diff options
| -rw-r--r-- | CMakeLists.txt | 5 | ||||
| -rw-r--r-- | src/cmake/modules/GUDHI_user_version_target.txt | 91 | ||||
| -rw-r--r-- | src/common/doc/main_page.h | 3 | ||||
| -rw-r--r-- | src/common/include/gudhi/reader_utils.h | 12 |
4 files changed, 10 insertions, 101 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt index b1bde390..a6f0a7f1 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -3,10 +3,7 @@ project(GUDHIdev) include(CMakeGUDHIVersion.txt) -set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") -set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") -message("CMAKE_PREFIX_PATH = ${CMAKE_PREFIX_PATH}") -message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}") +list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") enable_testing() diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt deleted file mode 100644 index 3172f6b1..00000000 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ /dev/null @@ -1,91 +0,0 @@ -# Some functionnalities requires CMake 2.8.11 minimum -if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) - - # Definition of the custom target user_version - add_custom_target(user_version) - - if(DEFINED USER_VERSION_DIR) - # set the GUDHI_USER_VERSION_DIR with USER_VERSION_DIR defined by the user - set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${USER_VERSION_DIR}) - else() - # set the GUDHI_USER_VERSION_DIR with timestamp and Gudhi version number - string(TIMESTAMP DATE_AND_TIME "%Y-%m-%d-%H-%M-%S") - set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${DATE_AND_TIME}_GUDHI_${GUDHI_VERSION}) - endif() - - set(GUDHI_DOXYGEN_DEPENDENCY user_version) - - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - make_directory ${GUDHI_USER_VERSION_DIR} - COMMENT "user_version creation in ${GUDHI_USER_VERSION_DIR}") - - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_SOURCE_DIR}/Conventions.txt ${GUDHI_USER_VERSION_DIR}/Conventions.txt) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_SOURCE_DIR}/README ${GUDHI_USER_VERSION_DIR}/README) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_SOURCE_DIR}/COPYING ${GUDHI_USER_VERSION_DIR}/COPYING) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_SOURCE_DIR}/src/CMakeLists.txt ${GUDHI_USER_VERSION_DIR}/CMakeLists.txt) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_SOURCE_DIR}/src/Doxyfile ${GUDHI_USER_VERSION_DIR}/Doxyfile) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfigVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfigVersion.cmake.in) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfig.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfig.cmake.in) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${CMAKE_SOURCE_DIR}/CMakeGUDHIVersion.txt ${GUDHI_USER_VERSION_DIR}/CMakeGUDHIVersion.txt) - - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${CMAKE_SOURCE_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${CMAKE_SOURCE_DIR}/src/cython ${GUDHI_USER_VERSION_DIR}/cython) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${CMAKE_SOURCE_DIR}/data ${GUDHI_USER_VERSION_DIR}/data) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${CMAKE_SOURCE_DIR}/src/cmake ${GUDHI_USER_VERSION_DIR}/cmake) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) - - set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistence_representations;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex") - set(GUDHI_DIRECTORIES "doc;example;concept;utilities") - set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches") - - foreach(GUDHI_MODULE ${GUDHI_MODULES}) - foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES}) - # Find files - file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*) - - foreach(GUDHI_FILE ${GUDHI_FILES}) - get_filename_component(GUDHI_FILE_NAME ${GUDHI_FILE} NAME) - # GUDHI_FILE can be a file or a directory - if(IS_DIRECTORY ${GUDHI_FILE}) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${GUDHI_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_DIRECTORY}/${GUDHI_MODULE}/${GUDHI_FILE_NAME}) - else() - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${GUDHI_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_DIRECTORY}/${GUDHI_MODULE}/${GUDHI_FILE_NAME}) - endif() - endforeach() - endforeach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES}) - - foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) - # include files - file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_INCLUDE_DIRECTORY}/*) - - foreach(GUDHI_INCLUDE_FILE ${GUDHI_INCLUDE_FILES}) - get_filename_component(GUDHI_INCLUDE_FILE_NAME ${GUDHI_INCLUDE_FILE} NAME) - # GUDHI_INCLUDE_FILE can be a file or a directory - if(IS_DIRECTORY ${GUDHI_INCLUDE_FILE}) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_INCLUDE_DIRECTORY}/${GUDHI_INCLUDE_FILE_NAME}) - else() - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_INCLUDE_DIRECTORY}/${GUDHI_INCLUDE_FILE_NAME}) - endif() - endforeach() - endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) - - endforeach(GUDHI_MODULE ${GUDHI_MODULES}) - -endif() diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index ec968558..e5f135db 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -152,6 +152,7 @@ </table> \section Toolbox Toolbox + \subsection BottleneckDistanceToolbox Bottleneck distance \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge" <table border="0"> @@ -485,4 +486,4 @@ make doxygen * @example Witness_complex/example_witness_complex_persistence.cpp * @example Witness_complex/example_witness_complex_sphere.cpp */ - +
\ No newline at end of file diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 35af09bd..1dc8a547 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -305,6 +305,7 @@ Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);` where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. **/ template <typename OutputIterator> void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) { @@ -326,7 +327,6 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu if (n >= 2) { //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1); int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1); - GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death."); *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]); } } @@ -338,13 +338,14 @@ Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>` where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. **/ -std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) { +inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) { std::map<int, std::vector<std::pair<double, double>>> ret; read_persistence_intervals_and_dimension( filename, - boost::make_function_output_iterator([&ret](auto t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); })); + boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); })); return ret; } // read_persistence_diagram_from_file @@ -357,13 +358,14 @@ If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` (or where dimension is not specified) are returned. The return value is an `std::vector<std::pair<birth, death>>` where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +Note: the function does not check that birth <= death. **/ -std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) { +inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) { std::vector<std::pair<double, double>> ret; read_persistence_intervals_and_dimension( filename, - boost::make_function_output_iterator([&ret](auto t) { ret.emplace_back(get<1>(t), get<2>(t)); })); + boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); })); return ret; } // read_persistence_diagram_from_file |