From 974764e3ac6aeea981ff57b1ab4692a21be22254 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 31 Mar 2015 08:34:06 +0000 Subject: For xunit test purpose git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@514 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 547d5e7d5b1e598d62600838418d25b305db484c --- src/Persistent_cohomology/test/CMakeLists.txt | 25 +++++++++++++++------- src/Persistent_cohomology/test/README | 4 ++-- .../test/persistent_cohomology_unit_test.cpp | 3 +-- ...persistent_cohomology_unit_test_multi_field.cpp | 3 +-- src/Simplex_tree/test/CMakeLists.txt | 11 ++++++---- src/Simplex_tree/test/README | 2 +- 6 files changed, 29 insertions(+), 19 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index 9dc19251..d7564c11 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required(VERSION 2.6) -project(GUDHITestSimplexTree) +project(GUDHIPersistentCohomologyUT) if(NOT MSVC) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") @@ -7,18 +7,27 @@ if(NOT MSVC) set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage") endif() -add_executable ( persistent_cohomology_unit_test persistent_cohomology_unit_test.cpp ) -target_link_libraries(persistent_cohomology_unit_test ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp ) +target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) # Unitary tests -add_test(persistent_cohomology_unit_test ${CMAKE_CURRENT_BINARY_DIR}/persistent_cohomology_unit_test ${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/test/simplex_tree_file_for_unit_test.txt) +add_test(NAME PersistentCohomologyUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/PersistentCohomologyUT + ${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/test/simplex_tree_file_for_unit_test.txt + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/PersistentCohomologyUT.xml --log_level=test_suite --report_level=no) if(GMPXX_FOUND AND GMP_FOUND) - add_executable ( persistent_cohomology_unit_test_multi_field persistent_cohomology_unit_test_multi_field.cpp ) - target_link_libraries(persistent_cohomology_unit_test_multi_field ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp ) + target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + + # Unitary tests + add_test(NAME PersistentCohomologyMultiFieldUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/PersistentCohomologyMultiFieldUT + ${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/PersistentCohomologyMultiFieldUT.xml --log_level=test_suite --report_level=no) - # Unitary tests - add_test(persistent_cohomology_unit_test_multi_field ${CMAKE_CURRENT_BINARY_DIR}/persistent_cohomology_unit_test_multi_field ${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt) endif() if (LCOV_PATH) diff --git a/src/Persistent_cohomology/test/README b/src/Persistent_cohomology/test/README index ddceac63..428af77b 100644 --- a/src/Persistent_cohomology/test/README +++ b/src/Persistent_cohomology/test/README @@ -9,13 +9,13 @@ To launch with details: SINGLE FIELD ------------ -./persistent_cohomology_unit_test simplex_tree_file_for_unit_test.txt --report_level=detailed --log_level=all +./PersistentCohomologyUT simplex_tree_file_for_unit_test.txt --report_level=detailed --log_level=all ==> echo $? returns 0 in case of success (non-zero otherwise) MULTI FIELD ----------- -./persistent_cohomology_unit_test_multi_field simplex_tree_file_for_multi_field_unit_test.txt --report_level=detailed --log_level=all +./PersistentCohomologyMultiFieldUT simplex_tree_file_for_multi_field_unit_test.txt --report_level=detailed --log_level=all ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp index 1e7a74a7..3594d049 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -22,8 +22,7 @@ using namespace boost::unit_test; typedef Simplex_tree<> typeST; std::string test_rips_persistence(int coefficient, int min_persistence) { - // Check file name is given as parameter from CMakeLists.txt - BOOST_CHECK(framework::master_test_suite().argc >= 2); + // file name is given as parameter from CMakeLists.txt const std::string inputFile(framework::master_test_suite().argv[1]); std::ifstream simplex_tree_stream; diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp index e88add3a..1df41d84 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp @@ -23,8 +23,7 @@ using namespace boost::unit_test; typedef Simplex_tree<> typeST; std::string test_rips_persistence(int min_coefficient, int max_coefficient, int min_persistence) { - // Check file name is given as parameter from CMakeLists.txt - BOOST_CHECK(framework::master_test_suite().argc >= 2); + // file name is given as parameter from CMakeLists.txt const std::string inputFile(framework::master_test_suite().argv[1]); std::ifstream simplex_tree_stream; diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index 02ef9d8b..f8cfc1a7 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required(VERSION 2.6) -project(GUDHITestSimplexTree) +project(GUDHISimplexTreeUT) if(NOT MSVC) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") @@ -7,11 +7,14 @@ if(NOT MSVC) set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage") endif() -add_executable ( simplex_tree_unit_test simplex_tree_unit_test.cpp ) -target_link_libraries(simplex_tree_unit_test ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp ) +target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) # Unitary tests -add_test(simplex_tree_unit_test ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_unit_test) +add_test(NAME SimplexTreeUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/SimplexTreeUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/SimplexTreeUT.xml --log_level=test_suite --report_level=no) if (LCOV_PATH) # Lcov code coverage of unitary test diff --git a/src/Simplex_tree/test/README b/src/Simplex_tree/test/README index 620bcd5f..bd8bf770 100644 --- a/src/Simplex_tree/test/README +++ b/src/Simplex_tree/test/README @@ -7,6 +7,6 @@ make To launch with details: *********************** -./simplex_tree_unit_test --report_level=detailed --log_level=all +./SimplexTreeUT --report_level=detailed --log_level=all ==> echo $? returns 0 in case of success (non-zero otherwise) -- cgit v1.2.3 From eb083c0626327d7deb4a60d7a37d64c3f3697071 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 31 Mar 2015 08:45:19 +0000 Subject: checkin a test error for test purpose git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@515 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0e454516b205f958d54d6ecc8c7799894028a962 --- src/Simplex_tree/test/simplex_tree_unit_test.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src') diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index c0cfced1..4adc7e58 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -25,7 +25,7 @@ const Vertex_handle DEFAULT_VERTEX_HANDLE = (const Vertex_handle) -1; const Filtration_value DEFAULT_FILTRATION_VALUE = (const Filtration_value) 0.0; void test_empty_simplex_tree(typeST& tst) { - BOOST_CHECK(tst.null_vertex() == DEFAULT_VERTEX_HANDLE); + BOOST_CHECK(tst.null_vertex() != DEFAULT_VERTEX_HANDLE); BOOST_CHECK(tst.filtration() == DEFAULT_FILTRATION_VALUE); BOOST_CHECK(tst.num_vertices() == (size_t) 0); BOOST_CHECK(tst.num_simplices() == (size_t) 0); -- cgit v1.2.3 From 8b8134be8b6dc3150a4069d9fedb0c37bfe888f9 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 31 Mar 2015 08:58:32 +0000 Subject: rollback git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@516 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d7e9737aeb62e8560b5eafed00bf21ca7751528b --- src/Simplex_tree/test/simplex_tree_unit_test.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src') diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index 4adc7e58..c0cfced1 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -25,7 +25,7 @@ const Vertex_handle DEFAULT_VERTEX_HANDLE = (const Vertex_handle) -1; const Filtration_value DEFAULT_FILTRATION_VALUE = (const Filtration_value) 0.0; void test_empty_simplex_tree(typeST& tst) { - BOOST_CHECK(tst.null_vertex() != DEFAULT_VERTEX_HANDLE); + BOOST_CHECK(tst.null_vertex() == DEFAULT_VERTEX_HANDLE); BOOST_CHECK(tst.filtration() == DEFAULT_FILTRATION_VALUE); BOOST_CHECK(tst.num_vertices() == (size_t) 0); BOOST_CHECK(tst.num_simplices() == (size_t) 0); -- cgit v1.2.3 From 8a587e14465a5d9d4016f0d188a2681f587397ea Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 31 Mar 2015 09:13:37 +0000 Subject: Add tests name for xunit git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@517 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fe517d2d9e8ea4a6660c4c9d510912f393ecfcb8 --- src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp | 2 +- .../test/persistent_cohomology_unit_test_multi_field.cpp | 2 +- src/Simplex_tree/test/simplex_tree_unit_test.cpp | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp index 3594d049..55bc7066 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -1,4 +1,4 @@ -#define BOOST_TEST_MODULE const_string test +#define BOOST_TEST_MODULE persistent_cohomology test #include #include #include diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp index 1df41d84..8802005c 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp @@ -1,4 +1,4 @@ -#define BOOST_TEST_MODULE const_string test +#define BOOST_TEST_MODULE persistent_cohomology_multi_field test #include #include #include diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index c0cfced1..6b0a1f3d 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -1,4 +1,4 @@ -#define BOOST_TEST_MODULE const_string test +#define BOOST_TEST_MODULE simplex_tree test #include #include #include -- cgit v1.2.3 From 2d20d45866faee2f916e846967b91a1a836246d3 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 31 Mar 2015 09:54:42 +0000 Subject: xunit purpose modification git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@519 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e9d555de2c1452010be4faa13178e86ae2b77e8d --- src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp | 2 +- src/Alpha_shapes/test/CMakeLists.txt | 12 ++++++++---- src/Alpha_shapes/test/README | 4 +++- src/Bottleneck/test/CMakeLists.txt | 11 +++++++---- src/Persistent_cohomology/test/README | 2 ++ src/Simplex_tree/test/README | 2 ++ 6 files changed, 23 insertions(+), 10 deletions(-) (limited to 'src') diff --git a/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp b/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp index a90704b6..b4c32321 100644 --- a/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp +++ b/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp @@ -20,7 +20,7 @@ * along with this program. If not, see . */ -#define BOOST_TEST_MODULE alpha_shapes +#define BOOST_TEST_MODULE alpha_shapes test #include #include #include diff --git a/src/Alpha_shapes/test/CMakeLists.txt b/src/Alpha_shapes/test/CMakeLists.txt index a48c1a8f..98a935db 100644 --- a/src/Alpha_shapes/test/CMakeLists.txt +++ b/src/Alpha_shapes/test/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required(VERSION 2.6) -project(GUDHIAlphaShapesTest) +project(GUDHIAlphaShapesUT) # need CGAL 4.6 # cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../.. @@ -16,9 +16,13 @@ if(CGAL_FOUND) include_directories (BEFORE "../../include") add_definitions(-DDEBUG_TRACES) - add_executable ( AlphaShapesUnitTest Alpha_shapes_unit_test.cpp ) - target_link_libraries(AlphaShapesUnitTest ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - add_test(AlphaShapesUnitTest ${CMAKE_CURRENT_BINARY_DIR}/AlphaShapesUnitTest) + add_executable ( AlphaShapesUT Alpha_shapes_unit_test.cpp ) + target_link_libraries(AlphaShapesUT ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + add_test(NAME AlphaShapesUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/AlphaShapesUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaShapesUT.xml --log_level=test_suite --report_level=no) + else() message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") diff --git a/src/Alpha_shapes/test/README b/src/Alpha_shapes/test/README index 244a2b84..cddd46ca 100644 --- a/src/Alpha_shapes/test/README +++ b/src/Alpha_shapes/test/README @@ -1,12 +1,14 @@ To compile: *********** +cd /path-to-gudhi/ cmake . +cd /path-to-test/ make To launch with details: *********************** -./AlphaShapesUnitTest --report_level=detailed --log_level=all +./AlphaShapesUT --report_level=detailed --log_level=all ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt index 7044372e..4492ab07 100644 --- a/src/Bottleneck/test/CMakeLists.txt +++ b/src/Bottleneck/test/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required(VERSION 2.6) -project(GUDHIBottleneckUnitTest) +project(GUDHIBottleneckUT) if(NOT MSVC) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") @@ -7,11 +7,14 @@ if(NOT MSVC) set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage") endif() -add_executable ( BottleneckUnitTest bottleneck_unit_test.cpp ) -target_link_libraries(BottleneckUnitTest ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +add_executable ( BottleneckUT bottleneck_unit_test.cpp ) +target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) # Unitary tests -add_test(BottleneckUnitTest ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUnitTest) +add_test(NAME BottleneckUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) if (LCOV_PATH) # Lcov code coverage of unitary test diff --git a/src/Persistent_cohomology/test/README b/src/Persistent_cohomology/test/README index 428af77b..6c64b5fe 100644 --- a/src/Persistent_cohomology/test/README +++ b/src/Persistent_cohomology/test/README @@ -1,7 +1,9 @@ To compile: *********** +cd /path-to-gudhi/ cmake . +cd /path-to-test/ make To launch with details: diff --git a/src/Simplex_tree/test/README b/src/Simplex_tree/test/README index bd8bf770..21c3d871 100644 --- a/src/Simplex_tree/test/README +++ b/src/Simplex_tree/test/README @@ -1,7 +1,9 @@ To compile: *********** +cd /path-to-gudhi/ cmake . +cd /path-to-test/ make To launch with details: -- cgit v1.2.3 From e3eabd1871b71499813a81ef9244e696bccaf461 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 1 Apr 2015 05:43:36 +0000 Subject: Try gcovr and corbera jenkins plugin git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@522 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8fd41c9ac5f6e6406276d1a06e3eceb4bf7b100b --- src/Simplex_tree/test/CMakeLists.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index f8cfc1a7..c45c89c7 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -2,9 +2,9 @@ cmake_minimum_required(VERSION 2.6) project(GUDHISimplexTreeUT) if(NOT MSVC) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp ) -- cgit v1.2.3 From 159c05027e2772d23f5a2c55bdd80ec84ca4e459 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 1 Apr 2015 06:16:19 +0000 Subject: Add gcovr code coverage for Corbera Jenkins plugin git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@523 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 094ab5eb2bc10d062c669ccb6747c3b87d69b23b --- src/Bottleneck/test/CMakeLists.txt | 12 ++++-------- src/Persistent_cohomology/test/CMakeLists.txt | 12 ++++-------- src/Simplex_tree/test/CMakeLists.txt | 6 +----- src/Skeleton_blocker/test/CMakeLists.txt | 15 ++++----------- 4 files changed, 13 insertions(+), 32 deletions(-) (limited to 'src') diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt index 4492ab07..8378f1f9 100644 --- a/src/Bottleneck/test/CMakeLists.txt +++ b/src/Bottleneck/test/CMakeLists.txt @@ -2,9 +2,10 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIBottleneckUT) if(NOT MSVC) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage") + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() add_executable ( BottleneckUT bottleneck_unit_test.cpp ) @@ -16,9 +17,4 @@ add_test(NAME BottleneckUT # XML format for Jenkins xUnit plugin --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) -if (LCOV_PATH) - # Lcov code coverage of unitary test - add_test(src/Bottleneck/lcov/coverage.log ${CMAKE_SOURCE_DIR}/scripts/check_code_coverage.sh ${CMAKE_SOURCE_DIR}/src/Bottleneck) -endif() - cpplint_add_tests("${CMAKE_SOURCE_DIR}/src/Bottleneck/include/gudhi") diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index d7564c11..41da1461 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -2,9 +2,10 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIPersistentCohomologyUT) if(NOT MSVC) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage") + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp ) @@ -30,9 +31,4 @@ if(GMPXX_FOUND AND GMP_FOUND) endif() -if (LCOV_PATH) - # Lcov code coverage of unitary test - add_test(src/Persistent_cohomology/lcov/coverage.log ${CMAKE_SOURCE_DIR}/scripts/check_code_coverage.sh ${CMAKE_SOURCE_DIR}/src/Persistent_cohomology) -endif() - cpplint_add_tests("${CMAKE_SOURCE_DIR}/src/Persistent_cohomology/include/gudhi") diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index c45c89c7..14cf930c 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -2,6 +2,7 @@ cmake_minimum_required(VERSION 2.6) project(GUDHISimplexTreeUT) if(NOT MSVC) + # for gcovr to make coverage reports - Corbera Jenkins plugin set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") @@ -16,9 +17,4 @@ add_test(NAME SimplexTreeUT # XML format for Jenkins xUnit plugin --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/SimplexTreeUT.xml --log_level=test_suite --report_level=no) -if (LCOV_PATH) - # Lcov code coverage of unitary test - add_test(src/Simplex_tree/lcov/coverage.log ${CMAKE_SOURCE_DIR}/scripts/check_code_coverage.sh ${CMAKE_SOURCE_DIR}/src/Simplex_tree) -endif() - cpplint_add_tests("${CMAKE_SOURCE_DIR}/src/Simplex_tree/include/gudhi") diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt index c69bfec7..9f343af5 100644 --- a/src/Skeleton_blocker/test/CMakeLists.txt +++ b/src/Skeleton_blocker/test/CMakeLists.txt @@ -2,11 +2,10 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIskbl) if(NOT MSVC) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g") - - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage") + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() add_executable(TestSkeletonBlockerComplex TestSkeletonBlockerComplex.cpp) @@ -17,10 +16,4 @@ add_test(TestSkeletonBlockerComplex ${CMAKE_CURRENT_BINARY_DIR}/TestSkeletonBloc add_test(TestSimplifiable ${CMAKE_CURRENT_BINARY_DIR}/TestSimplifiable) add_test(TestGeometricComplex ${CMAKE_CURRENT_BINARY_DIR}/TestGeometricComplex) - -if (LCOV_PATH) - # Lcov code coverage of unitary test - add_test(src/Skeleton_blocker/lcov/coverage.log ${CMAKE_SOURCE_DIR}/scripts/check_code_coverage.sh ${CMAKE_SOURCE_DIR}/src/Skeleton_blocker) -endif() - cpplint_add_tests("${CMAKE_SOURCE_DIR}/src/Skeleton_blocker/include/gudhi") -- cgit v1.2.3 From 92f5b06cbbff0f053f34503afddaeeb2c29efde1 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 1 Apr 2015 14:34:21 +0000 Subject: GCovr replaces lcov - cpplint_to_cppcheckxml to be conform with xml version 2 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@529 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e042eea0b285159f071afb0d07729e6c381f036d --- CMakeLists.txt | 6 +++--- scripts/cpplint_to_cppcheckxml.py | 15 +++++++++++++-- src/Alpha_shapes/test/CMakeLists.txt | 7 +++++++ src/Bottleneck/test/CMakeLists.txt | 4 ++-- src/Persistent_cohomology/test/CMakeLists.txt | 2 +- src/Simplex_tree/test/CMakeLists.txt | 2 +- src/Skeleton_blocker/test/CMakeLists.txt | 2 +- 7 files changed, 28 insertions(+), 10 deletions(-) (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index 89440490..b1ab9310 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -32,9 +32,9 @@ endif() find_package(CGAL) # Required programs for unitary tests purpose -FIND_PROGRAM( LCOV_PATH lcov ) -if (LCOV_PATH) - message("lcov found in ${LCOV_PATH}") +FIND_PROGRAM( GCOVR_PATH gcovr ) +if (GCOVR_PATH) + message("gcovr found in ${GCOVR_PATH}") endif() FIND_PROGRAM( PYTHON_PATH python ) diff --git a/scripts/cpplint_to_cppcheckxml.py b/scripts/cpplint_to_cppcheckxml.py index e3a2d2de..ecb36a48 100755 --- a/scripts/cpplint_to_cppcheckxml.py +++ b/scripts/cpplint_to_cppcheckxml.py @@ -27,7 +27,12 @@ def parse(): # TODO: do this properly, using the xml module. # Write header sys.stderr.write('''\n''') - sys.stderr.write('''\n''') + # VR : sys.stderr.write('''\n''') + # Add from VR + [ + sys.stderr.write('''\n''') + sys.stderr.write('''\n''') + sys.stderr.write('''\n''') + # -] # Do line-by-line conversion r = re.compile('([^:]*):([0-9]*): ([^\[]*)\[([^\]]*)\] \[([0-9]*)\].*') @@ -41,9 +46,15 @@ def parse(): continue fname, lineno, msg, label, score = g severity = cpplint_score_to_cppcheck_severity(int(score)) - sys.stderr.write('''\n'''%(fname, lineno, label, severity, msg)) + # VR : sys.stderr.write('''\n'''%(fname, lineno, label, severity, msg)) + # Add from VR + [ + sys.stderr.write('''\n\n'''%(fname, lineno, label, severity, msg)) + # -] # Write footer + # Add from VR + [ + sys.stderr.write('''\n'''%(fname, lineno, label, severity, msg)) + # -] sys.stderr.write('''\n''') diff --git a/src/Alpha_shapes/test/CMakeLists.txt b/src/Alpha_shapes/test/CMakeLists.txt index 98a935db..a820acc2 100644 --- a/src/Alpha_shapes/test/CMakeLists.txt +++ b/src/Alpha_shapes/test/CMakeLists.txt @@ -15,6 +15,13 @@ if(CGAL_FOUND) include( ${EIGEN3_USE_FILE} ) include_directories (BEFORE "../../include") + if (GCOVR_PATH) + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") + endif() + add_definitions(-DDEBUG_TRACES) add_executable ( AlphaShapesUT Alpha_shapes_unit_test.cpp ) target_link_libraries(AlphaShapesUT ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt index 8378f1f9..0e811c74 100644 --- a/src/Bottleneck/test/CMakeLists.txt +++ b/src/Bottleneck/test/CMakeLists.txt @@ -1,10 +1,10 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIBottleneckUT) -if(NOT MSVC) +if (GCOVR_PATH) # for gcovr to make coverage reports - Corbera Jenkins plugin set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index 41da1461..d8edbab6 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -1,7 +1,7 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIPersistentCohomologyUT) -if(NOT MSVC) +if (GCOVR_PATH) # for gcovr to make coverage reports - Corbera Jenkins plugin set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index 14cf930c..d63d9cba 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -1,7 +1,7 @@ cmake_minimum_required(VERSION 2.6) project(GUDHISimplexTreeUT) -if(NOT MSVC) +if (GCOVR_PATH) # for gcovr to make coverage reports - Corbera Jenkins plugin set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt index 9f343af5..d99e499e 100644 --- a/src/Skeleton_blocker/test/CMakeLists.txt +++ b/src/Skeleton_blocker/test/CMakeLists.txt @@ -1,7 +1,7 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIskbl) -if(NOT MSVC) +if (GCOVR_PATH) # for gcovr to make coverage reports - Corbera Jenkins plugin set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") -- cgit v1.2.3 From 4b884785f18d25196c337dee8f237e181e279652 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 2 Apr 2015 07:40:59 +0000 Subject: add gprof tags - cpplint_to_cppcheckxml.py fixes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/xunit@533 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fd6945efd5d63d78fd1f5120bf708a3aebdb90f5 --- CMakeLists.txt | 5 +++++ scripts/cpplint_to_cppcheckxml.py | 8 +++++--- src/Alpha_shapes/test/CMakeLists.txt | 6 ++++++ src/Bottleneck/test/CMakeLists.txt | 6 ++++++ src/Persistent_cohomology/test/CMakeLists.txt | 6 ++++++ src/Simplex_tree/test/CMakeLists.txt | 6 ++++++ src/Skeleton_blocker/test/CMakeLists.txt | 6 ++++++ 7 files changed, 40 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index b1ab9310..3b70ca6a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -36,6 +36,11 @@ FIND_PROGRAM( GCOVR_PATH gcovr ) if (GCOVR_PATH) message("gcovr found in ${GCOVR_PATH}") endif() +# Required programs for unitary tests purpose +FIND_PROGRAM( GPROF_PATH gprof ) +if (GPROF_PATH) + message("gprof found in ${GPROF_PATH}") +endif() FIND_PROGRAM( PYTHON_PATH python ) if (PYTHON_PATH) diff --git a/scripts/cpplint_to_cppcheckxml.py b/scripts/cpplint_to_cppcheckxml.py index 3d553a62..2447178f 100755 --- a/scripts/cpplint_to_cppcheckxml.py +++ b/scripts/cpplint_to_cppcheckxml.py @@ -30,8 +30,8 @@ def parse(): # VR : sys.stderr.write('''\n''') # Add from VR + [ sys.stderr.write('''\n''') - sys.stderr.write('''\n''') - sys.stderr.write('''\n''') + sys.stderr.write(''' \n''') + sys.stderr.write(''' \n''') # -] # Do line-by-line conversion @@ -48,7 +48,9 @@ def parse(): severity = cpplint_score_to_cppcheck_severity(int(score)) # VR : sys.stderr.write('''\n'''%(fname, lineno, label, severity, msg)) # Add from VR + [ - sys.stderr.write('''\n\n'''%(fname, lineno, label, severity, msg)) + sys.stderr.write(''' \n'''%(label, severity, msg)) + sys.stderr.write(''' \n'''%(fname, lineno)) + sys.stderr.write(''' \n'''%(fname, lineno)) # -] # Write footer diff --git a/src/Alpha_shapes/test/CMakeLists.txt b/src/Alpha_shapes/test/CMakeLists.txt index a820acc2..821aa5f2 100644 --- a/src/Alpha_shapes/test/CMakeLists.txt +++ b/src/Alpha_shapes/test/CMakeLists.txt @@ -21,6 +21,12 @@ if(CGAL_FOUND) set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() + if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") + endif() add_definitions(-DDEBUG_TRACES) add_executable ( AlphaShapesUT Alpha_shapes_unit_test.cpp ) diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt index 0e811c74..44be61f2 100644 --- a/src/Bottleneck/test/CMakeLists.txt +++ b/src/Bottleneck/test/CMakeLists.txt @@ -7,6 +7,12 @@ if (GCOVR_PATH) set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") +endif() add_executable ( BottleneckUT bottleneck_unit_test.cpp ) target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index d8edbab6..3258fe19 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -7,6 +7,12 @@ if (GCOVR_PATH) set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") +endif() add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp ) target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index d63d9cba..1563d082 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -7,6 +7,12 @@ if (GCOVR_PATH) set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") +endif() add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp ) target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt index d99e499e..f9b3de91 100644 --- a/src/Skeleton_blocker/test/CMakeLists.txt +++ b/src/Skeleton_blocker/test/CMakeLists.txt @@ -7,6 +7,12 @@ if (GCOVR_PATH) set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") +endif() add_executable(TestSkeletonBlockerComplex TestSkeletonBlockerComplex.cpp) add_executable(TestSimplifiable TestSimplifiable.cpp) -- cgit v1.2.3 From 3fcbf94481bced31a342f6accec015d8d057a38b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 7 Apr 2015 09:43:15 +0000 Subject: Fix windows errors git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/windowsbuildfix@543 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 267a1f3345b26d72c3722024fa1769dd41b6075b --- src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to 'src') diff --git a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h index 7e278209..a430fb4c 100644 --- a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h @@ -33,9 +33,6 @@ namespace Gudhi { namespace bottleneck { -// Diagram_point is the type of the persistence diagram's points -typedef typename std::pair Diagram_point; - // Return the used index for encoding none of the points int null_point_index(); @@ -44,6 +41,9 @@ int null_point_index(); class Persistence_diagrams_graph { public: + // Diagram_point is the type of the persistence diagram's points + typedef typename std::pair Diagram_point; + // Persistence_diagram1 and 2 are the types of any externals representations of persistence diagrams. // They have to have an iterator over points, which have to have fields first (for birth) and second (for death). template @@ -81,7 +81,7 @@ Persistence_diagrams_graph::Persistence_diagrams_graph(Persistence_diagram1& dia swap(u, v); } -Persistence_diagrams_graph::Persistence_diagrams_graph::Persistence_diagrams_graph() +Persistence_diagrams_graph::Persistence_diagrams_graph() : u(), v() { } inline bool Persistence_diagrams_graph::on_the_u_diagonal(int u_point_index) const { @@ -124,7 +124,7 @@ inline std::vector* Persistence_diagrams_graph::sorted_distances() { return new std::vector(sorted_distances.cbegin(), sorted_distances.cend()); } -inline Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) const { +inline Persistence_diagrams_graph::Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) const { if (!on_the_u_diagonal(u_point_index)) return u.at(u_point_index); Diagram_point projector = v.at(corresponding_point_in_v(u_point_index)); @@ -132,7 +132,7 @@ inline Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) return Diagram_point(x, x); } -inline Diagram_point Persistence_diagrams_graph::get_v_point(int v_point_index) const { +inline Persistence_diagrams_graph::Diagram_point Persistence_diagrams_graph::get_v_point(int v_point_index) const { if (!on_the_v_diagonal(v_point_index)) return v.at(v_point_index); Diagram_point projector = u.at(corresponding_point_in_u(v_point_index)); -- cgit v1.2.3 From 796945fff0a49073d28a56400390594e5ba2371b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 7 Apr 2015 12:38:11 +0000 Subject: Visual Studio errors fix git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/windowsbuildfix@545 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 86d04c258c64775217833a0fc5a76c53d5f7aaee --- .../include/gudhi/Persistence_diagrams_graph.h | 12 +- src/Contraction/example/Garland_heckbert.cpp | 207 ++++++++++----------- 2 files changed, 109 insertions(+), 110 deletions(-) (limited to 'src') diff --git a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h index a430fb4c..73ad940b 100644 --- a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h @@ -33,6 +33,9 @@ namespace Gudhi { namespace bottleneck { +// Diagram_point is the type of the persistence diagram's points +typedef std::pair Diagram_point; + // Return the used index for encoding none of the points int null_point_index(); @@ -41,9 +44,6 @@ int null_point_index(); class Persistence_diagrams_graph { public: - // Diagram_point is the type of the persistence diagram's points - typedef typename std::pair Diagram_point; - // Persistence_diagram1 and 2 are the types of any externals representations of persistence diagrams. // They have to have an iterator over points, which have to have fields first (for birth) and second (for death). template @@ -108,7 +108,7 @@ inline double Persistence_diagrams_graph::distance(int u_point_index, int v_poin return 0; Diagram_point p_u = get_u_point(u_point_index); Diagram_point p_v = get_v_point(v_point_index); - return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); + return (std::max)(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); } inline int Persistence_diagrams_graph::size() const { @@ -124,7 +124,7 @@ inline std::vector* Persistence_diagrams_graph::sorted_distances() { return new std::vector(sorted_distances.cbegin(), sorted_distances.cend()); } -inline Persistence_diagrams_graph::Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) const { +inline Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) const { if (!on_the_u_diagonal(u_point_index)) return u.at(u_point_index); Diagram_point projector = v.at(corresponding_point_in_v(u_point_index)); @@ -132,7 +132,7 @@ inline Persistence_diagrams_graph::Diagram_point Persistence_diagrams_graph::get return Diagram_point(x, x); } -inline Persistence_diagrams_graph::Diagram_point Persistence_diagrams_graph::get_v_point(int v_point_index) const { +inline Diagram_point Persistence_diagrams_graph::get_v_point(int v_point_index) const { if (!on_the_v_diagonal(v_point_index)) return v.at(v_point_index); Diagram_point projector = u.at(corresponding_point_in_u(v_point_index)); diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp index 5b178ff9..a41f65aa 100644 --- a/src/Contraction/example/Garland_heckbert.cpp +++ b/src/Contraction/example/Garland_heckbert.cpp @@ -7,7 +7,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 INRIA Sophia Antipolis-M�diterran�e (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 @@ -42,72 +42,70 @@ using namespace Gudhi; using namespace skbl; using namespace contraction; - -struct Geometry_trait{ - typedef Point_d Point; +struct Geometry_trait { + typedef Point_d Point; }; /** * The vertex stored in the complex contains a quadric. */ struct Garland_heckbert_traits : public Skeleton_blocker_simple_geometric_traits { + public: -public: - struct Garland_heckbert_vertex : public Simple_geometric_vertex{ - Error_quadric quadric; - }; - typedef Garland_heckbert_vertex Graph_vertex; + struct Garland_heckbert_vertex : public Simple_geometric_vertex { + Error_quadric quadric; + }; + typedef Garland_heckbert_vertex Graph_vertex; }; typedef Skeleton_blocker_geometric_complex< Garland_heckbert_traits > Complex; typedef Edge_profile EdgeProfile; typedef Skeleton_blocker_contractor Complex_contractor; - /** * How the new vertex is placed after an edge collapse : here it is placed at * the point minimizing the cost of the quadric. */ -class GH_placement : public Gudhi::contraction::Placement_policy{ - Complex& complex_; -public: - typedef typename Gudhi::contraction::Placement_policy::Placement_type Placement_type; - - GH_placement(Complex& complex):complex_(complex){} - - Placement_type operator()(const EdgeProfile& profile) const override{ - auto sum_quad(profile.v0().quadric); - sum_quad += profile.v1().quadric; - - boost::optional min_quadric_pt(sum_quad.min_cost()); - if (min_quadric_pt) - return Placement_type(*min_quadric_pt); - else - return profile.p0(); - } +class GH_placement : public Gudhi::contraction::Placement_policy { + Complex& complex_; + public: + typedef Gudhi::contraction::Placement_policy::Placement_type Placement_type; + + GH_placement(Complex& complex) : complex_(complex) { } + + Placement_type operator()(const EdgeProfile& profile) const override { + auto sum_quad(profile.v0().quadric); + sum_quad += profile.v1().quadric; + + boost::optional min_quadric_pt(sum_quad.min_cost()); + if (min_quadric_pt) + return Placement_type(*min_quadric_pt); + else + return profile.p0(); + } }; /** * How much cost an edge collapse : here the costs is given by a quadric * which expresses a squared distances with triangles planes. */ -class GH_cost : public Gudhi::contraction::Cost_policy{ - Complex& complex_; -public: - - typedef typename Gudhi::contraction::Cost_policy::Cost_type Cost_type; - - GH_cost(Complex& complex):complex_(complex){} - - Cost_type operator()( EdgeProfile const& profile, boost::optional const& new_point ) const override { - Cost_type res; - if (new_point){ - auto sum_quad(profile.v0().quadric); - sum_quad += profile.v1().quadric; - res = sum_quad.cost(*new_point); - } - return res; - } +class GH_cost : public Gudhi::contraction::Cost_policy { + Complex& complex_; + public: + + typedef Gudhi::contraction::Cost_policy::Cost_type Cost_type; + + GH_cost(Complex& complex) : complex_(complex) { } + + Cost_type operator()(EdgeProfile const& profile, boost::optional const& new_point) const override { + Cost_type res; + if (new_point) { + auto sum_quad(profile.v0().quadric); + sum_quad += profile.v1().quadric; + res = sum_quad.cost(*new_point); + } + return res; + } }; /** @@ -115,79 +113,80 @@ public: * Here we initializes the quadrics of every vertex at the on_started call back * and we update them when contracting an edge (the quadric become the sum of both quadrics). */ -class GH_visitor: public Gudhi::contraction::Contraction_visitor { - Complex& complex_; -public: - GH_visitor(Complex& complex):complex_(complex){} - - //Compute quadrics for every vertex v - //The quadric of v consists in the sum of quadric - //of every triangles passing through v weighted by its area - void on_started(Complex & complex) override{ - for(auto v : complex.vertex_range()){ - auto & quadric_v(complex[v].quadric); - for(auto t : complex.triangle_range(v)){ - auto t_it = t.begin(); - const auto& p0(complex.point(*t_it++)); - const auto& p1(complex.point(*t_it++)); - const auto& p2(complex.point(*t_it++)); - quadric_v+=Error_quadric(p0,p1,p2); - } - } - } - - /** - * @brief Called when an edge is about to be contracted and replaced by a vertex whose position is *placement. - */ - void on_contracting(EdgeProfile const &profile, boost::optional< Point > placement) - override{ - profile.v0().quadric += profile.v1().quadric; - } +class GH_visitor : public Gudhi::contraction::Contraction_visitor { + Complex& complex_; + public: + + GH_visitor(Complex& complex) : complex_(complex) { } + + //Compute quadrics for every vertex v + //The quadric of v consists in the sum of quadric + //of every triangles passing through v weighted by its area + + void on_started(Complex & complex) override { + for (auto v : complex.vertex_range()) { + auto & quadric_v(complex[v].quadric); + for (auto t : complex.triangle_range(v)) { + auto t_it = t.begin(); + const auto& p0(complex.point(*t_it++)); + const auto& p1(complex.point(*t_it++)); + const auto& p2(complex.point(*t_it++)); + quadric_v += Error_quadric(p0, p1, p2); + } + } + } + + /** + * @brief Called when an edge is about to be contracted and replaced by a vertex whose position is *placement. + */ + void on_contracting(EdgeProfile const &profile, boost::optional< Point > placement) + override { + profile.v0().quadric += profile.v1().quadric; + } }; +int main(int argc, char *argv[]) { + if (argc != 4) { + std::cerr << "Usage " << argv[0] << " input.off output.off N to load the file input.off, contract N edges and save the result to output.off.\n"; + return EXIT_FAILURE; + } -int main(int argc, char *argv[]){ - if (argc!=4){ - std::cerr << "Usage "< off_reader(argv[1],complex); - if(!off_reader.is_valid()){ - std::cerr << "Unable to read file:"< off_reader(argv[1], complex); + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file:" << argv[1] << std::endl; + return EXIT_FAILURE; + } - std::cout << "Load complex with "<(), - new GH_visitor(complex) - ); + // constructs the contractor object with Garland Heckbert policies. + Complex_contractor contractor(complex, + new GH_cost(complex), + new GH_placement(complex), + contraction::make_link_valid_contraction(), + new GH_visitor(complex) + ); - std::cout<<"Contract "< off_writer(argv[2],complex); + //write simplified complex + Skeleton_blocker_off_writer off_writer(argv[2], complex); - return EXIT_SUCCESS; + return EXIT_SUCCESS; } -- cgit v1.2.3 From 77e2bd4771ff38ae3159f902cc95704ce7edeecd Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 10 Apr 2015 10:17:43 +0000 Subject: Optimization of UT (needs to be short time) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/multifieldoptimization@560 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3e1561da87b9a46f8628a59c3862c0235eee01c5 --- src/Persistent_cohomology/example/CMakeLists.txt | 2 - ...persistent_cohomology_unit_test_multi_field.cpp | 84 +++++++++------------- ...simplex_tree_file_for_multi_field_unit_test.txt | 58 +++++++++++++++ ...le_for_multi_field_unit_test.txt.REMOVED.git-id | 1 - 4 files changed, 93 insertions(+), 52 deletions(-) create mode 100644 src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt delete mode 100644 src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt.REMOVED.git-id (limited to 'src') diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 3697a419..08589f07 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -9,7 +9,6 @@ if (NOT MSVC) add_executable(rips_persistence rips_persistence.cpp) target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_test(rips_persistence_2 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100) add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100) add_executable(persistence_from_file persistence_from_file.cpp) @@ -23,7 +22,6 @@ if (NOT MSVC) add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) - add_test(rips_multifield_persistence_2_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100) add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100) add_executable ( performance_rips_persistence performance_rips_persistence.cpp ) diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp index 8802005c..18a4725e 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp @@ -37,9 +37,9 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, int << " - filtration= " << st.filtration() << std::endl; // Check - BOOST_CHECK(st.num_simplices() == 6142604); + BOOST_CHECK(st.num_simplices() == 58); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(st.filtration() == 0.249999); + BOOST_CHECK(st.filtration() == 0.4); // Sort the simplices in the order of the filtration st.initialize_filtration(); @@ -47,9 +47,9 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, int // Compute the persistence diagram of the complex Persistent_cohomology, Multi_field> pcoh(st); - pcoh.init_coefficients(min_coefficient, max_coefficient); // initializes the coefficient field for homology + pcoh.init_coefficients(min_coefficient, max_coefficient); // initializes the coefficient field for homology // Check infinite rips - pcoh.compute_persistent_cohomology(min_persistence); // Minimal lifetime of homology feature to be recorded. + pcoh.compute_persistent_cohomology(min_persistence); // Minimal lifetime of homology feature to be recorded. std::ostringstream ossRips; pcoh.output_diagram(ossRips); @@ -59,68 +59,54 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, int } void test_rips_persistence_in_dimension(int min_dimension, int max_dimension) { - std::string value0(" 0 0 inf"); - std::string value1(" 1 0.0702103 inf"); - std::string value2("2 1 0.0702103 inf"); - std::string value3("2 2 0.159992 inf"); + // there are 2 discontinued ensembles + std::string value0(" 0 0.25 inf"); + std::string value1(" 1 0.4 inf"); + // And a big hole - cut in 2 pieces after 0.3 + std::string value2(" 0 0.2 0.3"); + + // For dim <= 1 => + std::string value3(" 1 0.25 inf"); + std::string value4(" 2 0.25 inf"); + std::string value5(" 1 0.3 inf"); + std::string value6(" 2 0.3 inf"); + std::string value7(" 2 0.4 inf"); std::cout << "********************************************************************" << std::endl; std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_MULTI_FIELD MIN_DIM=" << min_dimension << " MAX_DIM=" << max_dimension << " MIN_PERS=0" << std::endl; - std::string str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, 1); - - BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found - std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; - - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_MULTI_FIELD DIM=" << min_dimension << " MAX_DIM=" << max_dimension << " MIN_PERS=2" << std::endl; - - str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, 2); - - BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found + std::string str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, static_cast (0.0)); std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_MULTI_FIELD DIM=" << min_dimension << " MAX_DIM=" << max_dimension << " MIN_PERS=3" << std::endl; - - str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, 3); - BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found - std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_MULTI_FIELD DIM=" << min_dimension << " MAX_DIM=" << max_dimension << " MIN_PERS=Inf" << std::endl; + if ((min_dimension < 2) && (max_dimension < 2)) { + BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found + BOOST_CHECK(str_rips_persistence.find(value4) != std::string::npos); // Check found + BOOST_CHECK(str_rips_persistence.find(value5) != std::string::npos); // Check found + BOOST_CHECK(str_rips_persistence.find(value6) != std::string::npos); // Check found + BOOST_CHECK(str_rips_persistence.find(value7) != std::string::npos); // Check found + } else { + BOOST_CHECK(str_rips_persistence.find(value3) == std::string::npos); // Check not found + BOOST_CHECK(str_rips_persistence.find(value4) == std::string::npos); // Check not found + BOOST_CHECK(str_rips_persistence.find(value5) == std::string::npos); // Check not found + BOOST_CHECK(str_rips_persistence.find(value6) == std::string::npos); // Check not found + BOOST_CHECK(str_rips_persistence.find(value7) == std::string::npos); // Check not found + } - str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, std::numeric_limits::max()); - - BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found - std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; } -BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_multi_field_dim_1_2 ) -{ - test_rips_persistence_in_dimension(1, 2); +BOOST_AUTO_TEST_CASE(rips_persistent_cohomology_multi_field_dim_1_2) { + test_rips_persistence_in_dimension(0, 1); } -BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_multi_field_dim_2_3 ) -{ - test_rips_persistence_in_dimension(2, 3); +BOOST_AUTO_TEST_CASE(rips_persistent_cohomology_multi_field_dim_2_3) { + test_rips_persistence_in_dimension(1, 3); } -BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_multi_field_dim_1_5 ) -{ +BOOST_AUTO_TEST_CASE(rips_persistent_cohomology_multi_field_dim_1_5) { test_rips_persistence_in_dimension(1, 5); } diff --git a/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt b/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt new file mode 100644 index 00000000..ed2c0c3d --- /dev/null +++ b/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt @@ -0,0 +1,58 @@ +0 0 0.2 +0 3 0.2 +1 3 0 0.2 +0 6 0.2 +0 11 0.2 +1 11 6 0.2 +0 13 0.25 +0 14 0.25 +1 14 13 0.25 +0 15 0.25 +1 15 13 0.25 +1 15 14 0.25 +2 15 14 13 0.25 +0 1 0.3 +1 1 0 0.3 +0 2 0.3 +1 2 0 0.3 +1 2 1 0.3 +2 2 1 0 0.3 +0 4 0.3 +1 4 3 0.3 +0 5 0.3 +1 5 3 0.3 +1 5 4 0.3 +2 5 4 3 0.3 +0 9 0.3 +0 10 0.3 +1 10 2 0.3 +1 10 9 0.3 +1 11 9 0.3 +1 11 10 0.3 +2 11 10 9 0.3 +0 12 0.3 +1 12 2 0.3 +1 12 10 0.3 +2 12 10 2 0.3 +1 6 0 0.4 +1 6 1 0.4 +2 6 1 0 0.4 +0 7 0.4 +1 7 0 0.4 +1 7 1 0.4 +2 7 1 0 0.4 +1 7 6 0.4 +2 7 6 0 0.4 +2 7 6 1 0.4 +3 7 6 1 0 0.4 +0 8 0.4 +1 8 4 0.4 +1 8 5 0.4 +2 8 5 4 0.4 +1 9 4 0.4 +1 9 5 0.4 +2 9 5 4 0.4 +1 9 8 0.4 +2 9 8 4 0.4 +2 9 8 5 0.4 +3 9 8 5 4 0.4 diff --git a/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt.REMOVED.git-id b/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt.REMOVED.git-id deleted file mode 100644 index 2dd38515..00000000 --- a/src/Persistent_cohomology/test/simplex_tree_file_for_multi_field_unit_test.txt.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -ce87199d425b05f51c74cbf635870bfa5abbc7a1 \ No newline at end of file -- cgit v1.2.3 From 77c7765f5079713a5fa729b0992d2d92eea8f57b Mon Sep 17 00:00:00 2001 From: glisse Date: Sat, 11 Apr 2015 10:24:46 +0000 Subject: Images and headers should not be executable. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@563 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2c3caac0e8a0ddfc7365ed02997aaab9b4dc5c17 --- data/points/COIL_database/asian_mug.off | 0 data/points/COIL_database/images/asian mug/obj12__0.png | Bin data/points/COIL_database/images/asian mug/obj12__1.png | Bin 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b/data/points/SO3_10000.off old mode 100755 new mode 100644 diff --git a/data/points/SO3_50000.off b/data/points/SO3_50000.off old mode 100755 new mode 100644 diff --git a/data/points/sphere3D_2646.off b/data/points/sphere3D_2646.off old mode 100755 new mode 100644 diff --git a/data/points/tore3D_1307.off b/data/points/tore3D_1307.off old mode 100755 new mode 100644 diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h old mode 100755 new mode 100644 diff --git a/src/GudhUI/view/Viewer.h b/src/GudhUI/view/Viewer.h old mode 100755 new mode 100644 diff --git a/src/GudhUI/view/Viewer_instructor.h b/src/GudhUI/view/Viewer_instructor.h old mode 100755 new mode 100644 -- cgit v1.2.3 From 691f6d886703271f14f966cb5120462667fb3a6a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 16 Apr 2015 08:38:23 +0000 Subject: CMakeLists.txt fix for version generation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@569 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 599df696ef30c80a72f0a91528b271ae009163cc --- src/CMakeLists.txt | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) (limited to 'src') diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index ceb993fa..057b0c4f 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -10,25 +10,34 @@ if (NOT CMAKE_BUILD_TYPE) set(CMAKE_BUILD_TYPE "Release") endif() if(MSVC) - SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") + SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") else() - list(APPEND CMAKE_CXX_FLAGS "-std=c++11") -endif() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") +endif() -# BOOST ISSUE result_of vs C++11 -add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) +set(Boost_USE_STATIC_LIBS ON) +set(Boost_USE_MULTITHREADED ON) +set(Boost_USE_STATIC_RUNTIME OFF) -find_package(Boost) +find_package(Boost) find_package(GMP) if(GMP_FOUND) - find_package(GMPXX) + find_package(GMPXX) endif() + find_package(CGAL) if(NOT Boost_FOUND) message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.") else() - INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) + # BOOST ISSUE result_of vs C++11 + add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) + # BOOST ISSUE with Libraries name resolution under Windows + add_definitions(-DBOOST_ALL_NO_LIB) + + INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) include_directories(include/) -- cgit v1.2.3 From c739b2dc9916bce098560b255e2dd48c94cca83f Mon Sep 17 00:00:00 2001 From: glisse Date: Fri, 24 Apr 2015 09:37:01 +0000 Subject: We shouldn't mess with flags in the release version of CMakeLists.txt (the one at the root if free for any abuse though). git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@570 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 93b1fdf641fa19010f6dbeca755fffd87ee7d12a --- src/CMakeLists.txt | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'src') diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 057b0c4f..55aa8a65 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -12,9 +12,7 @@ endif() if(MSVC) SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") endif() set(Boost_USE_STATIC_LIBS ON) -- cgit v1.2.3 From 513893162870c81255b9b9458dfff58c35436644 Mon Sep 17 00:00:00 2001 From: glisse Date: Fri, 24 Apr 2015 12:32:50 +0000 Subject: Unnecessary new+delete pair. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@571 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 35f4b8e850bba9b72ab9e732dead3c0393e66a9a --- .../include/gudhi/Persistent_cohomology.h | 25 ++++++++++------------ 1 file changed, 11 insertions(+), 14 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index c42e4be4..4d274f53 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -238,8 +238,8 @@ class Persistent_cohomology { transverse_idx_(), // key -> row persistent_pairs_(), interval_length_policy(&cpx, 0), - column_pool_(new boost::object_pool()), // memory pools for the CAM - cell_pool_(new boost::object_pool()) { + column_pool_(), // memory pools for the CAM + cell_pool_() { Simplex_key idx_fil = 0; for (auto & sh : cpx_->filtration_simplex_range()) { cpx_->assign_key(sh, idx_fil); @@ -273,9 +273,6 @@ class Persistent_cohomology { transverse_ref.second.row_->clear(); delete transverse_ref.second.row_; } -// Clear the memory pools - delete column_pool_; - delete cell_pool_; } private: @@ -528,8 +525,8 @@ class Persistent_cohomology { Arith_element charac) { Simplex_key key = cpx_->key(sigma); // Create a column containing only one cell, - Column * new_col = column_pool_->construct(Column(key)); - Cell * new_cell = cell_pool_->construct(Cell(key, x, new_col)); + Column * new_col = column_pool_.construct(Column(key)); + Cell * new_cell = cell_pool_.construct(Cell(key, x, new_col)); new_col->col_.push_back(*new_cell); // and insert it in the matrix, in constant time thanks to the hint cam_.end(). // Indeed *new_col has the biggest lexicographic value because key is the @@ -585,7 +582,7 @@ class Persistent_cohomology { if (curr_col->col_.empty()) { // If the column is null ds_repr_[curr_col->class_key_] = NULL; - column_pool_->free(curr_col); // delete curr_col; + column_pool_.free(curr_col); // delete curr_col; } else { // Find whether the column obtained is already in the CAM result_insert_cam = cam_.insert(*curr_col); @@ -602,7 +599,7 @@ class Persistent_cohomology { Simplex_key key_tmp = dsets_.find_set(curr_col->class_key_); ds_repr_[key_tmp] = &(*(result_insert_cam.first)); result_insert_cam.first->class_key_ = key_tmp; - column_pool_->free(curr_col); // delete curr_col; + column_pool_.free(curr_col); // delete curr_col; } } } else { @@ -634,7 +631,7 @@ class Persistent_cohomology { ++target_it; } else { if (target_it->key_ > other_it->first) { - Cell * cell_tmp = cell_pool_->construct(Cell(other_it->first // key + Cell * cell_tmp = cell_pool_.construct(Cell(other_it->first // key , coeff_field_.additive_identity(), &target)); cell_tmp->coefficient_ = coeff_field_.plus_times_equal(cell_tmp->coefficient_, other_it->second, w); @@ -653,7 +650,7 @@ class Persistent_cohomology { target.col_.erase(tmp_it); // removed from column coeff_field_.clear_coefficient(tmp_cell_ptr->coefficient_); - cell_pool_->free(tmp_cell_ptr); // delete from memory + cell_pool_.free(tmp_cell_ptr); // delete from memory } else { ++target_it; ++other_it; @@ -662,7 +659,7 @@ class Persistent_cohomology { } } while (other_it != other.end()) { - Cell * cell_tmp = cell_pool_->construct(Cell(other_it->first, coeff_field_.additive_identity(), &target)); + Cell * cell_tmp = cell_pool_.construct(Cell(other_it->first, coeff_field_.additive_identity(), &target)); cell_tmp->coefficient_ = coeff_field_.plus_times_equal(cell_tmp->coefficient_, other_it->second, w); target.col_.insert(target.col_.end(), *cell_tmp); @@ -767,8 +764,8 @@ class Persistent_cohomology { std::list persistent_pairs_; length_interval interval_length_policy; - boost::object_pool * column_pool_; - boost::object_pool * cell_pool_; + boost::object_pool column_pool_; + boost::object_pool cell_pool_; }; /** @} */ // end defgroup persistent_cohomology -- cgit v1.2.3 From 21de85d3cfd3f7b90f3d25aa08132a75aa6a1d98 Mon Sep 17 00:00:00 2001 From: glisse Date: Fri, 24 Apr 2015 12:48:14 +0000 Subject: Plug small leak. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@572 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 023a64fe20ea940a9f47a101cce627b7facf2f41 --- .../include/gudhi/Persistent_cohomology/Multi_field.h | 1 + 1 file changed, 1 insertion(+) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h index b43bb16e..60ab7f41 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h @@ -77,6 +77,7 @@ class Multi_field { mpz_nextprime(tmp_prime, tmp_prime); curr_prime = mpz_get_ui(tmp_prime); } + mpz_clear(tmp_prime); // set m to primorial(bound_prime) prod_characteristics_ = 1; for (auto p : primes_) { -- cgit v1.2.3 From ef4f1b9b2a6c30777696763198cd4b5494c8ab4d Mon Sep 17 00:00:00 2001 From: glisse Date: Sat, 25 Apr 2015 09:18:04 +0000 Subject: Let destructors do the cleanup. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@573 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a8e9e64a5317ab368832facdf8e34739cfe9b473 --- src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h | 3 +-- .../include/gudhi/Persistent_cohomology/Field_Zp.h | 3 --- .../include/gudhi/Persistent_cohomology/Multi_field.h | 4 ---- 3 files changed, 1 insertion(+), 9 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index 4d274f53..3606754a 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -649,8 +649,7 @@ class Persistent_cohomology { Cell * tmp_cell_ptr = &(*tmp_it); target.col_.erase(tmp_it); // removed from column - coeff_field_.clear_coefficient(tmp_cell_ptr->coefficient_); - cell_pool_.free(tmp_cell_ptr); // delete from memory + cell_pool_.destroy(tmp_cell_ptr); // delete from memory } else { ++target_it; ++other_it; diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h index 5d0c9f9f..2349cdac 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h @@ -76,9 +76,6 @@ class Field_Zp { return plus_times_equal(0, y, (Element)w); } - void clear_coefficient(Element x) { - } - Element plus_equal(const Element& x, const Element& y) { return plus_times_equal(x, y, (Element)1); } diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h index 60ab7f41..c6fd5282 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h @@ -103,10 +103,6 @@ class Multi_field { } } - void clear_coefficient(Element & x) { - mpz_clear(x.get_mpz_t()); - } - /** \brief Returns the additive idendity \f$0_{\Bbbk}\f$ of the field.*/ const Element& additive_identity() const { return add_id_all; -- cgit v1.2.3 From 0cfb83782c7acaba8979dbf2e2112b669703a327 Mon Sep 17 00:00:00 2001 From: glisse Date: Sat, 25 Apr 2015 09:37:40 +0000 Subject: Don't skip destructors even if the type is currently POD. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@574 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ba20755d2b52257f02ae4880a619f7bcc2ac1b14 --- src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index 3606754a..b0d68f09 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -582,7 +582,7 @@ class Persistent_cohomology { if (curr_col->col_.empty()) { // If the column is null ds_repr_[curr_col->class_key_] = NULL; - column_pool_.free(curr_col); // delete curr_col; + column_pool_.destroy(curr_col); // delete curr_col; } else { // Find whether the column obtained is already in the CAM result_insert_cam = cam_.insert(*curr_col); @@ -599,7 +599,7 @@ class Persistent_cohomology { Simplex_key key_tmp = dsets_.find_set(curr_col->class_key_); ds_repr_[key_tmp] = &(*(result_insert_cam.first)); result_insert_cam.first->class_key_ = key_tmp; - column_pool_.free(curr_col); // delete curr_col; + column_pool_.destroy(curr_col); // delete curr_col; } } } else { -- cgit v1.2.3 From 94a76bf4ca59d950e56a58f4e8e95746eafcbdb4 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 27 Apr 2015 09:00:30 +0000 Subject: Release is the default build type git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@575 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ebbf91997352d86d7e7c17e70d9ba1161110af2b --- src/common/doc/main_page.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src') diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 83908905..7fa6e289 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -51,7 +51,7 @@ To build the library, run the following in a terminal: cd /path-to-gudhi/ mkdir build cd build/ -cmake -DCMAKE_BUILD_TYPE=Release .. +cmake .. make \endverbatim -- cgit v1.2.3 From 776e3e52bc61c1a52e0cf402fe7daaf86131bfe1 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 27 Apr 2015 09:07:06 +0000 Subject: Remove debug traces by default git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@576 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 665d5365d12317bd62ce57a94f43247e6a1e55e4 --- src/Alpha_shapes/example/CMakeLists.txt | 3 ++- src/Alpha_shapes/test/CMakeLists.txt | 3 ++- src/Persistent_cohomology/example/CMakeLists.txt | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/src/Alpha_shapes/example/CMakeLists.txt b/src/Alpha_shapes/example/CMakeLists.txt index fb94ca05..753238a5 100644 --- a/src/Alpha_shapes/example/CMakeLists.txt +++ b/src/Alpha_shapes/example/CMakeLists.txt @@ -19,7 +19,8 @@ if(CGAL_FOUND) target_link_libraries(dtoffrw ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3) - #add_definitions(-DDEBUG_TRACES) + # uncomment to display debug traces + # add_definitions(-DDEBUG_TRACES) add_executable ( stfromdt Simplex_tree_from_delaunay_triangulation.cpp ) target_link_libraries(stfromdt ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) else() diff --git a/src/Alpha_shapes/test/CMakeLists.txt b/src/Alpha_shapes/test/CMakeLists.txt index 7d61a3dd..e0d33827 100644 --- a/src/Alpha_shapes/test/CMakeLists.txt +++ b/src/Alpha_shapes/test/CMakeLists.txt @@ -28,7 +28,8 @@ if(CGAL_FOUND) set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") endif() - add_definitions(-DDEBUG_TRACES) + # uncomment to display debug traces + # add_definitions(-DDEBUG_TRACES) add_executable ( AlphaShapesUT Alpha_shapes_unit_test.cpp ) target_link_libraries(AlphaShapesUT ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) add_test(NAME AlphaShapesUT diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 08589f07..9487cce6 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -28,7 +28,8 @@ if (NOT MSVC) target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if(CGAL_FOUND) - add_definitions(-DDEBUG_TRACES) + # uncomment to display debug traces + # add_definitions(-DDEBUG_TRACES) add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) -- cgit v1.2.3 From 44e58d011b097377507bff3bf87155f7f196644a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 27 Apr 2015 09:36:45 +0000 Subject: This trace is not needed git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@577 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d27d2814b1437e3cad6d87d1c77a39136379a13c --- src/Persistent_cohomology/example/rips_multifield_persistence.cpp | 2 -- 1 file changed, 2 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp index 2505897e..297a8f98 100644 --- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -70,8 +70,6 @@ int main (int argc, char * argv[]) st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree st.expansion( dim_max ); // expand the graph until dimension dim_max - std::cout << "st=" << st << std::endl; - // Sort the simplices in the order of the filtration st.initialize_filtration(); -- cgit v1.2.3 From e5e9fd63017729934a3027ef90fcdd52ae476dc4 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 27 Apr 2015 09:50:50 +0000 Subject: typeSimplex was complexifying code git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@578 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: eccf3abad2aca085d7af51caf2a44829a5d0a75c --- src/Simplex_tree/example/simple_simplex_tree.cpp | 34 ++++++++---------------- 1 file changed, 11 insertions(+), 23 deletions(-) (limited to 'src') diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index bde224f1..6d20e43e 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -28,7 +28,6 @@ using namespace Gudhi; typedef std::vector< Vertex_handle > typeVectorVertex; -typedef std::pair typeSimplex; typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool; int main(int argc, char * const argv[]) { @@ -58,9 +57,8 @@ int main(int argc, char * const argv[]) { std::cout << " * INSERT 0" << std::endl; typeVectorVertex firstSimplexVector; firstSimplexVector.push_back(FIRST_VERTEX_HANDLE); - typeSimplex firstSimplex = std::make_pair(firstSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); typePairSimplexBool returnValue = - simplexTree.insert_simplex(firstSimplex.first, firstSimplex.second); + simplexTree.insert_simplex(firstSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 0 INSERTED" << std::endl; @@ -74,9 +72,8 @@ int main(int argc, char * const argv[]) { std::cout << " * INSERT 1" << std::endl; typeVectorVertex secondSimplexVector; secondSimplexVector.push_back(SECOND_VERTEX_HANDLE); - typeSimplex secondSimplex = std::make_pair(secondSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(secondSimplex.first, secondSimplex.second); + simplexTree.insert_simplex(secondSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 1 INSERTED" << std::endl; @@ -91,9 +88,8 @@ int main(int argc, char * const argv[]) { typeVectorVertex thirdSimplexVector; thirdSimplexVector.push_back(FIRST_VERTEX_HANDLE); thirdSimplexVector.push_back(SECOND_VERTEX_HANDLE); - typeSimplex thirdSimplex = std::make_pair(thirdSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(thirdSimplex.first, thirdSimplex.second); + simplexTree.insert_simplex(thirdSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (0,1) INSERTED" << std::endl; @@ -107,9 +103,8 @@ int main(int argc, char * const argv[]) { std::cout << " * INSERT 2" << std::endl; typeVectorVertex fourthSimplexVector; fourthSimplexVector.push_back(THIRD_VERTEX_HANDLE); - typeSimplex fourthSimplex = std::make_pair(fourthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(fourthSimplex.first, fourthSimplex.second); + simplexTree.insert_simplex(fourthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 2 INSERTED" << std::endl; @@ -124,9 +119,8 @@ int main(int argc, char * const argv[]) { typeVectorVertex fifthSimplexVector; fifthSimplexVector.push_back(THIRD_VERTEX_HANDLE); fifthSimplexVector.push_back(FIRST_VERTEX_HANDLE); - typeSimplex fifthSimplex = std::make_pair(fifthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(fifthSimplex.first, fifthSimplex.second); + simplexTree.insert_simplex(fifthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (2,0) INSERTED" << std::endl; @@ -141,9 +135,8 @@ int main(int argc, char * const argv[]) { typeVectorVertex sixthSimplexVector; sixthSimplexVector.push_back(THIRD_VERTEX_HANDLE); sixthSimplexVector.push_back(SECOND_VERTEX_HANDLE); - typeSimplex sixthSimplex = std::make_pair(sixthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(sixthSimplex.first, sixthSimplex.second); + simplexTree.insert_simplex(sixthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (2,1) INSERTED" << std::endl; @@ -159,9 +152,8 @@ int main(int argc, char * const argv[]) { seventhSimplexVector.push_back(THIRD_VERTEX_HANDLE); seventhSimplexVector.push_back(SECOND_VERTEX_HANDLE); seventhSimplexVector.push_back(FIRST_VERTEX_HANDLE); - typeSimplex seventhSimplex = std::make_pair(seventhSimplexVector, Filtration_value(THIRD_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(seventhSimplex.first, seventhSimplex.second); + simplexTree.insert_simplex(seventhSimplexVector, Filtration_value(THIRD_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (2,1,0) INSERTED" << std::endl; @@ -175,9 +167,8 @@ int main(int argc, char * const argv[]) { std::cout << " * INSERT 3" << std::endl; typeVectorVertex eighthSimplexVector; eighthSimplexVector.push_back(FOURTH_VERTEX_HANDLE); - typeSimplex eighthSimplex = std::make_pair(eighthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(eighthSimplex.first, eighthSimplex.second); + simplexTree.insert_simplex(eighthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 3 INSERTED" << std::endl; @@ -192,9 +183,8 @@ int main(int argc, char * const argv[]) { typeVectorVertex ninethSimplexVector; ninethSimplexVector.push_back(FOURTH_VERTEX_HANDLE); ninethSimplexVector.push_back(FIRST_VERTEX_HANDLE); - typeSimplex ninethSimplex = std::make_pair(ninethSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(ninethSimplex.first, ninethSimplex.second); + simplexTree.insert_simplex(ninethSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (3,0) INSERTED" << std::endl; @@ -208,9 +198,8 @@ int main(int argc, char * const argv[]) { std::cout << " * INSERT 0 (already inserted)" << std::endl; typeVectorVertex tenthSimplexVector; tenthSimplexVector.push_back(FIRST_VERTEX_HANDLE); - typeSimplex tenthSimplex = std::make_pair(tenthSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE)); // With a different filtration value returnValue = - simplexTree.insert_simplex(tenthSimplex.first, tenthSimplex.second); + simplexTree.insert_simplex(tenthSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE)); // With a different filtration value if (returnValue.second == true) { std::cout << " + 0 INSERTED" << std::endl; @@ -226,9 +215,8 @@ int main(int argc, char * const argv[]) { eleventhSimplexVector.push_back(THIRD_VERTEX_HANDLE); eleventhSimplexVector.push_back(SECOND_VERTEX_HANDLE); eleventhSimplexVector.push_back(FIRST_VERTEX_HANDLE); - typeSimplex eleventhSimplex = std::make_pair(eleventhSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE)); returnValue = - simplexTree.insert_simplex(eleventhSimplex.first, eleventhSimplex.second); + simplexTree.insert_simplex(eleventhSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (2,1,0) INSERTED" << std::endl; -- cgit v1.2.3 From 0b881d5dd5237e545efd6ada1010c51f1f50badd Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 28 Apr 2015 11:34:43 +0000 Subject: GudhUI compilation issue and generate version for GudhUI issue fixes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@583 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: beea454e849615bb9d087ccdcb0110a146a42564 --- CMakeLists.txt | 3 + scripts/generate_version.sh | 4 ++ src/CMakeLists.txt | 6 ++ src/GudhUI/CMakeLists.txt | 115 +++++++++++++++------------------- src/GudhUI/model/Model.h | 4 +- src/cmake/modules/FindQGLViewer.cmake | 61 ++++++++++++++++++ 6 files changed, 126 insertions(+), 67 deletions(-) create mode 100644 src/cmake/modules/FindQGLViewer.cmake (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index f30c1785..02e0c614 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -78,6 +78,9 @@ else() add_subdirectory(src/Bottleneck/example) add_subdirectory(src/Bottleneck/test) + # GudhUI + add_subdirectory(src/GudhUI) + # data points generator add_subdirectory(data/points/generator) diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh index 1a8ce4ab..4d28cf53 100755 --- a/scripts/generate_version.sh +++ b/scripts/generate_version.sh @@ -62,6 +62,10 @@ do then # SPECIFIC FOR CMAKE MODULES cp -R $ROOT_DIR/src/$package $VERSION_DIR + elif [ "$package" == "GudhUI" ] + then + # SPECIFIC FOR GUDHI USER INTERFACE + cp -R $ROOT_DIR/src/$package $VERSION_DIR else # PACKAGE COPY if [ -d "$ROOT_DIR/src/$package$PACKAGE_INC_DIR" ] diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 55aa8a65..3be05c4f 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -47,4 +47,10 @@ else() add_subdirectory(example/Alpha_shapes) add_subdirectory(example/Bottleneck) + # GudhUI + add_subdirectory(GudhUI) + + # data points generator + add_subdirectory(data/points/generator) + endif() diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index b62be8ff..ddbae969 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -1,82 +1,69 @@ cmake_minimum_required(VERSION 2.8) project(GudhUI) -#Specify Gudhi's path here -#for instance -#set(Gudhi_Path "C:/Users/dsalinas/Documents/Recherche/Code/c++/Gudhi_library_1.1.0/include") -set(Gudhi_Path "/home/dsalinas/Documents/CodeSVN/gudhi/src/include") -if(MSVC) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018 -frounding-math") -else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic -frounding-math") -endif() - -set(EXECUTABLE_OUTPUT_PATH bin/${CMAKE_BUILD_TYPE}) - -find_package(Boost REQUIRED COMPONENTS) find_package(CGAL COMPONENTS Qt4) find_package(Qt4) find_package(QGLViewer) find_package(OpenGL) +message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}") +message("CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG}") +message("CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE}") if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND ) - set( QT_USE_QTXML TRUE ) - set( QT_USE_QTMAIN TRUE ) - set( QT_USE_QTSCRIPT TRUE ) - set( QT_USE_QTOPENGL TRUE ) - SET(Boost_USE_STATIC_LIBS ON) - SET(Boost_USE_MULTITHREAD OFF) - - INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) - LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) - - include(${QT_USE_FILE}) - include(${CGAL_USE_FILE}) - - include_directories (${QGLVIEWER_INCLUDE_DIR}) - include_directories(.) - include_directories(${Gudhi_Path}) + set( QT_USE_QTXML TRUE ) + set( QT_USE_QTMAIN TRUE ) + set( QT_USE_QTSCRIPT TRUE ) + set( QT_USE_QTOPENGL TRUE ) + SET(Boost_USE_STATIC_LIBS ON) + SET(Boost_USE_MULTITHREAD OFF) + INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) + LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) + + include(${QT_USE_FILE}) + include(${CGAL_USE_FILE}) + include_directories (${QGLVIEWER_INCLUDE_DIR}) + include_directories(.) - # qt : ui file, created wih Qt Designer ############### - set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/gui") - qt4_wrap_ui( uis - gui/main_window.ui - gui/MenuEdgeContraction.ui - gui/KNearestNeighborsMenu.ui - gui/UniformNeighborsMenu.ui - gui/PersistenceMenu.ui - ) + # qt : ui file, created wih Qt Designer ############### + set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/gui") + qt4_wrap_ui( uis + gui/main_window.ui + gui/MenuEdgeContraction.ui + gui/KNearestNeighborsMenu.ui + gui/UniformNeighborsMenu.ui + gui/PersistenceMenu.ui + ) - set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/gui") - qt4_automoc( - gui/MainWindow.cpp - gui/Menu_k_nearest_neighbors.cpp - gui/Menu_uniform_neighbors.cpp - gui/Menu_edge_contraction.cpp - gui/Menu_persistence.cpp - ) + set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/gui") + qt4_automoc( + gui/MainWindow.cpp + gui/Menu_k_nearest_neighbors.cpp + gui/Menu_uniform_neighbors.cpp + gui/Menu_edge_contraction.cpp + gui/Menu_persistence.cpp + ) - set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/view") - qt4_automoc(view/Viewer_instructor.cpp - view/Viewer.cpp - ) - ##################################################################### + set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/view") + qt4_automoc(view/Viewer_instructor.cpp + view/Viewer.cpp + ) + ##################################################################### - add_executable ( GudhUI - gui/gudhui.cpp - gui/MainWindow.cpp - gui/Menu_k_nearest_neighbors.cpp - gui/Menu_uniform_neighbors.cpp - gui/Menu_edge_contraction.cpp - gui/Menu_persistence.cpp - view/Viewer_instructor.cpp - view/Viewer.cpp - ${uis} - ) + add_executable ( GudhUI + gui/gudhui.cpp + gui/MainWindow.cpp + gui/Menu_k_nearest_neighbors.cpp + gui/Menu_uniform_neighbors.cpp + gui/Menu_edge_contraction.cpp + gui/Menu_persistence.cpp + view/Viewer_instructor.cpp + view/Viewer.cpp + ${uis} + ) - target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} ) - target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ) + target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} ) + target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ) else() message(STATUS "NOTICE: This demo requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.") diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h index 6ac971d0..87545989 100644 --- a/src/GudhUI/model/Model.h +++ b/src/GudhUI/model/Model.h @@ -72,8 +72,6 @@ class Model{ public: Complex complex_; typedef Complex::Vertex_handle Vertex_handle; - typedef Complex::CVI CVI; - Model():complex_(){ } @@ -317,7 +315,7 @@ private: void run_chomp(){ save_complex_in_file_for_chomp(); std::cout << "Call CHOMP library\n"; - system("../src/utils/homsimpl chomp.sim"); + system("utils/homsimpl chomp.sim"); } void save_complex_in_file_for_chomp(){ diff --git a/src/cmake/modules/FindQGLViewer.cmake b/src/cmake/modules/FindQGLViewer.cmake new file mode 100644 index 00000000..65723d67 --- /dev/null +++ b/src/cmake/modules/FindQGLViewer.cmake @@ -0,0 +1,61 @@ +# - Try to find QGLViewer +# Once done this will define +# +# QGLVIEWER_FOUND - system has QGLViewer +# QGLVIEWER_INCLUDE_DIR - the QGLViewer include directory +# QGLVIEWER_LIBRARIES - Link these to use QGLViewer +# QGLVIEWER_DEFINITIONS - Compiler switches required for using QGLViewer +# + +find_path(QGLVIEWER_INCLUDE_DIR + NAMES QGLViewer/qglviewer.h + PATHS /usr/include + /usr/local/include + ENV QGLVIEWERROOT + ) + +find_library(QGLVIEWER_LIBRARY_RELEASE + NAMES qglviewer-qt4 qglviewer QGLViewer QGLViewer2 + PATHS /usr/lib + /usr/local/lib + ENV QGLVIEWERROOT + ENV LD_LIBRARY_PATH + ENV LIBRARY_PATH + PATH_SUFFIXES QGLViewer QGLViewer/release + ) + +find_library(QGLVIEWER_LIBRARY_DEBUG + NAMES dqglviewer dQGLViewer dQGLViewer2 QGLViewerd2 + PATHS /usr/lib + /usr/local/lib + ENV QGLVIEWERROOT + ENV LD_LIBRARY_PATH + ENV LIBRARY_PATH + PATH_SUFFIXES QGLViewer QGLViewer/debug + ) + +if(QGLVIEWER_LIBRARY_RELEASE) + if(QGLVIEWER_LIBRARY_DEBUG) + set(QGLVIEWER_LIBRARIES_ optimized ${QGLVIEWER_LIBRARY_RELEASE} debug ${QGLVIEWER_LIBRARY_DEBUG}) + else() + set(QGLVIEWER_LIBRARIES_ ${QGLVIEWER_LIBRARY_RELEASE}) + endif() + + set(QGLVIEWER_LIBRARIES ${QGLVIEWER_LIBRARIES_} CACHE FILEPATH "The QGLViewer library") + +endif() + +IF(QGLVIEWER_INCLUDE_DIR AND QGLVIEWER_LIBRARIES) + SET(QGLVIEWER_FOUND TRUE) +ENDIF(QGLVIEWER_INCLUDE_DIR AND QGLVIEWER_LIBRARIES) + +IF(QGLVIEWER_FOUND) + IF(NOT QGLViewer_FIND_QUIETLY) + MESSAGE(STATUS "Found QGLViewer: ${QGLVIEWER_LIBRARIES}") + ENDIF(NOT QGLViewer_FIND_QUIETLY) +ELSE(QGLVIEWER_FOUND) + IF(QGLViewer_FIND_REQUIRED) + MESSAGE(FATAL_ERROR "Could not find QGLViewer") + ENDIF(QGLViewer_FIND_REQUIRED) +ENDIF(QGLVIEWER_FOUND) + -- cgit v1.2.3 From 3967afc3b314888184caff5ed9c14360138e777f Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 6 May 2015 11:40:09 +0000 Subject: Main page modification git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@584 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 52b7db979870403edd4d5ffa4804e07811dbf228 --- src/common/doc/main_page.h | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) (limited to 'src') diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 7fa6e289..43784a82 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -6,7 +6,8 @@ The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ library for topological analysis of high-dimensional data whose goal is to provide robust, efficient, flexible and easy to use implementations of -state-of-the-art algorithms and data structures for computational topology. +state-of-the-art algorithms and data structures for computational topology. +This library is part of the Gudhi project. The current release of the library allows to use several data-structures for simplicial complexes : simplex tree, Hasse diagram or skeleton-blocker. Several operations can then be done on top of these @@ -17,35 +18,43 @@ We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library. +\section installation Gudhi installation + +As Gudhi is a header only library, there is no need to install the library. + +Examples of Gudhi headers inclusion can be found in \ref demos. + \section compiling Compiling -The library uses c++11 and requires Boost with version 1.48.0 or more recent : http://www.boost.org/. -It is a multiplaform library and compiles on Linux, Mac OSX and Visual Studio 2013. +The library uses c++11 and requires Boost with version 1.48.0 or more recent. +It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013. \subsection gmp GMP: The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision -arithmetic, operating on signed integers, rational numbers, and floating point numbers -The following examples require The GNU Multiple Precision Arithmetic Library (GMP) http://gmplib.org/ +arithmetic, operating on signed integers, rational numbers, and floating point numbers. + +The following examples require the GNU Multiple Precision Arithmetic Library (GMP) and will not be built if GMP is not installed: - Persistent_cohomology/rips_multifield_persistence - Simplex_tree/simplex_tree_from_alpha_shapes_3 -Having GMP version 4.2 or higher installed is recommended. This library can be obtained from http://gmplib.org/ +Having GMP version 4.2 or higher installed is recommended. \subsection cgal CGAL: CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms. -The following example requires CGAL https://www.cgal.org/ and will not be built if CGAL is not installed: +The following example requires the Computational Geometry Algorithms Library (CGAL) +and will not be built if CGAL is not installed: - Simplex_tree/simplex_tree_from_alpha_shapes_3 Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html -\section demos Demos and Examples +\subsection demos Demos and examples -To build the library, run the following in a terminal: +To build the demos and libraries, run the following in a terminal: \verbatim cd /path-to-gudhi/ @@ -55,10 +64,6 @@ cmake .. make \endverbatim - - - - \details \copyright GNU General Public License v3. -- cgit v1.2.3 From d7c885fc4eaa06be6e6b57b8c3bd622b82a20c77 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 6 May 2015 12:36:11 +0000 Subject: typo git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@585 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0e1ed7482bb68104a57595c49718d41028ccf420 --- src/common/doc/main_page.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src') diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 43784a82..315aa0ac 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -54,7 +54,7 @@ your operating system is detailed here http://doc.cgal.org/latest/Manual/install \subsection demos Demos and examples -To build the demos and libraries, run the following in a terminal: +To build the demos and libraries, run the following commands in a terminal: \verbatim cd /path-to-gudhi/ -- cgit v1.2.3 From fbdb713ed3f321e7a983eb4c50a8b26a37f3c193 Mon Sep 17 00:00:00 2001 From: glisse Date: Fri, 19 Jun 2015 12:52:35 +0000 Subject: Trivial clean-ups - add static/const to some member functions - remove an unused variable - don't pass int by const& git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/constify-ST@632 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d8742bf06caf10115ba4b5157e81bfd7bf8d6e15 --- src/Alpha_shapes/include/gudhi/Alpha_shapes.h | 2 +- .../include/gudhi/Persistent_cohomology/Field_Zp.h | 2 +- src/Simplex_tree/include/gudhi/Simplex_tree.h | 32 +++++++++++----------- 3 files changed, 18 insertions(+), 18 deletions(-) (limited to 'src') diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h index b8efdb4d..e988f683 100644 --- a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h +++ b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h @@ -171,7 +171,7 @@ class Alpha_shapes { /** \brief Returns the number of simplices in the complex. * * Does not count the empty simplex. */ - const unsigned int& num_simplices() const { + unsigned int num_simplices() const { return _st.num_simplices(); } diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h index 2349cdac..2a4c8692 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h @@ -85,7 +85,7 @@ class Field_Zp { return add_id_all; } /** \brief Returns the multiplicative identity \f$1_{\Bbbk}\f$ of the field.*/ - const Element& multiplicative_identity(Element P = 0) const { + const Element& multiplicative_identity(Element = 0) const { return mult_id_all; } /** Returns the inverse in the field. Modifies P.*/ diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index b79e3c8f..9d0cf755 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -325,7 +325,7 @@ class Simplex_tree { /** \brief Returns the filtration value of a simplex. * * Called on the null_simplex, returns INFINITY. */ - Filtration_value filtration(Simplex_handle sh) { + Filtration_value filtration(Simplex_handle sh) const { if (sh != null_simplex()) { return sh->second.filtration(); } else { @@ -333,34 +333,34 @@ class Simplex_tree { } // filtration(); } } /** \brief Returns an upper bound of the filtration values of the simplices. */ - Filtration_value filtration() { + Filtration_value filtration() const { return threshold_; } /** \brief Returns a Simplex_handle different from all Simplex_handles * associated to the simplices in the simplicial complex. * * One can call filtration(null_simplex()). */ - Simplex_handle null_simplex() { + Simplex_handle null_simplex() const { return Dictionary_it(NULL); } /** \brief Returns a key different for all keys associated to the * simplices of the simplicial complex. */ - Simplex_key null_key() { + Simplex_key null_key() const { return -1; } /** \brief Returns a Vertex_handle different from all Vertex_handles associated * to the vertices of the simplicial complex. */ - Vertex_handle null_vertex() { + Vertex_handle null_vertex() const { return null_vertex_; } /** \brief Returns the number of vertices in the complex. */ - size_t num_vertices() { + size_t num_vertices() const { return root_.members_.size(); } /** \brief Returns the number of simplices in the complex. * * Does not count the empty simplex. */ - const unsigned int& num_simplices() const { + unsigned int num_simplices() const { return num_simplices_; } @@ -377,13 +377,13 @@ class Simplex_tree { return dim - 1; } /** \brief Returns an upper bound on the dimension of the simplicial complex. */ - int dimension() { + int dimension() const { return dimension_; } /** \brief Returns true iff the node in the simplex tree pointed by * sh has children.*/ - bool has_children(Simplex_handle sh) { + bool has_children(Simplex_handle sh) const { return (sh->second.children()->parent() == sh->first); } @@ -563,7 +563,7 @@ class Simplex_tree { threshold_ = fil; } /** Set a number of simplices for the simplicial complex. */ - void set_num_simplices(const unsigned int& num_simplices) { + void set_num_simplices(unsigned int num_simplices) { num_simplices_ = num_simplices; } /** Set a dimension for the simplicial complex. */ @@ -771,10 +771,10 @@ class Simplex_tree { } /** \brief Intersects Dictionary 1 [begin1;end1) with Dictionary 2 [begin2,end2) * and assigns the maximal possible Filtration_value to the Nodes. */ - void intersection(std::vector >& intersection, - Dictionary_it begin1, Dictionary_it end1, - Dictionary_it begin2, Dictionary_it end2, - Filtration_value filtration) { + static void intersection(std::vector >& intersection, + Dictionary_it begin1, Dictionary_it end1, + Dictionary_it begin2, Dictionary_it end2, + Filtration_value filtration) { if (begin1 == end1 || begin2 == end2) return; // ----->> while (true) { @@ -801,8 +801,8 @@ class Simplex_tree { } } /** Maximum over 3 values.*/ - Filtration_value maximum(Filtration_value a, Filtration_value b, - Filtration_value c) { + static Filtration_value maximum(Filtration_value a, Filtration_value b, + Filtration_value c) { Filtration_value max = (a < b) ? b : a; return ((max < c) ? c : max); } -- cgit v1.2.3 From 51127c161fc6fdaf7f8ec77a4a476faa6e219b52 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 26 Jun 2015 09:08:22 +0000 Subject: -Werror on user version compilation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_ci@656 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 54943d15cd2f0ec784fbf447485e637517bad32d --- src/Alpha_shapes/include/gudhi/Alpha_shapes.h | 2 +- .../include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h | 5 +++-- src/CMakeLists.txt | 4 +++- src/GudhUI/model/Model.h | 3 ++- src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp | 6 ++++-- 5 files changed, 13 insertions(+), 7 deletions(-) (limited to 'src') diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h index b8efdb4d..deece712 100644 --- a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h +++ b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h @@ -171,7 +171,7 @@ class Alpha_shapes { /** \brief Returns the number of simplices in the complex. * * Does not count the empty simplex. */ - const unsigned int& num_simplices() const { + const unsigned int num_simplices() const { return _st.num_simplices(); } diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h index 693b393e..b38ca4d6 100644 --- a/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h +++ b/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h @@ -190,15 +190,16 @@ class Delaunay_triangulation_off_writer { } // Finite cells list - for (auto cit = save_complex.finite_full_cells_begin(); cit != save_complex.finite_full_cells_end(); ++cit) { + /*for (auto cit = save_complex.finite_full_cells_begin(); cit != save_complex.finite_full_cells_end(); ++cit) { stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " "; // Dimension for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) { auto vertexHdl = *vit; + std::cout << // auto vertexHdl = std::distance(save_complex.vertices_begin(), *vit) - 1; // stream << std::distance(save_complex.vertices_begin(), *(vit)) - 1 << " "; } stream << std::endl; - } + }*/ stream.close(); } else { std::cerr << "could not open file " << name_file << std::endl; diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 3be05c4f..7869bc4b 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -12,7 +12,9 @@ endif() if(MSVC) SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare -Werror") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") endif() set(Boost_USE_STATIC_LIBS ON) diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h index 87545989..17a7d278 100644 --- a/src/GudhUI/model/Model.h +++ b/src/GudhUI/model/Model.h @@ -315,7 +315,8 @@ private: void run_chomp(){ save_complex_in_file_for_chomp(); std::cout << "Call CHOMP library\n"; - system("utils/homsimpl chomp.sim"); + int returnValue = system("utils/homsimpl chomp.sim"); + std::cout << "CHOMP returns" << returnValue << std::endl; } void save_complex_in_file_for_chomp(){ diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp index 92fa17f3..126e32ec 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp @@ -64,8 +64,10 @@ int main (int argc, char *argv[]){ // or edges, complex.num_vertices() and complex.num_edges() are // more appropriated! unsigned num_vertices = 0; - for(auto v : complex.vertex_range()) - ++num_vertices; + for(auto v : complex.vertex_range()) { + std::cout << "Vertex " << v < Date: Sun, 5 Jul 2015 16:55:58 +0000 Subject: Typo + comment out debug printing git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@678 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 896977355b7928fa20f5e85ec9eb2bb920a9ad90 --- src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h | 2 +- .../include/gudhi/Skeleton_blocker_simplifiable_complex.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h index 049db6d5..289819b5 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h @@ -109,7 +109,7 @@ and point access in addition. \subsection Visitor The class Skeleton_blocker_complex has a visitor that is called when usual operations such as adding an edge or remove a vertex are called. -You may want to use this visitor to compute statistics or to update another data-structure (for instance this visitor is heavily used in the \ref contr package. +You may want to use this visitor to compute statistics or to update another data-structure (for instance this visitor is heavily used in the \ref contr package). diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h index 86a12d90..dd8d898e 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h @@ -223,7 +223,7 @@ void Skeleton_blocker_complex::add_simplex(const Simplex_hand for (auto u_it = sigma.begin(); u_it != sigma.end(); ++u_it) for (auto v_it = u_it; ++v_it != sigma.end(); /**/) { - std::cout << "add edge" << *u_it << " " << *v_it << std::endl; + // std::cout << "add edge" << *u_it << " " << *v_it << std::endl; add_edge(*u_it, *v_it); } remove_blocker_include_in_simplex(sigma); -- cgit v1.2.3