From 4ba017094d3246cd8fe917a6c45443ba25d74b1d Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 2 Jun 2017 14:00:20 +0000 Subject: Fix some cpplint git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2502 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0a6422b0fa27105b9aaba743371da3328d9039be --- .../example/CMakeLists.txt | 7 ++----- .../example/persistence_heat_maps.cpp | 23 ++++++++++------------ .../example/persistence_intervals.cpp | 4 +--- .../example/persistence_landscape.cpp | 3 +-- .../example/persistence_landscape_on_grid.cpp | 3 +-- .../example/persistence_vectors.cpp | 13 +++++------- .../test/persistence_heat_maps_test.cpp | 2 +- .../test/persistence_intervals_test.cpp | 2 +- .../persistence_intervals_with_distances_test.cpp | 2 +- .../test/persistence_lanscapes_on_grid_test.cpp | 2 +- .../test/persistence_lanscapes_test.cpp | 2 +- .../utilities/CMakeLists.txt | 6 ++++++ .../utilities/persistence_heat_maps/CMakeLists.txt | 3 +-- .../average_persistence_heat_maps.cpp | 12 +++++------ .../compute_distance_of_persistence_heat_maps.cpp | 10 +++++----- ...ute_scalar_product_of_persistence_heat_maps.cpp | 10 +++++----- ...h_m_weighted_by_arctan_of_their_persistence.cpp | 12 +++++------ ...te_p_h_m_weighted_by_distance_from_diagonal.cpp | 12 +++++------ ...ate_p_h_m_weighted_by_squared_diag_distance.cpp | 12 +++++------ .../create_persistence_heat_maps.cpp | 11 +++++------ .../persistence_heat_maps/create_pssk.cpp | 7 +++---- .../plot_persistence_heat_map.cpp | 8 ++++---- ...te_birth_death_range_in_persistence_diagram.cpp | 3 +-- .../compute_bottleneck_distance.cpp | 5 ++--- .../compute_number_of_dominant_intervals.cpp | 3 +-- .../plot_histogram_of_intervals_lengths.cpp | 3 +-- .../plot_persistence_Betti_numbers.cpp | 3 +-- .../plot_persistence_intervals.cpp | 7 ++----- .../persistence_landscapes/average_landscapes.cpp | 5 ++--- .../compute_distance_of_landscapes.cpp | 6 +++--- .../compute_scalar_product_of_landscapes.cpp | 5 ++--- .../persistence_landscapes/create_landscapes.cpp | 5 ++--- .../persistence_landscapes/plot_landscapes.cpp | 5 ++--- .../average_landscapes_on_grid.cpp | 6 +++--- .../compute_distance_of_landscapes_on_grid.cpp | 5 ++--- ...ompute_scalar_product_of_landscapes_on_grid.cpp | 5 ++--- .../create_landscapes_on_grid.cpp | 5 ++--- .../plot_landscapes_on_grid.cpp | 5 ++--- 38 files changed, 108 insertions(+), 134 deletions(-) create mode 100644 src/Persistence_representations/utilities/CMakeLists.txt (limited to 'src/Persistence_representations') diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index 3c783d36..3357017a 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -1,27 +1,24 @@ cmake_minimum_required(VERSION 2.6) -project(GUDHI_STAT) +project(Persistence_representations_example) file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_executable ( persistence_landscape_on_grid persistence_landscape_on_grid.cpp ) target_link_libraries(persistence_landscape_on_grid ${Boost_SYSTEM_LIBRARY}) add_test ( persistence_landscape_on_grid ${CMAKE_CURRENT_BINARY_DIR}/persistence_landscape_on_grid ) -file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_executable ( persistence_landscape persistence_landscape.cpp ) target_link_libraries(persistence_landscape ${Boost_SYSTEM_LIBRARY}) add_test ( persistence_landscape ${CMAKE_CURRENT_BINARY_DIR}/persistence_landscape ) -file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_executable ( persistence_intervals persistence_intervals.cpp ) target_link_libraries(persistence_intervals ${Boost_SYSTEM_LIBRARY}) add_test ( persistence_intervals ${CMAKE_CURRENT_BINARY_DIR}/persistence_intervals simple_diagram.txt ) -file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_executable ( persistence_vectors persistence_vectors.cpp ) target_link_libraries(persistence_vectors ${Boost_SYSTEM_LIBRARY}) add_test ( persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/persistence_vectors ) -file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_executable ( persistence_heat_maps persistence_heat_maps.cpp ) target_link_libraries(persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) add_test ( persistence_heat_maps ${CMAKE_CURRENT_BINARY_DIR}/persistence_heat_maps ) diff --git a/src/Persistence_representations/example/persistence_heat_maps.cpp b/src/Persistence_representations/example/persistence_heat_maps.cpp index a9ac5df5..2a472ac6 100644 --- a/src/Persistence_representations/example/persistence_heat_maps.cpp +++ b/src/Persistence_representations/example/persistence_heat_maps.cpp @@ -20,17 +20,14 @@ * along with this program. If not, see . */ -#include #include #include #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - -double epsilon = 0.0000005; +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; int main(int argc, char** argv) { // create two simple vectors with birth--death pairs: @@ -50,30 +47,30 @@ int main(int argc, char** argv) { // over here we define a function we sill put on a top on every birth--death pair in the persistence interval. It can // be anything. Over here we will use standard Gaussian - std::vector > filter = create_Gaussian_filter(5, 1); + std::vector > filter = Gudhi::Persistence_representations::create_Gaussian_filter(5, 1); // creating two heat maps. - Persistence_heat_maps hm1(persistence1, filter, false, 20, 0, 11); - Persistence_heat_maps hm2(persistence2, filter, false, 20, 0, 11); + Persistence_heat_maps hm1(persistence1, filter, false, 20, 0, 11); + Persistence_heat_maps hm2(persistence2, filter, false, 20, 0, 11); - std::vector*> vector_of_maps; + std::vector vector_of_maps; vector_of_maps.push_back(&hm1); vector_of_maps.push_back(&hm2); // compute median/mean of a vector of heat maps: - Persistence_heat_maps mean; + Persistence_heat_maps mean; mean.compute_mean(vector_of_maps); - Persistence_heat_maps median; + Persistence_heat_maps median; median.compute_median(vector_of_maps); // to compute L^1 distance between hm1 and hm2: std::cout << "The L^1 distance is : " << hm1.distance(hm2, 1) << std::endl; // to average of hm1 and hm2: - std::vector*> to_average; + std::vector to_average; to_average.push_back(&hm1); to_average.push_back(&hm2); - Persistence_heat_maps av; + Persistence_heat_maps av; av.compute_average(to_average); // to compute scalar product of hm1 and hm2: diff --git a/src/Persistence_representations/example/persistence_intervals.cpp b/src/Persistence_representations/example/persistence_intervals.cpp index 29cd66f3..c1ceb458 100644 --- a/src/Persistence_representations/example/persistence_intervals.cpp +++ b/src/Persistence_representations/example/persistence_intervals.cpp @@ -20,15 +20,13 @@ * along with this program. If not, see . */ -#include #include #include #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { if (argc != 2) { diff --git a/src/Persistence_representations/example/persistence_landscape.cpp b/src/Persistence_representations/example/persistence_landscape.cpp index 1bcc524a..400a9ae1 100644 --- a/src/Persistence_representations/example/persistence_landscape.cpp +++ b/src/Persistence_representations/example/persistence_landscape.cpp @@ -26,8 +26,7 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; +using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; int main(int argc, char** argv) { // create two simple vectors with birth--death pairs: diff --git a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp index 0cede07e..b201b397 100644 --- a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp +++ b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp @@ -26,8 +26,7 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; +using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; int main(int argc, char** argv) { // create two simple vectors with birth--death pairs: diff --git a/src/Persistence_representations/example/persistence_vectors.cpp b/src/Persistence_representations/example/persistence_vectors.cpp index c6581039..59eca152 100644 --- a/src/Persistence_representations/example/persistence_vectors.cpp +++ b/src/Persistence_representations/example/persistence_vectors.cpp @@ -21,7 +21,6 @@ */ #include -#include #include #include @@ -30,8 +29,8 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; +using Vector_distances_in_diagram = + Gudhi::Persistence_representations::Vector_distances_in_diagram; int main(int argc, char** argv) { // create two simple vectors with birth--death pairs: @@ -50,17 +49,15 @@ int main(int argc, char** argv) { persistence2.push_back(std::make_pair(6, 10)); // create two persistence vectors based on persistence1 and persistence2: - Vector_distances_in_diagram v1 = - Vector_distances_in_diagram(persistence1, std::numeric_limits::max()); - Vector_distances_in_diagram v2 = - Vector_distances_in_diagram(persistence2, std::numeric_limits::max()); + Vector_distances_in_diagram v1(persistence1, std::numeric_limits::max()); + Vector_distances_in_diagram v2(persistence2, std::numeric_limits::max()); // writing to a stream: std::cout << "v1 : " << v1 << std::endl; std::cout << "v2 : " << v2 << std::endl; // averages: - Vector_distances_in_diagram average; + Vector_distances_in_diagram average; average.compute_average({&v1, &v2}); std::cout << "Average : " << average << std::endl; diff --git a/src/Persistence_representations/test/persistence_heat_maps_test.cpp b/src/Persistence_representations/test/persistence_heat_maps_test.cpp index fef397a3..1f1502f5 100644 --- a/src/Persistence_representations/test/persistence_heat_maps_test.cpp +++ b/src/Persistence_representations/test/persistence_heat_maps_test.cpp @@ -21,7 +21,7 @@ */ #define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "Persistence_representations" +#define BOOST_TEST_MODULE "Persistence_heat_maps_test" #include #include #include diff --git a/src/Persistence_representations/test/persistence_intervals_test.cpp b/src/Persistence_representations/test/persistence_intervals_test.cpp index 7a3a058f..51d8a0f9 100644 --- a/src/Persistence_representations/test/persistence_intervals_test.cpp +++ b/src/Persistence_representations/test/persistence_intervals_test.cpp @@ -21,7 +21,7 @@ */ #define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "Persistence_representations" +#define BOOST_TEST_MODULE "Persistence_intervals_test" #include #include #include "gudhi/Persistence_intervals.h" diff --git a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp index c6d4796c..7b70eee3 100644 --- a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp +++ b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp @@ -21,7 +21,7 @@ */ #define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "Persistence_representations" +#define BOOST_TEST_MODULE "Persistence_intervals_with_distances_test" #include #include #include "gudhi/Persistence_intervals_with_distances.h" diff --git a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp index 098e08b2..8ab7449e 100644 --- a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp +++ b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp @@ -21,7 +21,7 @@ */ #define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "Persistence_representations" +#define BOOST_TEST_MODULE "Persistence_landscapes_on_grid_test" #include #include #include diff --git a/src/Persistence_representations/test/persistence_lanscapes_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_test.cpp index 6749fbd8..1141edfb 100644 --- a/src/Persistence_representations/test/persistence_lanscapes_test.cpp +++ b/src/Persistence_representations/test/persistence_lanscapes_test.cpp @@ -21,7 +21,7 @@ */ #define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "Persistence_representations" +#define BOOST_TEST_MODULE "Persistence_landscapes_test" #include #include #include diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt new file mode 100644 index 00000000..66524666 --- /dev/null +++ b/src/Persistence_representations/utilities/CMakeLists.txt @@ -0,0 +1,6 @@ +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 c90c637d..4ad924cb 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt @@ -1,11 +1,10 @@ cmake_minimum_required(VERSION 2.6) -project(GUDHI_STAT) +project(Persistence_representations_heat_maps_utilities) #persitence heat maps add_executable ( create_persistence_heat_maps create_persistence_heat_maps.cpp ) target_link_libraries(create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) -#add_test ( create_persistence_heat_maps ${CMAKE_CURRENT_BINARY_DIR}/create_persistence_heat_maps 10 -1 -1 4 -1 simple_diagram.txt ) add_test ( create_persistence_heat_maps ${CMAKE_CURRENT_BINARY_DIR}/create_persistence_heat_maps 10 -1 -1 4 -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" ) add_executable ( create_pssk create_pssk.cpp ) 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 b4e2be89..4e81375a 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 @@ -22,12 +22,12 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + 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 " @@ -44,14 +44,14 @@ int main(int argc, char** argv) { } std::cout << "Creating persistence landscapes...\n"; - std::vector*> maps; + std::vector maps; for (size_t i = 0; i != filenames.size(); ++i) { - Persistence_heat_maps* l = new Persistence_heat_maps; + Persistence_heat_maps* l = new Persistence_heat_maps; l->load_from_file(filenames[i]); maps.push_back(l); } - Persistence_heat_maps av; + Persistence_heat_maps av; av.compute_average(maps); av.print_to_file("average.mps"); 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 56b2d336..a9e8821f 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 @@ -22,14 +22,14 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + int main(int argc, char** argv) { std::cout << "This program compute distance of persistence heat maps stored in a file (the file needs to be created " "beforehand). \n"; @@ -52,10 +52,10 @@ int main(int argc, char** argv) { for (int i = 2; i < argc; ++i) { filenames.push_back(argv[i]); } - std::vector > maps; + std::vector maps; maps.reserve(filenames.size()); for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - Persistence_heat_maps l; + Persistence_heat_maps l; l.load_from_file(filenames[file_no]); maps.push_back(l); } 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 ec9482f0..1cee1f82 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 @@ -22,13 +22,13 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + 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"; @@ -38,10 +38,10 @@ int main(int argc, char** argv) { for (int i = 1; i < argc; ++i) { filenames.push_back(argv[i]); } - std::vector > maps; + std::vector maps; maps.reserve(filenames.size()); for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - Persistence_heat_maps l; + Persistence_heat_maps l; l.load_from_file(filenames[file_no]); maps.push_back(l); } 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 68c75059..2bf185a3 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 @@ -22,14 +22,15 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +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; + 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"; @@ -68,12 +69,11 @@ int main(int argc, char** argv) { } std::cout << "Creating persistence heat maps...\n"; - std::vector > filter = create_Gaussian_filter(stdiv, 1); + std::vector > 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); + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); std::stringstream ss; ss << filenames[i] << ".mps"; 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 a56393a3..ec9477f1 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 @@ -22,14 +22,15 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +using distance_from_diagonal_scaling = Gudhi::Persistence_representations::distance_from_diagonal_scaling; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps; + 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"; @@ -68,12 +69,11 @@ int main(int argc, char** argv) { } std::cout << "Creating persistence heat maps...\n"; - std::vector > filter = create_Gaussian_filter(stdiv, 1); + std::vector > 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); + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); std::stringstream ss; ss << filenames[i] << ".mps"; 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 44115329..cb7e282c 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 @@ -22,14 +22,15 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +using squared_distance_from_diagonal_scaling = Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps; + 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"; @@ -68,12 +69,11 @@ int main(int argc, char** argv) { } std::cout << "Creating persistence heat maps...\n"; - std::vector > filter = create_Gaussian_filter(stdiv, 1); + std::vector > 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); + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); std::stringstream ss; ss << filenames[i] << ".mps"; 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 ebc82f82..bd5ec89a 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 @@ -22,14 +22,14 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + 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"; @@ -65,12 +65,11 @@ int main(int argc, char** argv) { } std::cout << "Creating persistence heat maps...\n"; - std::vector > filter = create_Gaussian_filter(stdiv, 1); + std::vector > 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); + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); std::stringstream ss; ss << filenames[i] << ".mps"; 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 7b24bb7c..6aefbb00 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp @@ -22,14 +22,13 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +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"; @@ -67,7 +66,7 @@ int main(int argc, char** argv) { } std::cout << "Creating persistence heat maps...\n"; - std::vector > filter = create_Gaussian_filter(stdiv, 1); + std::vector > 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; 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 0b7841d1..a7c9f2d8 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 @@ -22,16 +22,16 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + 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"; - Persistence_heat_maps l; + Persistence_heat_maps l; l.load_from_file(argv[1]); l.plot(argv[1]); return 0; 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 72c56e92..66fa31ca 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 @@ -28,8 +28,7 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; +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 " 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 6a872b7a..0b1b526d 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -23,14 +23,13 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +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 " 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 5fbbef14..1286ca57 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 @@ -28,8 +28,7 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of " 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 b8f96b60..d68f4584 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 @@ -28,8 +28,7 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; +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 " 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 521621b2..da2b9319 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 @@ -28,8 +28,7 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; +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 " 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 e76906e9..e7d29e84 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -29,10 +29,7 @@ #include #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - -double epsilon = 0.0000005; +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; int main(int argc, char** argv) { if (argc < 2) { @@ -50,7 +47,7 @@ int main(int argc, char** argv) { dimension = (unsigned)dim; } std::vector > intervals = - read_persistence_intervals_in_one_dimension_from_file(argv[1], dimension); + Gudhi::Persistence_representations::read_persistence_intervals_in_one_dimension_from_file(argv[1], dimension); Persistence_intervals b(intervals); b.plot(argv[1]); return 0; diff --git a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp index f885a7a7..526130e9 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp @@ -22,12 +22,11 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include +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"; 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 7028b98b..b3881d6a 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 @@ -22,12 +22,12 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include +#include + +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 " 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 76a9d433..8dad7b4d 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 @@ -22,13 +22,12 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include +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"; diff --git a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp index a6b33225..325081d1 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp @@ -22,14 +22,13 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +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 " diff --git a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp index 35262fe2..ebdb20a1 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp @@ -22,12 +22,11 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include +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"; 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 a17a8998..d50118a0 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 @@ -22,10 +22,10 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include +#include + +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 " 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 4694e897..859c6991 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 @@ -22,14 +22,13 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +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"; 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 75c33cb1..e95bf8ad 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 @@ -22,13 +22,12 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include +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"; 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 490a1c25..8d747c14 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 @@ -22,14 +22,13 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include #include #include +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"; 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 f5a70826..42822a01 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 @@ -22,12 +22,11 @@ #include -using namespace Gudhi; -using namespace Gudhi::Persistence_representations; - #include #include +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"; -- cgit v1.2.3