diff options
Diffstat (limited to 'src/common')
| -rw-r--r-- | src/common/doc/header.html | 3 | ||||
| -rw-r--r-- | src/common/doc/main_page.h | 10 | ||||
| -rw-r--r-- | src/common/example/CMakeLists.txt | 18 | ||||
| -rw-r--r-- | src/common/example/example_CGAL_3D_points_off_reader.cpp (renamed from src/common/example/CGAL_3D_points_off_reader.cpp) | 0 | ||||
| -rw-r--r-- | src/common/example/example_CGAL_points_off_reader.cpp (renamed from src/common/example/CGAL_points_off_reader.cpp) | 2 | ||||
| -rw-r--r-- | src/common/example/example_vector_double_points_off_reader.cpp | 41 | ||||
| -rw-r--r-- | src/common/include/gudhi/Points_off_io.h | 11 | ||||
| -rw-r--r-- | src/common/include/gudhi/Test.h | 105 | ||||
| -rw-r--r-- | src/common/test/CMakeLists.txt | 27 | ||||
| -rw-r--r-- | src/common/test/test_points_off_reader.cpp (renamed from src/common/test/points_off_reader_unit_test.cpp) | 21 |
10 files changed, 82 insertions, 156 deletions
diff --git a/src/common/doc/header.html b/src/common/doc/header.html index c958390c..a6f3ed9c 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -40,6 +40,7 @@ $extrastylesheet <li><a href="http://gudhi.gforge.inria.fr/getinvolved/">Get involved</a></li> <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li> <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li> + <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li> </ul> </li> <li class="divider"></li> @@ -52,7 +53,7 @@ $extrastylesheet </ul> </li> <li class="divider"></li> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/modules.html">Documentation</a></li> + <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">Documentation</a></li> <li class="divider"></li> <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li> <li class="divider"></li> diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 9146bed1..0983051d 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -13,8 +13,8 @@ * The current release of the GUDHI library includes: * * \li Data structures to represent, construct and manipulate simplicial complexes. - * \li Algorithms to compute persistent homology and multi-field persistent homology. - * \li Simplication of simplicial complexes by edge contraction. + * \li Simplification of simplicial complexes by edge contraction. + * \li Algorithms to compute persistent homology persistent homology. * * All data-structures are generic and several of their aspects can be parameterized via template classes. * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library. @@ -266,8 +266,10 @@ make \endverbatim * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a> * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html"> * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_shapes_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> + * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html"> diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index 0da3dcc0..b0c6d69a 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -1,17 +1,21 @@ cmake_minimum_required(VERSION 2.6) project(Common_examples) -# need CGAL 4.7 +add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp ) +target_link_libraries(vector_double_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) +add_test(vector_double_off_reader ${CMAKE_CURRENT_BINARY_DIR}/vector_double_off_reader ${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off) + if(CGAL_FOUND) - add_executable ( cgal3Doffreader CGAL_3D_points_off_reader.cpp ) - target_link_libraries(cgal3Doffreader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - add_test(cgal3Doffreader ${CMAKE_CURRENT_BINARY_DIR}/cgal3Doffreader ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp ) + target_link_libraries(cgal_3D_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(cgal_3D_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_3D_off_reader ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + # need CGAL 4.7 if (NOT CGAL_VERSION VERSION_LESS 4.7.0) if (EIGEN3_FOUND) - add_executable ( cgaloffreader CGAL_points_off_reader.cpp ) - target_link_libraries(cgaloffreader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - add_test(cgaloffreader ${CMAKE_CURRENT_BINARY_DIR}/cgaloffreader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off) + add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp ) + target_link_libraries(cgal_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off) endif(EIGEN3_FOUND) endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) endif() diff --git a/src/common/example/CGAL_3D_points_off_reader.cpp b/src/common/example/example_CGAL_3D_points_off_reader.cpp index d48bb17d..d48bb17d 100644 --- a/src/common/example/CGAL_3D_points_off_reader.cpp +++ b/src/common/example/example_CGAL_3D_points_off_reader.cpp diff --git a/src/common/example/CGAL_points_off_reader.cpp b/src/common/example/example_CGAL_points_off_reader.cpp index d1ca166d..4522174a 100644 --- a/src/common/example/CGAL_points_off_reader.cpp +++ b/src/common/example/example_CGAL_points_off_reader.cpp @@ -37,7 +37,7 @@ int main(int argc, char **argv) { int n {0}; for (auto point : point_cloud) { std::cout << "Point[" << n << "] = "; - for (int i {0}; i < point.dimension(); i++) + for (std::size_t i {0}; i < point.size(); i++) std::cout << point[i] << " "; std::cout << "\n"; ++n; diff --git a/src/common/example/example_vector_double_points_off_reader.cpp b/src/common/example/example_vector_double_points_off_reader.cpp new file mode 100644 index 00000000..8aecb26e --- /dev/null +++ b/src/common/example/example_vector_double_points_off_reader.cpp @@ -0,0 +1,41 @@ +#include <gudhi/Points_off_io.h> + +#include <iostream> +#include <string> +#include <vector> + +using Point_d = std::vector<double>; + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " inputFile.off" << std::endl; + exit(-1); +} + +int main(int argc, char **argv) { + if (argc != 2) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + usage(argv[0]); + } + + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_off_reader<Point_d> off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector<Point_d> point_cloud = off_reader.get_point_cloud(); + + int n {0}; + for (auto point : point_cloud) { + std::cout << "Point[" << n << "] = "; + for (std::size_t i {0}; i < point.size(); i++) + std::cout << point[i] << " "; + std::cout << "\n"; + ++n; + } + return 0; +} diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h index 74b49386..18b23e84 100644 --- a/src/common/include/gudhi/Points_off_io.h +++ b/src/common/include/gudhi/Points_off_io.h @@ -73,9 +73,8 @@ class Points_off_visitor_reader { * @details * Point_d must have a constructor with the following form: * - * @code template<class InputIterator > Point_d::Point_d(int d, InputIterator first, InputIterator last) @endcode + * @code template<class InputIterator > Point_d::Point_d(InputIterator first, InputIterator last) @endcode * - * where d is the point dimension. */ void point(const std::vector<double>& point) { #ifdef DEBUG_TRACES @@ -86,7 +85,7 @@ class Points_off_visitor_reader { std::cout << std::endl; #endif // DEBUG_TRACES // Fill the point cloud - point_cloud.push_back(Point_d(point.size(), point.begin(), point.end())); + point_cloud.push_back(Point_d(point.begin(), point.end())); } // Off_reader visitor maximal_face implementation - Only points are read @@ -117,14 +116,14 @@ class Points_off_visitor_reader { * * \section Example * - * This example loads points from an OFF file and builds a vector of CGAL points in dimension d. + * This example loads points from an OFF file and builds a vector of points (vector of double). * Then, it is asked to display the points. * - * \include common/CGAL_points_off_reader.cpp + * \include common/example_vector_double_points_off_reader.cpp * * When launching: * - * \code $> ./cgaloffreader ../../data/points/alphacomplexdoc.off + * \code $> ./vector_double_off_reader ../../data/points/alphacomplexdoc.off * \endcode * * the program output is: diff --git a/src/common/include/gudhi/Test.h b/src/common/include/gudhi/Test.h deleted file mode 100644 index 6024c822..00000000 --- a/src/common/include/gudhi/Test.h +++ /dev/null @@ -1,105 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): David Salinas - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - * - */ - -#ifndef TEST_H_ -#define TEST_H_ - -#include <list> -#include <string> -#include <vector> -#include <sstream> -#include <iostream> - - -#define TEST(a) std::cout << "TEST: " << (a) << std::endl -#define TESTMSG(a, b) std::cout << "TEST: " << a << b << std::endl -#define TESTVALUE(a) std::cout << "TEST: " << #a << ": " << a << std::endl - -/** - * Class to perform test - */ - -class Test { - private: - std::string name; - bool (*test)(); - - std::string separation() const { - return "+++++++++++++++++++++++++++++++++++++++++++++++++\n"; - } - - std::string print_between_plus(std::string& s) const { - std::stringstream res; - res << "+++++++++++++++++" << s << "+++++++++++++++++\n"; - return res.str(); - } - - public: - Test(std::string name_, bool (*test_)()) { - name = name_; - test = test_; - } - - bool run() { - std::cout << print_between_plus(name); - return test(); - } - - std::string getName() { - return name; - } -}; - -class Tests { - private: - std::list<Test> tests; - - public: - void add(std::string name_, bool (*test_)()) { - Test test(name_, test_); - tests.push_back(test); - } - - bool run() { - bool tests_succesful(true); - std::vector<bool> res; - for (Test test : tests) { - res.push_back(test.run()); - } - std::cout << "\n\n results of tests : " << std::endl; - int i = 0; - for (Test t : tests) { - std::cout << "Test " << i << " \"" << t.getName() << "\" --> "; - if (res[i++]) { - std::cout << "OK" << std::endl; - } else { - std::cout << "Fail" << std::endl; - tests_succesful = false; - break; - } - } - return tests_succesful; - } -}; - -#endif // TEST_H_ diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt index 0a88cf8e..7ccdb752 100644 --- a/src/common/test/CMakeLists.txt +++ b/src/common/test/CMakeLists.txt @@ -10,26 +10,15 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -# need CGAL 4.7 -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - if (EIGEN3_FOUND) - add_executable ( poffreader_UT points_off_reader_unit_test.cpp ) - target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +add_executable ( poffreader_UT test_points_off_reader.cpp ) +target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - # Do not forget to copy test files in current binary dir - file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - # Unitary tests - add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no) +# Unitary tests +add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no) - else() - message(WARNING "Eigen3 not found. Version 3.1.0 is required for points_off_reader unitary tests.") - endif() - else() - message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile points_off_reader unitary tests. Version 4.7.0 is required.") - endif () -endif() diff --git a/src/common/test/points_off_reader_unit_test.cpp b/src/common/test/test_points_off_reader.cpp index dbcc0434..b4f71182 100644 --- a/src/common/test/points_off_reader_unit_test.cpp +++ b/src/common/test/test_points_off_reader.cpp @@ -22,10 +22,6 @@ #include <gudhi/Points_off_io.h> -// For CGAL points type in dimension d -// cf. http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Point__d.html -#include <CGAL/Epick_d.h> - #include <iostream> #include <string> #include <vector> @@ -34,8 +30,7 @@ #define BOOST_TEST_MODULE "points_off_read_write" #include <boost/test/unit_test.hpp> -typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; -typedef Kernel::Point_d Point_d; +using Point_d = std::vector<double>; BOOST_AUTO_TEST_CASE( points_doc_test ) { @@ -50,19 +45,19 @@ BOOST_AUTO_TEST_CASE( points_doc_test ) std::vector<Point_d> expected_points; std::vector<double> point = {1.0, 1.0}; - expected_points.push_back(Point_d(2, point.begin(), point.end())); + expected_points.push_back(Point_d(point.begin(), point.end())); point = {7.0, 0.0}; - expected_points.push_back(Point_d(2, point.begin(), point.end())); + expected_points.push_back(Point_d(point.begin(), point.end())); point = {4.0, 6.0}; - expected_points.push_back(Point_d(2, point.begin(), point.end())); + expected_points.push_back(Point_d(point.begin(), point.end())); point = {9.0, 6.0}; - expected_points.push_back(Point_d(2, point.begin(), point.end())); + expected_points.push_back(Point_d(point.begin(), point.end())); point = {0.0, 14.0}; - expected_points.push_back(Point_d(2, point.begin(), point.end())); + expected_points.push_back(Point_d(point.begin(), point.end())); point = {2.0, 19.0}; - expected_points.push_back(Point_d(2, point.begin(), point.end())); + expected_points.push_back(Point_d(point.begin(), point.end())); point = {9.0, 17.0}; - expected_points.push_back(Point_d(2, point.begin(), point.end())); + expected_points.push_back(Point_d(point.begin(), point.end())); BOOST_CHECK(point_cloud == expected_points); } |