${plot_utility}> + # "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") + if(GNUPLOT_PATH) + add_test(NAME Persistence_representation_utilities_${plot_utility}_first_gnuplot COMMAND ${GNUPLOT_PATH} + "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}_GnuplotScript'") + #add_test(NAME Persistence_representation_utilities_${plot_utility}_second_gnuplot COMMAND ${GNUPLOT_PATH} + # "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}_GnuplotScript'") + endif() +endfunction(add_persistence_representation_plot_utility) + +function(add_persistence_representation_function_utility function_utility tool_extension) + add_executable ( ${function_utility} ${function_utility}.cpp ) + + # ARGV2 is an optional argument + if (${ARGV2}) + # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files + add_test(NAME Persistence_representation_utilities_${function_utility} COMMAND $<TARGET_FILE:${function_utility}> + "${ARGV2}" + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") + else() + # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files + add_test(NAME Persistence_representation_utilities_${function_utility} COMMAND $<TARGET_FILE:${function_utility}> + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") + endif() +endfunction(add_persistence_representation_function_utility) + add_subdirectory(persistence_heat_maps) add_subdirectory(persistence_intervals) add_subdirectory(persistence_landscapes) add_subdirectory(persistence_landscapes_on_grid) add_subdirectory(persistence_vectors) - diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt index 0dd63852..386e9fa5 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt @@ -1,63 +1,15 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_representations_heat_maps_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") - -add_executable ( create_persistence_heat_maps create_persistence_heat_maps.cpp ) -target_link_libraries(create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_persistence_heat_maps COMMAND $<TARGET_FILE:create_persistence_heat_maps> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - - -add_executable ( create_pssk create_pssk.cpp ) -target_link_libraries(create_pssk ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_pssk COMMAND $<TARGET_FILE:create_pssk> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( create_p_h_m_weighted_by_distance_from_diagonal create_p_h_m_weighted_by_distance_from_diagonal.cpp ) -target_link_libraries(create_p_h_m_weighted_by_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_p_h_m_weighted_by_distance_from_diagonal COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_distance_from_diagonal> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( create_p_h_m_weighted_by_squared_diag_distance create_p_h_m_weighted_by_squared_diag_distance.cpp ) -target_link_libraries(create_p_h_m_weighted_by_squared_diag_distance ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_p_h_m_weighted_by_squared_diag_distance COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_squared_diag_distance> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( create_p_h_m_weighted_by_arctan_of_their_persistence create_p_h_m_weighted_by_arctan_of_their_persistence.cpp ) -target_link_libraries(create_p_h_m_weighted_by_arctan_of_their_persistence ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME create_p_h_m_weighted_by_arctan_of_their_persistence COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_arctan_of_their_persistence> - "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( average_persistence_heat_maps average_persistence_heat_maps.cpp ) -target_link_libraries(average_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME average_persistence_heat_maps COMMAND $<TARGET_FILE:average_persistence_heat_maps> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( plot_persistence_heat_map plot_persistence_heat_map.cpp ) -target_link_libraries(plot_persistence_heat_map ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_persistence_heat_map COMMAND $<TARGET_FILE:plot_persistence_heat_map> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( compute_distance_of_persistence_heat_maps compute_distance_of_persistence_heat_maps.cpp ) -target_link_libraries(compute_distance_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_distance_of_persistence_heat_maps COMMAND $<TARGET_FILE:compute_distance_of_persistence_heat_maps> - "1" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( compute_scalar_product_of_persistence_heat_maps compute_scalar_product_of_persistence_heat_maps.cpp ) -target_link_libraries(compute_scalar_product_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_scalar_product_of_persistence_heat_maps COMMAND $<TARGET_FILE:compute_scalar_product_of_persistence_heat_maps> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") +add_persistence_representation_creation_utility(create_pssk "10" "-1" "-1" "4" "-1") +add_persistence_representation_creation_utility(create_p_h_m_weighted_by_arctan_of_their_persistence "10" "-1" "-1" "4" "-1") +add_persistence_representation_creation_utility(create_p_h_m_weighted_by_distance_from_diagonal "10" "-1" "-1" "4" "-1") +add_persistence_representation_creation_utility(create_p_h_m_weighted_by_squared_diag_distance "10" "-1" "-1" "4" "-1") +# Need to set grid min and max for further average, distance and scalar_product +add_persistence_representation_creation_utility(create_persistence_heat_maps "10" "0" "35" "10" "-1") + +add_persistence_representation_plot_utility(plot_persistence_heat_map ".mps") + +add_persistence_representation_function_utility(average_persistence_heat_maps ".mps") +add_persistence_representation_function_utility(compute_distance_of_persistence_heat_maps ".mps" "1") +add_persistence_representation_function_utility(compute_scalar_product_of_persistence_heat_maps ".mps") diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp index 4e81375a..6739e0b6 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp @@ -29,21 +29,20 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program computes average persistence landscape of persistence landscapes created based on " - "persistence diagrams provided as an input. Please call this program with the names of files with " - "persistence diagrams \n"; - std::vector<const char*> filenames; + std::cout << "This program computes average of persistence heat maps stored in files (the files needs to be " + << "created beforehand).\n" + << "The parameters of this programs are names of files with persistence heat maps.\n"; - if (argc == 1) { - std::cout << "No input files given, the program will now terminate \n"; + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } + std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; std::vector<Persistence_heat_maps*> maps; for (size_t i = 0; i != filenames.size(); ++i) { Persistence_heat_maps* l = new Persistence_heat_maps; @@ -53,13 +52,12 @@ int main(int argc, char** argv) { Persistence_heat_maps av; av.compute_average(maps); - av.print_to_file("average.mps"); for (size_t i = 0; i != filenames.size(); ++i) { delete maps[i]; } - std::cout << "Done \n"; + std::cout << "Average can be found in 'average.mps' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp index befb0837..ed8278a2 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp @@ -31,11 +31,11 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program computes distance of persistence heat maps stored in a file (the file needs to be created " - "beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " - "maps. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this program are names of files with persistence heat maps.\n"; + std::cout << "This program computes distance of persistence heat maps stored in files (the files needs to be " + << "created beforehand).\n" + << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " + << "maps. For L^infty distance choose p = -1. \n" + << "The remaining parameters of this program are names of files with persistence heat maps.\n"; if (argc < 3) { std::cout << "Wrong number of parameters, the program will now terminate \n"; @@ -78,7 +78,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.mps"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -89,5 +89,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.mps' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp index c684a336..63626853 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp @@ -30,9 +30,14 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program computes scalar product of persistence landscapes stored in a file (the file needs to be " - "created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + std::cout << "This program computes scalar product of persistence heat maps stored in a file (the file needs to be " + << "created beforehand). \n" + << "The parameters of this programs are names of files with persistence heat maps.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { @@ -64,7 +69,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("scalar_product"); + out.open("scalar_product.mps"); for (size_t i = 0; i != scalar_product.size(); ++i) { for (size_t j = 0; j != scalar_product.size(); ++j) { std::cout << scalar_product[i][j] << " "; @@ -75,5 +80,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'scalar_product.mps' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp index 2bf185a3..b4a1daa5 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp @@ -29,25 +29,25 @@ using arc_tan_of_persistence_of_point = Gudhi::Persistence_representations::arc_tan_of_persistence_of_point; using Persistence_heat_maps = - Gudhi::Persistence_representations::Persistence_heat_maps<arc_tan_of_persistence_of_point>; + Gudhi::Persistence_representations::Persistence_heat_maps<arc_tan_of_persistence_of_point>; int main(int argc, char** argv) { - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " - "weighted by the arc tangential of their persistence.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) " + << "provided as an input.The Gaussian kernels are weighted by the arc tangential of their persistence.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -68,9 +68,7 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); @@ -79,6 +77,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".mps"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp index ec9477f1..c50f9ddb 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp @@ -28,26 +28,26 @@ #include <vector> using distance_from_diagonal_scaling = Gudhi::Persistence_representations::distance_from_diagonal_scaling; -using Persistence_heat_maps = - Gudhi::Persistence_representations::Persistence_heat_maps<distance_from_diagonal_scaling>; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<distance_from_diagonal_scaling>; int main(int argc, char** argv) { - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " - "weighted by the distance of a center from the diagonal.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) " + << "provided as an input.The Gaussian kernels are weighted by the distance of a center from the " + << "diagonal.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -68,9 +68,7 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); @@ -79,6 +77,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".mps"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp index ffec8b3d..59ff3c24 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp @@ -28,27 +28,28 @@ #include <vector> using squared_distance_from_diagonal_scaling = - Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling; + Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling; using Persistence_heat_maps = - Gudhi::Persistence_representations::Persistence_heat_maps<squared_distance_from_diagonal_scaling>; + Gudhi::Persistence_representations::Persistence_heat_maps<squared_distance_from_diagonal_scaling>; int main(int argc, char** argv) { - std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " - "weighted by the square of distance of a center from the diagonal.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) " + << "provided as an input.The Gaussian kernels are weighted by the square of distance of a center from the " + << "diagonal.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -69,9 +70,7 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); @@ -80,6 +79,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".mps"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp index db2f0008..25cd1067 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -31,21 +31,22 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program creates persistence heat map of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; + std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) " + << "provided as an input.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If your input file contains persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -64,17 +65,14 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + std::cout << "Creating a heat map based on file : " << filenames[i] << std::endl; Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); std::stringstream ss; ss << filenames[i] << ".mps"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp index 6aefbb00..97ddb8f0 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp @@ -30,21 +30,22 @@ using PSSK = Gudhi::Persistence_representations::PSSK; int main(int argc, char** argv) { - std::cout << "This program creates PSSK of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - "of pixels \n"; - std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " - "persistence heat maps."; - std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " - "procedure please provide the dimension of persistence you want to use."; - std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates PSSK files (*.pssk) of persistence diagrams files (*.pers) " + << "provided as an input.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + << "of pixels.\n" + << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " + << "the PSSK." + << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 7) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -65,17 +66,14 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence heat maps...\n"; std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); - for (size_t i = 0; i != filenames.size(); ++i) { - std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + std::cout << "Creating a PSSK based on a file : " << filenames[i] << std::endl; PSSK l(filenames[i], filter, size_of_grid, min_, max_, dimension); std::stringstream ss; ss << filenames[i] << ".pssk"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp index a7c9f2d8..63711d83 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -29,8 +29,12 @@ using constant_scaling_function = Gudhi::Persistence_representations::constant_s using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; int main(int argc, char** argv) { - std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). " - "Please call the code with the name of a landscape file \n"; + std::cout << "This program creates a gnuplot script from a persistence heat maps stored in a file (the file needs " + << "to be created beforehand). Please call the code with the name of a single heat maps file \n"; + if (argc != 2) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } Persistence_heat_maps l; l.load_from_file(argv[1]); l.plot(argv[1]); diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps b/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps deleted file mode 100644 index b7643887..00000000 --- a/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps +++ /dev/null @@ -1,11 +0,0 @@ -0.93 8.0707 -0.0492104 0.03889 0.0190956 0.00603584 0.00131569 0.000120934 2.10152e-05 0 0 0 -0.0650745 0.0539306 0.0296488 0.011745 0.00357642 0.000695928 0.000120934 0 0 0 -0.0572665 0.0559446 0.0409942 0.0230905 0.00937173 0.00242903 0.000422102 0 0 0 -0.0409942 0.0559656 0.0573874 0.0408475 0.0192639 0.00628964 0.00178718 0.000422102 0.000120934 2.10152e-05 -0.0296488 0.0540515 0.0657704 0.0519133 0.0283092 0.0132056 0.00628964 0.00242903 0.000695928 0.000120934 -0.0190956 0.0393121 0.0516395 0.0465955 0.0359385 0.0283092 0.0192639 0.00937173 0.00357642 0.00131569 -0.00847814 0.0188418 0.0281882 0.0358964 0.0465955 0.0519133 0.0408475 0.0230905 0.011745 0.00603584 -0.00242903 0.00628964 0.0132056 0.0281882 0.0516395 0.0657704 0.0573874 0.0409942 0.0296488 0.0190956 -0.000422102 0.00178718 0.00628964 0.0188418 0.0393121 0.0540515 0.0559656 0.0559446 0.0539306 0.03889 -0 0.000422102 0.00242903 0.00847814 0.0190956 0.0296488 0.0409942 0.0572665 0.0650745 0.0492104 diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt index 105b7efb..897e12a3 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt @@ -1,46 +1,32 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_representations_intervals_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") -add_executable ( plot_persistence_intervals plot_persistence_intervals.cpp ) -target_link_libraries( plot_persistence_intervals ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_persistence_intervals COMMAND $<TARGET_FILE:plot_persistence_intervals> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( compute_birth_death_range_in_persistence_diagram compute_birth_death_range_in_persistence_diagram.cpp ) -target_link_libraries( compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_birth_death_range_in_persistence_diagram COMMAND $<TARGET_FILE:compute_birth_death_range_in_persistence_diagram> - "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") +add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) -add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) -target_link_libraries( compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY}) +add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1") -add_test(NAME compute_number_of_dominant_intervals COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" "-1" "2") +add_persistence_representation_plot_utility(plot_persistence_intervals "") +add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "") -add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) -target_link_libraries( plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY}) +add_persistence_representation_creation_utility(compute_birth_death_range_in_persistence_diagram "-1") -add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" "2") -add_executable ( plot_persistence_Betti_numbers plot_persistence_Betti_numbers.cpp ) -target_link_libraries( plot_persistence_Betti_numbers ${Boost_SYSTEM_LIBRARY}) +add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) +add_test(NAME Persistence_representation_utilities_compute_number_of_dominant_intervals + COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals> + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1" "2") -add_test(NAME plot_persistence_Betti_numbers COMMAND $<TARGET_FILE:plot_persistence_Betti_numbers> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp ) - target_link_libraries( compute_bottleneck_distance ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) target_link_libraries(compute_bottleneck_distance ${TBB_LIBRARIES}) endif(TBB_FOUND) - - add_test(NAME compute_bottleneck_distance COMMAND $<TARGET_FILE:compute_bottleneck_distance> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + add_test(NAME Persistence_representation_utilities_compute_bottleneck_distance + COMMAND $<TARGET_FILE:compute_bottleneck_distance> + "-1" + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp index 66fa31ca..9102da79 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> #include <iostream> @@ -31,16 +30,21 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { - std::cout << "This program compute the range of birth and death times of persistence pairs in diagrams provided as " - "an input. \n"; - std::cout << "The first parameter of the program is the dimension of persistence to be used. If your file contains "; - std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence " - "pairs you want to use. If your input files consist only "; - std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; - std::cout << "The remaining parameters of the program are the names of files with persistence diagrams. \n"; + std::cout << "This program computes the range of birth and death times of persistence pairs in diagrams provided as " + << "an input.\n" + << "The first parameter is the dimension of persistence to be used to create persistence intervals. " + << "If your file contains the information about dimension of persistence pairs, please provide here the " + << "dimension of persistence pairs you want to use. " + << "If your input files consist only of birth-death pairs, please set this first parameter to -1.\n" + << "The remaining parameters of the program are the names of files with persistence diagrams.\n"; + + if (argc < 3) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } - int dim = atoi(argv[1]); unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[1]); if (dim >= 0) { dimension = (unsigned)dim; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp index 0b1b526d..c8290845 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -21,7 +21,6 @@ */ #include <gudhi/Persistence_intervals_with_distances.h> -#include <gudhi/read_persistence_from_file.h> #include <iostream> #include <sstream> @@ -31,21 +30,21 @@ using Persistence_intervals_with_distances = Gudhi::Persistence_representations::Persistence_intervals_with_distances; int main(int argc, char** argv) { - std::cout << "This program compute the bottleneck distance of persistence diagrams stored in a files. \n"; - std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence " - "landscapes. If your file contains "; - std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence " - "pairs you want to use. If your input files consist only "; - std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence diagrams.\n"; + std::cout << "This program computes the bottleneck distance of persistence pairs in diagrams provided as " + << "an input.\n" + << "The first parameter is the dimension of persistence to be used to create persistence intervals. " + << "If your file contains the information about dimension of persistence pairs, please provide here the " + << "dimension of persistence pairs you want to use. " + << "If your input files consist only of birth-death pairs, please set this first parameter to -1.\n" + << "The remaining parameters of the program are the names of files with persistence diagrams.\n"; if (argc < 3) { std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } - int dim = atoi(argv[1]); unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[1]); if (dim >= 0) { dimension = (unsigned)dim; } @@ -80,7 +79,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.itv"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -91,5 +90,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.itv' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp index 1286ca57..b3d126f0 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> #include <iostream> diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp index d68f4584..ccb5b645 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> #include <iostream> @@ -31,30 +30,34 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { - std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter " - "of this program. \n"; - if (argc != 3) { + std::cout << "This program computes a histogram of barcode's length. A number of bins in the histogram is a " + << "parameter of this program. \n"; + if ((argc != 3) && (argc != 4)) { std::cout << "To run this program, please provide the name of a file with persistence diagram and number of " - "dominant intervals you would like to get \n"; - std::cout << "The third parameter of a program is the dimension of the persistence that is to be used. If your " - "file contains only birth-death pairs, you can skip this parameter\n"; + << "dominant intervals you would like to get. Set a negative number dominant intervals value " + << "If your file contains only birth-death pairs.\n" + << "The third parameter is the dimension of the persistence that is to be used. If your " + << "file contains only birth-death pairs, you can skip this parameter\n"; return 1; } - unsigned dimension = std::numeric_limits<unsigned>::max(); - int dim = -1; - if (argc > 2) { - dim = atoi(argv[2]); + + unsigned dominant_interval_number = std::numeric_limits<unsigned>::max(); + int nbr = atoi(argv[2]); + if (nbr >= 0) { + dominant_interval_number = static_cast<unsigned>(nbr); } - if (dim >= 0) { - dimension = (unsigned)dim; + + int persistence_dimension = -1; + if (argc == 4) { + persistence_dimension = atoi(argv[3]); } - Persistence_intervals p(argv[1], dimension); - std::vector<std::pair<double, double> > dominant_intervals = p.dominant_intervals(atoi(argv[2])); + Persistence_intervals p(argv[1], dominant_interval_number); + std::vector<std::pair<double, double> > dominant_intervals = p.dominant_intervals(persistence_dimension); std::vector<size_t> histogram = p.histogram_of_lengths(10); std::stringstream gnuplot_script; - gnuplot_script << argv[1] << "_Gnuplot_script"; + gnuplot_script << argv[1] << "_GnuplotScript"; std::ofstream out; out.open(gnuplot_script.str().c_str()); @@ -66,7 +69,9 @@ int main(int argc, char** argv) { out << histogram[i] << std::endl; } out << std::endl; - std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; out.close(); + + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp index da2b9319..b433c2b3 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -20,7 +20,6 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> #include <iostream> @@ -31,29 +30,24 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { - std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with " - "persistence intervals. \n"; - std::cout << "The second optional parameter of a program is the dimension of the persistence that is to be used. If " - "your file contains only birth-death pairs, you can skip this parameter\n"; - if (argc < 2) { - std::cout << "To run this program, please provide the name of a file with persistence diagram and number of " - "dominant intervals you would like to get \n"; + if ((argc != 3) && (argc != 2)) { + std::cout << "This program creates a gnuplot script of Betti numbers from a single persistence diagram file" + << "(*.pers).\n" + << "To run this program, please provide the name of a file with persistence diagram.\n" + << "The second optional parameter of a program is the dimension of the persistence that is to be used. " + << "If your file contains only birth-death pairs, you can skip this parameter.\n"; return 1; } + unsigned dimension = std::numeric_limits<unsigned>::max(); int dim = -1; - if (argc > 2) { + if (argc == 3) { dim = atoi(argv[2]); } if (dim >= 0) { dimension = (unsigned)dim; } - std::stringstream gnuplot_script; - gnuplot_script << argv[1] << "_Gnuplot_script"; - std::ofstream out; - out.open(gnuplot_script.str().c_str()); - Persistence_intervals p(argv[1], dimension); std::vector<std::pair<double, size_t> > pbns = p.compute_persistent_betti_numbers(); @@ -69,6 +63,11 @@ int main(int argc, char** argv) { xRangeEnd += (xRangeEnd - xRangeBegin) / 100.0; yRangeEnd += yRangeEnd / 100; + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_GnuplotScript"; + std::ofstream out; + out.open(gnuplot_script.str().c_str()); + out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << std::endl; out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << std::endl; out << "plot '-' using 1:2 notitle with lp " << std::endl; @@ -81,7 +80,8 @@ int main(int argc, char** argv) { out << std::endl; out.close(); - std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" + << gnuplot_script.str().c_str() << "\'\"" << std::endl; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp index e7d29e84..33387802 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -20,9 +20,7 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> #include <gudhi/Persistence_intervals.h> -#include <gudhi/read_persistence_from_file.h> #include <iostream> #include <limits> @@ -32,15 +30,16 @@ using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { - if (argc < 2) { - std::cout << "To run this program, please provide the name of a file with persistence diagram \n"; - std::cout << "The second optional parameter of a program is the dimension of the persistence that is to be used. " - "If your file contains only birth-death pairs, you can skip this parameter\n"; + if ((argc != 3) && (argc != 2)) { + std::cout << "This program creates a gnuplot script from a single persistence diagram file (*.pers).\n" + << "To run this program, please provide the name of a file with persistence diagram.\n" + << "The second optional parameter of a program is the dimension of the persistence that is to be used. " + << "If your file contains only birth-death pairs, you can skip this parameter.\n"; return 1; } unsigned dimension = std::numeric_limits<unsigned>::max(); int dim = -1; - if (argc > 2) { + if (argc == 3) { dim = atoi(argv[2]); } if (dim >= 0) { diff --git a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt index baf8de3c..d7087ed8 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt @@ -1,38 +1,10 @@ cmake_minimum_required(VERSION 2.6) -project(Persistence_representations_lanscapes_utilities) +project(Persistence_representations_landscapes_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") +add_persistence_representation_creation_utility(create_landscapes "-1") -add_executable ( create_landscapes create_landscapes.cpp ) -target_link_libraries(create_landscapes ${Boost_SYSTEM_LIBRARY}) +add_persistence_representation_plot_utility(plot_landscapes ".land") -# Will create simple_diagram.txt.land -add_test(NAME create_landscapes COMMAND $<TARGET_FILE:create_landscapes> - "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( average_landscapes average_landscapes.cpp ) -target_link_libraries(average_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME average_landscapes COMMAND $<TARGET_FILE:average_landscapes> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( plot_landscapes plot_landscapes.cpp ) -target_link_libraries(plot_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_landscapes COMMAND $<TARGET_FILE:plot_landscapes> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( compute_distance_of_landscapes compute_distance_of_landscapes.cpp ) -target_link_libraries(compute_distance_of_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_distance_of_landscapes COMMAND $<TARGET_FILE:compute_distance_of_landscapes> - "1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land") - -add_executable ( compute_scalar_product_of_landscapes compute_scalar_product_of_landscapes.cpp ) -target_link_libraries(compute_scalar_product_of_landscapes ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_scalar_product_of_landscapes COMMAND $<TARGET_FILE:compute_scalar_product_of_landscapes> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land") +add_persistence_representation_function_utility(average_landscapes ".land") +add_persistence_representation_function_utility(compute_distance_of_landscapes ".land" "1") +add_persistence_representation_function_utility(compute_scalar_product_of_landscapes ".land") diff --git a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp index 526130e9..1a59be8c 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp @@ -28,14 +28,13 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program computes average persistence landscape of persistence landscapes created based on " - "persistence diagrams provided as an input (you must create them first).\n"; - std::cout << "Please call this program with the names of files with persistence landscapes. The program will create " - "a persistence landscape which will be their average \n"; + std::cout << "This program computes average of persistence landscapes stored in files (the files needs to be " + << "created beforehand).\n" + << "The parameters of this programs are names of files with persistence landscapes.\n"; std::vector<const char*> filenames; - if (argc == 1) { - std::cout << "No input files given, the program will now terminate \n"; + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } @@ -43,7 +42,6 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; std::vector<Persistence_landscape*> lands; for (size_t i = 0; i != filenames.size(); ++i) { Persistence_landscape* l = new Persistence_landscape; @@ -60,7 +58,6 @@ int main(int argc, char** argv) { delete lands[i]; } - std::cout << "Done \n"; - + std::cout << "Average can be found in 'average.land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp index b3881d6a..5062f521 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -30,11 +30,11 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program compute distance of persistence landscapes stored in a file (the file needs to be created " - "beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the given " - "landscapes. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence landscapes."; + std::cout << "This program computes distance of persistence landscapes stored in files (the files needs to be " + << "created beforehand).\n" + << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " + << "maps. For L^infty distance choose p = -1. \n" + << "The remaining parameters of this program are names of files with persistence landscapes.\n"; if (argc < 3) { std::cout << "Wrong number of parameters, the program will now terminate \n"; @@ -54,7 +54,6 @@ int main(int argc, char** argv) { std::vector<Persistence_landscape> landscaspes; landscaspes.reserve(filenames.size()); for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - std::cout << "Loading persistence landscape from a file : " << filenames[file_no] << std::endl; Persistence_landscape l; l.load_landscape_from_file(filenames[file_no]); landscaspes.push_back(l); @@ -78,7 +77,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.land"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -89,5 +88,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp index 8dad7b4d..5b5e9fa3 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp @@ -29,9 +29,14 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be " - "created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + std::cout << "This program computes scalar product of persistence landscapes stored in a file (the file needs to be " + << "created beforehand). \n" + << "The parameters of this programs are names of files with persistence landscapes.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { @@ -40,7 +45,6 @@ int main(int argc, char** argv) { std::vector<Persistence_landscape> landscaspes; landscaspes.reserve(filenames.size()); for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - std::cout << "Reading persistence landscape from a file : " << filenames[file_no] << std::endl; Persistence_landscape l; l.load_landscape_from_file(filenames[file_no]); landscaspes.push_back(l); @@ -64,7 +68,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("scalar_product"); + out.open("scalar_product.land"); for (size_t i = 0; i != scalar_product.size(); ++i) { for (size_t j = 0; j != scalar_product.size(); ++j) { std::cout << scalar_product[i][j] << " "; @@ -75,5 +79,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'scalar_product.land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp index 325081d1..6030e994 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp @@ -30,13 +30,20 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program creates persistence landscapes of diagrams provided as an input. \n"; - std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence " - "landscapes. If your file contains "; - std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence " - "pairs you want to use. If your input files consist only "; - std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; - std::cout << "The remaining parameters of the program are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence landscapes files (*.land) of persistence diagrams files (*.pers) " + << "provided as an input.\n" + << "The first parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a first parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 3) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; int dim = atoi(argv[1]); unsigned dimension = std::numeric_limits<unsigned>::max(); @@ -47,13 +54,12 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a landscape based on file : " << filenames[i] << std::endl; Persistence_landscape l(filenames[i], dimension); std::stringstream ss; ss << filenames[i] << ".land"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp index ebdb20a1..c797a7a8 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp @@ -28,16 +28,16 @@ using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { - std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). " - "Please call the code with the name of a landscape file \n"; + std::cout << "This program creates a gnuplot script from a persistence landscape stored in a file (the file needs " + << "to be created beforehand). Please call the code with the name of a single landscape file.\n"; + if (argc != 2) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + Persistence_landscape l; l.load_landscape_from_file(argv[1]); - - std::stringstream ss; - ss << argv[1] << "_gnuplot_script"; - l.plot(ss.str().c_str()); - - std::cout << "Done \n"; + l.plot(argv[1]); return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land b/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land deleted file mode 100644 index b99d2f62..00000000 --- a/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land +++ /dev/null @@ -1,13 +0,0 @@ -#lambda_0 -1 0 -1.5 0.5 -2 0 -3 0 -3.5 0.5 -4 0 -5 0 -5.5 0.5 -6 0 -7 0 -7.5 0.5 -8 0 diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt index 55a4fd50..c5ea4bbf 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt @@ -1,38 +1,11 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_representations_lanscapes_on_grid_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") +# Need to set grid min and max for further average, distance and scalar_product +add_persistence_representation_creation_utility(create_landscapes_on_grid "100" "0" "35" "-1") -add_executable ( create_landscapes_on_grid create_landscapes_on_grid.cpp ) -target_link_libraries(create_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) +add_persistence_representation_plot_utility(plot_landscapes_on_grid ".g_land") -# Will create simple_diagram.txt.land -add_test(NAME create_landscapes_on_grid COMMAND $<TARGET_FILE:create_landscapes_on_grid> - "100" "-1" "-1" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( average_landscapes_on_grid average_landscapes_on_grid.cpp ) -target_link_libraries(average_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME average_landscapes_on_grid COMMAND $<TARGET_FILE:average_landscapes_on_grid> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") - -add_executable ( plot_landscapes_on_grid plot_landscapes_on_grid.cpp ) -target_link_libraries(plot_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_landscapes_on_grid COMMAND $<TARGET_FILE:plot_landscapes_on_grid> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") - -add_executable ( compute_distance_of_landscapes_on_grid compute_distance_of_landscapes_on_grid.cpp ) -target_link_libraries(compute_distance_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_distance_of_landscapes_on_grid COMMAND $<TARGET_FILE:compute_distance_of_landscapes_on_grid> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") - -add_executable ( compute_scalar_product_of_landscapes_on_grid compute_scalar_product_of_landscapes_on_grid.cpp ) -target_link_libraries(compute_scalar_product_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_scalar_product_of_landscapes_on_grid COMMAND $<TARGET_FILE:compute_scalar_product_of_landscapes_on_grid> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") +add_persistence_representation_function_utility(average_landscapes_on_grid ".g_land") +add_persistence_representation_function_utility(compute_distance_of_landscapes_on_grid ".g_land" "1") +add_persistence_representation_function_utility(compute_scalar_product_of_landscapes_on_grid ".g_land") diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp index d50118a0..0b098d1a 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp @@ -28,21 +28,20 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program computes average persistence landscape on grid of persistence landscapes on grid created " - "based on persistence diagrams provided as an input. Please call this program with the names of files " - "with persistence diagrams \n"; - std::vector<const char*> filenames; + std::cout << "This program computes average of persistence landscapes on grid stored in files (the files needs to " + << "be created beforehand).\n" + << "The parameters of this programs are names of files with persistence landscapes on grid.\n"; - if (argc == 1) { - std::cout << "No input files given, the program will now terminate \n"; + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } + std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; std::vector<Persistence_landscape_on_grid*> lands; for (size_t i = 0; i != filenames.size(); ++i) { Persistence_landscape_on_grid* l = new Persistence_landscape_on_grid; @@ -59,7 +58,6 @@ int main(int argc, char** argv) { delete lands[i]; } - std::cout << "Done \n"; - + std::cout << "Average can be found in 'average.g_land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp index 859c6991..fd0fcd15 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp @@ -30,11 +30,11 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program compute distance of persistence landscapes on grid stored in a file (the file needs to be " - "created beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the landscapes " - "on grid. For L^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence landscapes on grid.\n"; + std::cout << "This program computes distance of persistence landscapes on grid stored in files (the files needs to " + << "be created beforehand).\n" + << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " + << "maps. For L^infty distance choose p = -1. \n" + << "The remaining parameters of this program are names of files with persistence landscapes on grid.\n"; if (argc < 3) { std::cout << "Wrong number of parameters, the program will now terminate \n"; @@ -77,7 +77,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.g_land"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -88,5 +88,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.g_land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp index e95bf8ad..01de3dee 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp @@ -29,9 +29,15 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program compute scalar product of persistence landscapes on grid stored in a file (the file needs " - "to be created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence landscapes on grid.\n"; + std::cout + << "This program computes scalar product of persistence landscapes on grid stored in a file (the file needs to " + << "be created beforehand). \n" + << "The parameters of this programs are names of files with persistence landscapes on grid.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { @@ -63,7 +69,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("scalar_product"); + out.open("scalar_product.g_land"); for (size_t i = 0; i != scalar_product.size(); ++i) { for (size_t j = 0; j != scalar_product.size(); ++j) { std::cout << scalar_product[i][j] << " "; @@ -74,5 +80,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'scalar_product.g_land' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp index 8d747c14..78e8ef57 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp @@ -30,18 +30,20 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program creates persistence landscape on grid of diagrams provided as an input.\n"; - std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; - std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " - "based on the data, set them both to -1 \n"; - std::cout << "The fourth parameter of the program is the dimension of persistence to be used to construct " - "persistence landscape on a grid. If your file contains "; - std::cout << "the information about dimension of birth-death pairs, please provide here the dimension of intervals " - "you want to use. If your input files consist only "; - std::cout << "of birth-death pairs, please set the fourth parameter to -1 \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "This program creates persistence landscapes on grid files (*.g_land) of persistence diagrams files " + << "(*.pers) provided as an input.\n" + << "The first parameter of a program is an integer, a size of a grid.\n" + << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + << "based on the data, set them both to -1 \n" + << "The fourth parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a fourth parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the fourth parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; - if (argc < 5) { + if (argc < 6) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } @@ -60,7 +62,6 @@ int main(int argc, char** argv) { filenames.push_back(argv[i]); } - std::cout << "Creating persistence landscapes...\n"; for (size_t i = 0; i != filenames.size(); ++i) { std::cout << "Creating persistence landscape on a grid based on a file : " << filenames[i] << std::endl; Persistence_landscape_on_grid l; @@ -74,6 +75,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".g_land"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp index 42822a01..dddb3615 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp @@ -28,20 +28,17 @@ using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { - std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created " - "beforehand). Please call the code with the name of a landscape on grid file \n"; - if (argc == 1) { - std::cout << "Wrong parameters of a program call, the program will now terminate \n"; + std::cout << "This program creates a gnuplot script from a persistence landscape on grid stored in a file (the file " + << "needs to be created beforehand). Please call the code with the name of a single landscape on grid file" + << ".\n"; + if (argc != 2) { + std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; } + Persistence_landscape_on_grid l; l.load_landscape_from_file(argv[1]); - - std::stringstream ss; - ss << argv[1] << "_gnuplot_script"; - l.plot(ss.str().c_str()); - - std::cout << "Done \n"; + l.plot(argv[1]); return 0; } diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land deleted file mode 100644 index dc53b932..00000000 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land +++ /dev/null @@ -1,104 +0,0 @@ -1 -8 -101 - -0.07 -0.14 -0.21 -0.28 -0.35 -0.42 -0.49 -0.42 -0.35 -0.28 -0.21 -0.14 -0.07 - - - - - - - - - - - - - - - -0.07 -0.14 -0.21 -0.28 -0.35 -0.42 -0.49 -0.42 -0.35 -0.28 -0.21 -0.14 -0.07 - - - - - - - - - - - - - - - - -0.07 -0.14 -0.21 -0.28 -0.35 -0.42 -0.49 -0.42 -0.35 -0.28 -0.21 -0.14 -0.07 - - - - - - - - - - - - - - - -0.07 -0.14 -0.21 -0.28 -0.35 -0.42 -0.49 -0.42 -0.35 -0.28 -0.21 -0.14 -0.07 - - diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt index e3d1013b..a401c955 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt @@ -1,38 +1,10 @@ cmake_minimum_required(VERSION 2.6) project(Persistence_vectors_utilities) -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") +add_persistence_representation_creation_utility(create_persistence_vectors "-1") -add_executable ( create_persistence_vectors create_persistence_vectors.cpp ) -target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) +add_persistence_representation_plot_utility(plot_persistence_vectors ".vect") -# Will create simple_diagram.txt.vect -add_test(NAME create_persistence_vectors COMMAND $<TARGET_FILE:create_persistence_vectors> - "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") - -add_executable ( average_persistence_vectors average_persistence_vectors.cpp ) -target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME average_persistence_vectors COMMAND $<TARGET_FILE:average_persistence_vectors> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") - -add_executable ( compute_distance_of_persistence_vectors compute_distance_of_persistence_vectors.cpp ) -target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_distance_of_persistence_vectors COMMAND $<TARGET_FILE:compute_distance_of_persistence_vectors> - "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") - -add_executable ( compute_scalar_product_of_persistence_vectors compute_scalar_product_of_persistence_vectors.cpp ) -target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME compute_scalar_product_of_persistence_vectors COMMAND $<TARGET_FILE:compute_scalar_product_of_persistence_vectors> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") - -add_executable ( plot_persistence_vectors plot_persistence_vectors.cpp ) -target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) - -add_test(NAME plot_persistence_vectors COMMAND $<TARGET_FILE:plot_persistence_vectors> - "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") +add_persistence_representation_function_utility(average_persistence_vectors ".vect") +add_persistence_representation_function_utility(compute_distance_of_persistence_vectors ".vect" "1") +add_persistence_representation_function_utility(compute_scalar_product_of_persistence_vectors ".vect") diff --git a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp index 366ee2bc..0144e76f 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -26,25 +26,23 @@ #include <vector> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { - std::cout << "This program computes average persistence vector of persistence vectors created based on persistence " - "diagrams provided as an input. \n"; - std::cout << "Please call this program with the names of files with persistence diagrams \n"; - std::vector<const char*> filenames; + std::cout << "This program computes average of persistence vectors stored in files (the files needs to " + << "be created beforehand).\n" + << "The parameters of this programs are names of files with persistence vectors.\n"; - if (argc == 1) { - std::cout << "No input files given, the program will now terminate \n"; + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; return 1; } + std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { filenames.push_back(argv[i]); } - std::cout << "Reading persistence vectors...\n"; std::vector<Vector_distances_in_diagram*> lands; for (size_t i = 0; i != filenames.size(); ++i) { Vector_distances_in_diagram* l = new Vector_distances_in_diagram; diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp index 3aed297e..7e66d25e 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -28,8 +28,7 @@ #include <vector> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created " @@ -79,7 +78,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("distance"); + out.open("distance.vect"); for (size_t i = 0; i != distance.size(); ++i) { for (size_t j = 0; j != distance.size(); ++j) { std::cout << distance[i][j] << " "; @@ -90,5 +89,6 @@ int main(int argc, char** argv) { } out.close(); + std::cout << "Distance can be found in 'distance.vect' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp index d9ad4360..303c6e3e 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -28,13 +28,17 @@ #include <vector> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { - std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be " - "created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence vectors.\n"; + std::cout << "This program computes scalar product of persistence vectors stored in a file (the file needs to " + << "be created beforehand). \n" + << "The parameters of this programs are names of files with persistence vectors.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } std::vector<const char*> filenames; for (int i = 1; i < argc; ++i) { @@ -66,7 +70,7 @@ int main(int argc, char** argv) { // and now output the result to the screen and a file: std::ofstream out; - out.open("scalar_product"); + out.open("scalar_product.vect"); for (size_t i = 0; i != scalar_product.size(); ++i) { for (size_t j = 0; j != scalar_product.size(); ++j) { std::cout << scalar_product[i][j] << " "; @@ -76,5 +80,7 @@ int main(int argc, char** argv) { out << std::endl; } out.close(); + + std::cout << "Distance can be found in 'scalar_product.vect' file\n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp index b618ca67..cc5e5393 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -28,17 +28,24 @@ #include <vector> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { - std::cout << "This program creates persistence vectors of diagrams provided as an input. The first parameter of this " - "program is a dimension of persistence "; - std::cout << " that will be used in creation of the persistence vectors. If our input files contain persistence " - "pairs of various dimension, as a second parameter of the "; - std::cout << " procedure please provide the dimension of persistence you want to use. If in your file there are only " - "birth-death pairs of the same dimension, set the first parameter to -1." - << std::endl; + std::cout << "This program creates persistence vectors files (*.vect) of persistence diagrams files (*.pers) " + << "provided as an input.\n" + << "The first parameter of this program is a dimension of persistence that will be used in creation of " + << "the persistence heat maps." + << "If your input files contains persistence pairs of various dimension, as a first parameter of the " + << "procedure please provide the dimension of persistence you want to use." + << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " + << "-1.\n" + << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 3) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; int dim = atoi(argv[1]); unsigned dimension = std::numeric_limits<unsigned>::max(); @@ -58,6 +65,5 @@ int main(int argc, char** argv) { ss << filenames[i] << ".vect"; l.print_to_file(ss.str().c_str()); } - std::cout << "Done \n"; return 0; } diff --git a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp index e52b8f7d..aa33107d 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -26,8 +26,7 @@ #include <sstream> using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; int main(int argc, char** argv) { std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the " diff --git a/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect deleted file mode 100644 index 1d4eeaaf..00000000 --- a/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect +++ /dev/null @@ -1 +0,0 @@ -0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107
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