From 74dcaacda1c887b008ea8c95b28962de1c02a2d0 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 2 Feb 2016 15:24:51 +0000 Subject: alpha off reader test strategy modification git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@995 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: aa4ba97eecefb03e01a53ae1e2b50248a0857043 --- src/Alpha_complex/doc/Intro_alpha_complex.h | 2 +- .../example/Alpha_complex_from_off.cpp | 33 +++++++++++++++------- .../example/Alpha_complex_from_points.cpp | 2 +- src/Alpha_complex/example/CMakeLists.txt | 19 +++++++++++-- .../example/alphaoffreader_for_doc_32.txt | 26 ++++++++--------- src/Alpha_complex/test/CMakeLists.txt | 14 +++++++++ src/Simplex_tree/include/gudhi/Simplex_tree.h | 15 ++++++---- 7 files changed, 78 insertions(+), 33 deletions(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 12d62ac0..8eea6ba7 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -67,7 +67,7 @@ namespace alphacomplex { * * When launching: * - * \code $> ./alphapoints 60.0 + * \code $> ./alphapoints * \endcode * * the program output is: diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index 780f904b..80445a22 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -5,14 +5,14 @@ #include void usage(char * const progName) { - std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value" << std::endl; - std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0" << std::endl; + std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value [ouput_file.txt]\n"; + std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n"; exit(-1); // ----- >> } int main(int argc, char **argv) { - if (argc != 3) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + if ((argc != 3) && (argc != 4)) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; usage(argv[0]); } @@ -25,21 +25,34 @@ int main(int argc, char **argv) { typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; Gudhi::alphacomplex::Alpha_complex alpha_complex_from_file(off_file_name, alpha_square_max_value); + std::streambuf* streambufffer; + std::ofstream ouput_file_stream; + + if (argc == 4) { + ouput_file_stream.open(std::string(argv[3])); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + std::ostream output_stream(streambufffer); + // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() << + output_stream << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() << " - " << alpha_complex_from_file.num_simplices() << " simplices - " << alpha_complex_from_file.num_vertices() << " vertices." << std::endl; - std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { - std::cout << " ( "; + output_stream << " ( "; for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; + output_stream << vertex << " "; } - std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] "; - std::cout << std::endl; + output_stream << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] "; + output_stream << std::endl; } + ouput_file_stream.close(); return 0; } diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index dab161c9..815e40d7 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -10,7 +10,7 @@ typedef Kernel::Point_d Point; typedef std::vector Vector_of_points; int main(int argc, char **argv) { - double alpha_square_max_value = 32.0; + double alpha_square_max_value = 60.0; // ---------------------------------------------------------------------------- // Init of a list of points diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 33ff6805..d93dd436 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -27,12 +27,25 @@ if(CGAL_FOUND) if (EIGEN3_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") include( ${EIGEN3_USE_FILE} ) - - add_executable ( alphaoffreader Alpha_complex_from_off.cpp ) - target_link_libraries(alphaoffreader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) add_executable ( alphapoints Alpha_complex_from_points.cpp ) target_link_libraries(alphapoints ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints) + + # Do not forget to copy test files in current binary dir + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + # Do not forget to copy test results files in current binary dir + file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_executable ( alphaoffreader Alpha_complex_from_off.cpp ) + target_link_libraries(alphaoffreader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt) + add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt) + if (DIFF_PATH) + add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) + endif() else() message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") endif() diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt index 553431a9..13183e86 100644 --- a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt @@ -7,16 +7,16 @@ Iterator on alpha complex simplices in the filtration order, with [filtration va ( 4 ) -> [0] ( 5 ) -> [0] ( 6 ) -> [0] - ( 5 4 ) -> [6.25] - ( 4 1 ) -> [20] - ( 4 2 ) -> [8.5] - ( 6 2 ) -> [9.25] - ( 6 5 ) -> [10] - ( 6 4 ) -> [11.25] - ( 6 5 4 ) -> [12.5] - ( 6 4 2 ) -> [12.9959] - ( 3 0 ) -> [13.25] - ( 4 1 ) -> [20] - ( 1 0 ) -> [22.7367] - ( 3 1 0 ) -> [22.7367] - ( 5 0 ) -> [30.25] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index fa24e1b1..52ec0a78 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -8,6 +8,20 @@ if(CGAL_FOUND) message(STATUS "CGAL version: ${CGAL_VERSION}.") include( ${CGAL_USE_FILE} ) + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. + # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 + # A workaround is to add "-std=c++11" again. + # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html + # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html + # but it implies to use cmake version 3.1 at least. + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index dbef8517..3911f497 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -307,7 +307,8 @@ class Simplex_tree { * of the simplex. * * @param[in] sh Simplex for which the boundary is computed. */ - Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) { + template + Boundary_simplex_range boundary_simplex_range(DictionaryIterator sh) { return Boundary_simplex_range(Boundary_simplex_iterator(this, sh), Boundary_simplex_iterator(this)); } @@ -528,7 +529,11 @@ class Simplex_tree { /** \brief Returns true if the node in the simplex tree pointed by * sh has children.*/ - bool has_children(Simplex_handle sh) const { + /*bool has_children(Simplex_handle sh) const { + return (sh->second.children()->parent() == sh->first); + }*/ + template + bool has_children(DictionaryIterator sh) const { return (sh->second.children()->parent() == sh->first); } @@ -1128,7 +1133,7 @@ class Simplex_tree { bool make_filtration_non_decreasing() { bool modified = false; // Loop must be from the end to the beginning, as higher dimension simplex are always on the left part of the tree - for (auto sh = (root_.members().end() - 1); sh >= root_.members().begin(); --sh) { + for (auto sh = root_.members().rbegin(); sh != root_.members().rend(); ++sh) { if (has_children(sh)) { modified |= rec_make_filtration_non_decreasing(sh->second.children()); } @@ -1144,10 +1149,11 @@ class Simplex_tree { bool rec_make_filtration_non_decreasing(Siblings * sib) { bool modified = false; + // Loop must be from the end to the beginning, as higher dimension simplex are always on the left part of the tree for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) { // Find the maximum filtration value in the border Boundary_simplex_range boundary = boundary_simplex_range(sh); - Boundary_simplex_iterator max_border = std::max_element( std::begin(boundary), std::end(boundary), + Boundary_simplex_iterator max_border = std::max_element(std::begin(boundary), std::end(boundary), [](Simplex_handle sh1, Simplex_handle sh2) { return filtration(sh1) < filtration(sh2); } ); @@ -1175,7 +1181,6 @@ class Simplex_tree { * call `initialize_filtration()` to recompute it. */ void prune_above_filtration(Filtration_value filtration) { -std::cout << "prune_above_filtration - filtration=" << filtration << std::endl; // No action if filtration is not stored if (Options::store_filtration) { if (filtration < threshold_) { -- cgit v1.2.3