From ec3f93103f5a1937d3f8bbf37af3837a1089bf03 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 19 May 2017 16:13:50 +0000 Subject: Move src/common/utilities/hypergenerator.cpp in src/common/utilities Management of Python distribution packages make install is now installing utilities and GUDHI python module git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cmake_modules_for_gudhi@2453 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a85576c7ae062718900f0db2bfb0dd3f26e87177 --- src/cython/CMakeLists.txt | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 96c2acb3..62f8d368 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -168,17 +168,23 @@ if(CYTHON_FOUND) configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY) add_custom_command( - OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + OUTPUT gudhi.so WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace") - add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + add_custom_target(cython ALL DEPENDS gudhi.so COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") if(UNIX) set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ ) endif(UNIX) + # For installation purpose + install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING + PATTERN "*.so" + PATTERN "*.dylib" + PATTERN "*.pyd") + # Test examples add_test(NAME alpha_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} -- cgit v1.2.3 From bb5e82c41e9d3a79f8e1dc53cd1dd2c117e06111 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 30 May 2017 07:36:17 +0000 Subject: Add a warning git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cmake_modules_for_gudhi@2465 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a873c9c6fff031968747c3dec197aec06738c32a --- src/cython/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 62f8d368..d9f356f9 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -180,6 +180,7 @@ if(CYTHON_FOUND) endif(UNIX) # For installation purpose + # TODO(VR) : files matching pattern mechanism is copying all cython directory install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING PATTERN "*.so" PATTERN "*.dylib" -- cgit v1.2.3 From c09268a046c43b4311f0f29ac4bfb14dcb2da30d Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 2 Jun 2017 14:10:20 +0000 Subject: Try to remove boost system git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2504 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fd12c45af5ebeb72c4b49142abab91b46ce1a9da --- src/Alpha_complex/example/CMakeLists.txt | 4 ++-- src/Rips_complex/example/CMakeLists.txt | 8 ++++---- src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 ++ src/cython/CMakeLists.txt | 10 +--------- 4 files changed, 9 insertions(+), 15 deletions(-) (limited to 'src/cython') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 4badcb91..5bf553e9 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -5,9 +5,9 @@ project(Alpha_complex_examples) # cmake -DCGAL_DIR=~/workspace/CGAL-4.7 .. if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp ) - target_link_libraries(Alpha_complex_example_from_points ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(Alpha_complex_example_from_points ${CGAL_LIBRARY}) add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp ) - target_link_libraries(Alpha_complex_example_from_off ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index 712db16e..d2d3e052 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -3,17 +3,17 @@ project(Rips_complex_examples) # Point cloud add_executable ( Rips_complex_example_from_off example_rips_complex_from_off_file.cpp ) -target_link_libraries(Rips_complex_example_from_off ${Boost_SYSTEM_LIBRARY}) +#target_link_libraries(Rips_complex_example_from_off ${Boost_SYSTEM_LIBRARY}) add_executable ( Rips_complex_example_one_skeleton_from_points example_one_skeleton_rips_from_points.cpp ) -target_link_libraries(Rips_complex_example_one_skeleton_from_points ${Boost_SYSTEM_LIBRARY}) +#target_link_libraries(Rips_complex_example_one_skeleton_from_points ${Boost_SYSTEM_LIBRARY}) # Distance matrix add_executable ( Rips_complex_example_one_skeleton_from_distance_matrix example_one_skeleton_rips_from_distance_matrix.cpp ) -target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix ${Boost_SYSTEM_LIBRARY}) +#target_link_libraries(Rips_complex_example_one_skeleton_from_distance_matrix ${Boost_SYSTEM_LIBRARY}) add_executable ( Rips_complex_example_from_csv_distance_matrix example_rips_complex_from_csv_distance_matrix_file.cpp ) -target_link_libraries(Rips_complex_example_from_csv_distance_matrix ${Boost_SYSTEM_LIBRARY}) +#target_link_libraries(Rips_complex_example_from_csv_distance_matrix ${Boost_SYSTEM_LIBRARY}) if (TBB_FOUND) target_link_libraries(Rips_complex_example_from_off ${TBB_LIBRARIES}) diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 8cb01d3c..7b0cda3b 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -99,6 +99,8 @@ add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) add_definitions(-DBOOST_ALL_NO_LIB) # problem with Visual Studio link on Boost program_options add_definitions( -DBOOST_ALL_DYN_LINK ) +# problem on Mac with boost_system and boost_thread +#add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED ) INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index d9f356f9..4b56122d 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -6,15 +6,7 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") - if(WIN32) - set( returnValue "" ) - find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY}) - set(BOOST_SYSTEM_LIB_NAME ${returnValue}) - else() - set(BOOST_SYSTEM_LIB_NAME "boost_system") - endif() - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") # Gudhi and CGAL compilation option if(MSVC) -- cgit v1.2.3 From 4adbd857ff2ac187b5dfcfa25c37f32b887ae69b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 9 Jun 2017 07:48:54 +0000 Subject: No more need of find_the_lib cmake macro to find Windows boost lib name Fix cmake warning on if with quotes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2527 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a352820ab0a596961b9851d4a30c40196a70ff98 --- src/cmake/modules/GUDHI_third_party_libraries.cmake | 13 ------------- src/cython/CMakeLists.txt | 4 ++-- 2 files changed, 2 insertions(+), 15 deletions(-) (limited to 'src/cython') diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 5bee774a..b4f3eb52 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -108,19 +108,6 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS}) message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) -macro( find_the_lib placeholder THE_LIBS ) - set (THE_LIB_WE_FOUND "NO") - foreach(THE_LIB ${THE_LIBS}) - if(EXISTS ${THE_LIB}) - get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE) - if (NOT THE_LIB_WE_FOUND) - set (THE_LIB_WE_FOUND "YES") - set(returnValue "${THE_LIB_WE}") - endif(NOT THE_LIB_WE_FOUND) - endif(EXISTS ${THE_LIB}) - endforeach(THE_LIB ${THE_LIBS}) -endmacro( find_the_lib ) - # Find the correct Python interpreter. # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance. find_package(Cython) diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 4b56122d..adcc64e4 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -17,9 +17,9 @@ if(CYTHON_FOUND) if(CMAKE_COMPILER_IS_GNUCXX) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") endif(CMAKE_COMPILER_IS_GNUCXX) - if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + if (CMAKE_CXX_COMPILER_ID MATCHES Intel) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") - endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + endif(CMAKE_CXX_COMPILER_ID MATCHES Intel) if (DEBUG_TRACES) # For programs to be more verbose set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") -- cgit v1.2.3 From 547a7c9cb50d1818c9412d10cca9655503db625c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 13 Jun 2017 20:42:51 +0000 Subject: Try to fix Windows compilation for Conda git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2541 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: afa1b10e300aafbc92a85b3519f4b39add2ae6e4 --- src/cmake/modules/GUDHI_third_party_libraries.cmake | 4 ++++ src/cython/CMakeLists.txt | 3 +++ 2 files changed, 7 insertions(+) (limited to 'src/cython') diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 8f486118..7cd57b25 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -10,6 +10,10 @@ find_package(GMP) if(GMP_FOUND) message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}") INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR}) + get_filename_component(lib_we ${GMP_LIBRARIES} NAME_WE) + + message("++ lib_we = ${lib_we}") + find_package(GMPXX) if(GMPXX_FOUND) message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index adcc64e4..2a0a3844 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -8,6 +8,9 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") + if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_thread', ") + endif() # Gudhi and CGAL compilation option if(MSVC) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") -- cgit v1.2.3 From f6d8aaaacf4a2802d3aaad6d326f9510fdb2ddf7 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 14 Jun 2017 05:24:01 +0000 Subject: Add traces for debug git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2542 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a9e8098443114a4fe6e9c19e6410169580c134c6 --- src/cmake/modules/GUDHI_third_party_libraries.cmake | 4 ---- src/cython/CMakeLists.txt | 10 ++++++++-- 2 files changed, 8 insertions(+), 6 deletions(-) (limited to 'src/cython') diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 7cd57b25..8f486118 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -10,10 +10,6 @@ find_package(GMP) if(GMP_FOUND) message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}") INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR}) - get_filename_component(lib_we ${GMP_LIBRARIES} NAME_WE) - - message("++ lib_we = ${lib_we}") - find_package(GMPXX) if(GMPXX_FOUND) message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 2a0a3844..eff36f93 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -8,6 +8,7 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") + message("++ Boost_THREAD_LIBRARY=${Boost_THREAD_LIBRARY} - Boost_thread_LIBRARY=${Boost_thread_LIBRARY} - ") if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_thread', ") endif() @@ -106,6 +107,7 @@ if(CYTHON_FOUND) if(CGAL_FOUND) # Add CGAL compilation args + message("++ CGAL_LIBRARIES = ${CGAL_LIBRARIES}") if(CGAL_HEADER_ONLY) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") else(CGAL_HEADER_ONLY) @@ -119,10 +121,14 @@ if(CYTHON_FOUND) # GMP and GMPXX are not required, but if present, CGAL will link with them. if(GMP_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") + get_filename_component(GMP_LIBRARY_FILE_NAME ${GMP_LIBRARIES} NAME_WE) + message("++ GMP_LIBRARY_FILE_NAME = ${GMP_LIBRARY_FILE_NAME}") if(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${GMP_LIBRARY_FILE_NAME}', ") else(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ") + STRING(REGEX REPLACE "lib" "" UNIX_GMP_LIBRARY_FILE_NAME ${GMP_LIBRARY_FILE_NAME}) + message("++ UNIX_GMP_LIBRARY_FILE_NAME = ${UNIX_GMP_LIBRARY_FILE_NAME}") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_GMP_LIBRARY_FILE_NAME}', ") endif(WIN32) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") if(GMPXX_FOUND) -- cgit v1.2.3 From e8c3b007c141551b68859ea178e79ddf618c6dca Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 14 Jun 2017 06:38:20 +0000 Subject: Fix try git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2543 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: da6eb0ef7b79c0d21d8e98d17d78459d1768a5db --- src/cython/CMakeLists.txt | 42 +++++++++++++++++++++------------------- src/cython/cythonize_gudhi.py.in | 2 +- 2 files changed, 23 insertions(+), 21 deletions(-) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index eff36f93..739e1a89 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -1,6 +1,20 @@ cmake_minimum_required(VERSION 2.8) project(Cython) +function( add_gudhi_cython_lib THE_LIB ) + if(EXISTS ${THE_LIB}) + get_filename_component(THE_LIB_FILE_NAME ${THE_LIB} NAME_WE) + if(WIN32) + message("++ ${THE_LIB} => THE_LIB_FILE_NAME = ${THE_LIB_FILE_NAME}") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${THE_LIB_FILE_NAME}', " PARENT_SCOPE) + else(WIN32) + STRING(REGEX REPLACE "lib" "" UNIX_LIB_FILE_NAME ${THE_LIB_FILE_NAME}) + message("++ ${THE_LIB} => UNIX_LIB_FILE_NAME = ${UNIX_LIB_FILE_NAME}") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_LIB_FILE_NAME}', " PARENT_SCOPE) + endif(WIN32) + endif(EXISTS ${THE_LIB}) +endfunction( add_gudhi_cython_lib ) + if(CYTHON_FOUND) message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}") @@ -8,9 +22,9 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") - message("++ Boost_THREAD_LIBRARY=${Boost_THREAD_LIBRARY} - Boost_thread_LIBRARY=${Boost_thread_LIBRARY} - ") if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_thread', ") + add_gudhi_cython_lib(${Boost_THREAD_LIBRARY}) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") endif() # Gudhi and CGAL compilation option if(MSVC) @@ -107,33 +121,20 @@ if(CYTHON_FOUND) if(CGAL_FOUND) # Add CGAL compilation args - message("++ CGAL_LIBRARIES = ${CGAL_LIBRARIES}") if(CGAL_HEADER_ONLY) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") else(CGAL_HEADER_ONLY) - if(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ") - else(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ") - endif(WIN32) + add_gudhi_cython_lib(${CGAL_LIBRARIES}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") endif(CGAL_HEADER_ONLY) # GMP and GMPXX are not required, but if present, CGAL will link with them. if(GMP_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") - get_filename_component(GMP_LIBRARY_FILE_NAME ${GMP_LIBRARIES} NAME_WE) - message("++ GMP_LIBRARY_FILE_NAME = ${GMP_LIBRARY_FILE_NAME}") - if(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${GMP_LIBRARY_FILE_NAME}', ") - else(WIN32) - STRING(REGEX REPLACE "lib" "" UNIX_GMP_LIBRARY_FILE_NAME ${GMP_LIBRARY_FILE_NAME}) - message("++ UNIX_GMP_LIBRARY_FILE_NAME = ${UNIX_GMP_LIBRARY_FILE_NAME}") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_GMP_LIBRARY_FILE_NAME}', ") - endif(WIN32) - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") + add_gudhi_cython_lib(${GMP_LIBRARIES}) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") if(GMPXX_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ") + add_gudhi_cython_lib(${GMPXX_LIBRARIES}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") endif(GMPXX_FOUND) endif(GMP_FOUND) @@ -154,7 +155,8 @@ if(CYTHON_FOUND) if (TBB_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ") + add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY}) + add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") endif() diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in index 5a97e9f3..cae4641b 100644 --- a/src/cython/cythonize_gudhi.py.in +++ b/src/cython/cythonize_gudhi.py.in @@ -42,7 +42,7 @@ setup( name = 'gudhi', author='Vincent Rouvreau', author_email='gudhi-contact@lists.gforge.inria.fr', - version='0.1.0', + version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', ext_modules = cythonize(gudhi), ) -- cgit v1.2.3 From 30d31a1aabc2035e23eca7bcf3867a30536f11b7 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Jun 2017 07:06:49 +0000 Subject: Fix Python module version numer Fix link with external libraries git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2547 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e2f47e860ea4608a4d298fa4772d750ac540be5a --- CMakeGUDHIVersion.txt | 2 +- src/cython/cythonize_gudhi.py.in | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) (limited to 'src/cython') diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index bd0c57ac..3d9add66 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,6 @@ set (GUDHI_MAJOR_VERSION 2) set (GUDHI_MINOR_VERSION 0) -set (GUDHI_PATCH_VERSION 0) +set (GUDHI_PATCH_VERSION 1.beta) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in index cae4641b..68a95916 100644 --- a/src/cython/cythonize_gudhi.py.in +++ b/src/cython/cythonize_gudhi.py.in @@ -35,6 +35,7 @@ gudhi = Extension( extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@], libraries=[@GUDHI_CYTHON_LIBRARIES@], library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@], + runtime_library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@], include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@], ) -- cgit v1.2.3 From 30b44fa282606a6a6b585e0e83b98dae4f2e6b2e Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Jun 2017 08:12:26 +0000 Subject: Add warning about boost_thread link for the Mac GUDHI python module git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2548 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4a9f6c43f4868bd4f303579c22fdc7a54728e68c --- src/cython/CMakeLists.txt | 9 +++++++++ 1 file changed, 9 insertions(+) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 739e1a89..84441591 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -22,6 +22,15 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") + # TODO: Something more clever could be done. + # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h + # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac). + # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h + # #if __has_feature(cxx_thread_local) || \ + # ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + # ( _MSC_VER >= 1900 ) + # #define CGAL_CAN_USE_CXX11_THREAD_LOCAL + # #endif if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") add_gudhi_cython_lib(${Boost_THREAD_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") -- cgit v1.2.3 From 06f595c9bbe1f7fbc1d4e9dae7f5a0a384fe62c2 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Jun 2017 09:27:12 +0000 Subject: Fix CUSTOMBUILD : error : don't know how to set runtime library search path for MSVC git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2549 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 94c7625b3bc8e943e3856e0e65dc65bb5d8cd0f7 --- src/cython/CMakeLists.txt | 8 ++++---- src/cython/cythonize_gudhi.py.in | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 84441591..7586188c 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -170,6 +170,10 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") endif() + if(UNIX) + set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") + endif(UNIX) + # set sphinx-build in make files configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY) configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) @@ -187,10 +191,6 @@ if(CYTHON_FOUND) add_custom_target(cython ALL DEPENDS gudhi.so COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") - if(UNIX) - set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ ) - endif(UNIX) - # For installation purpose # TODO(VR) : files matching pattern mechanism is copying all cython directory install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in index 68a95916..c1a1717a 100644 --- a/src/cython/cythonize_gudhi.py.in +++ b/src/cython/cythonize_gudhi.py.in @@ -35,8 +35,8 @@ gudhi = Extension( extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@], libraries=[@GUDHI_CYTHON_LIBRARIES@], library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@], - runtime_library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@], include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@], + runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@], ) setup( -- cgit v1.2.3 From 34487e33517c36ad65407743c46fd4c1df963628 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 28 Jun 2017 10:53:42 +0000 Subject: Add a comment git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2566 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 64cd59ca30ff82a1c116df20c4cee38a795dc518 --- src/cython/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 5c98b09a..d801fb0b 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -151,6 +151,7 @@ if(CYTHON_FOUND) else(CGAL_HEADER_ONLY) add_gudhi_cython_lib(${CGAL_LIBRARIES}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") + # If CGAL is not header only, CGAL library may link with boost system, add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") endif(CGAL_HEADER_ONLY) -- cgit v1.2.3 From 2e7447cf1deb3a1ac08f2fe90cd780901da65016 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 3 Jul 2017 13:16:54 +0000 Subject: Rename cythonize_gudhi.py in setup.py to be conform with Python convention (for easy_install and pip) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2578 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c514a7c5096293380254339e7e60782194040823 --- src/cython/CMakeLists.txt | 6 ++--- src/cython/cythonize_gudhi.py.in | 49 ---------------------------------------- src/cython/setup.py.in | 49 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 52 insertions(+), 52 deletions(-) delete mode 100644 src/cython/cythonize_gudhi.py.in create mode 100644 src/cython/setup.py.in (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index d801fb0b..99badffb 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -197,15 +197,15 @@ if(CYTHON_FOUND) configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY) configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) - # Generate cythonize_gudhi.py file to cythonize Gudhi - configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY) + # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention + configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY) # Generate gudhi.pyx - Gudhi cython file configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY) add_custom_command( OUTPUT gudhi.so WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace") + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace") add_custom_target(cython ALL DEPENDS gudhi.so COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in deleted file mode 100644 index c1a1717a..00000000 --- a/src/cython/cythonize_gudhi.py.in +++ /dev/null @@ -1,49 +0,0 @@ -from distutils.core import setup, Extension -from Cython.Build import cythonize - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2016 INRIA - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" -__license__ = "GPL v3" - -gudhi = Extension( - "gudhi", - sources = ['gudhi.pyx',], - language = 'c++', - extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@], - extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@], - libraries=[@GUDHI_CYTHON_LIBRARIES@], - library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@], - include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@], - runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@], -) - -setup( - name = 'gudhi', - author='Vincent Rouvreau', - author_email='gudhi-contact@lists.gforge.inria.fr', - version='@GUDHI_VERSION@', - url='http://gudhi.gforge.inria.fr/', - ext_modules = cythonize(gudhi), -) diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in new file mode 100644 index 00000000..c1a1717a --- /dev/null +++ b/src/cython/setup.py.in @@ -0,0 +1,49 @@ +from distutils.core import setup, Extension +from Cython.Build import cythonize + +"""This file is part of the Gudhi Library. The Gudhi library + (Geometric Understanding in Higher Dimensions) is a generic C++ + library for computational topology. + + Author(s): Vincent Rouvreau + + Copyright (C) 2016 INRIA + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +gudhi = Extension( + "gudhi", + sources = ['gudhi.pyx',], + language = 'c++', + extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@], + extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@], + libraries=[@GUDHI_CYTHON_LIBRARIES@], + library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@], + include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@], + runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@], +) + +setup( + name = 'gudhi', + author='Vincent Rouvreau', + author_email='gudhi-contact@lists.gforge.inria.fr', + version='@GUDHI_VERSION@', + url='http://gudhi.gforge.inria.fr/', + ext_modules = cythonize(gudhi), +) -- cgit v1.2.3 From a4b7d528893f992115711225c7d4396de55c6c58 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 4 Jul 2017 13:37:29 +0000 Subject: Add Gudhi namespace for reader_utils Add confidence band in persistence_graphical_tools.py Persistence_diagram returns a plot that is no more showed. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2582 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4125f4f525057e89c8b0d5d164ea0b9d1df1bd72 --- .../example/bottleneck_read_file_example.cpp | 4 ++-- .../example/rips_distance_matrix_persistence.cpp | 2 +- ..._rips_complex_from_csv_distance_matrix_file.cpp | 2 +- src/Rips_complex/test/test_rips_complex.cpp | 2 +- src/common/include/gudhi/reader_utils.h | 10 +++++++--- src/common/test/test_distance_matrix_reader.cpp | 4 ++-- src/cython/cython/persistence_graphical_tools.py | 23 +++++++++++++++------- .../doc/persistence_graphical_tools_user.rst | 10 ++++++---- ...ex_diagram_persistence_from_off_file_example.py | 4 +++- 9 files changed, 39 insertions(+), 22 deletions(-) (limited to 'src/cython') diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp index 238d99ad..1408681a 100644 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp @@ -36,8 +36,8 @@ int main(int argc, char** argv) { " distance (set by default to zero). The program will now terminate \n"; return -1; } - std::vector> diag1 = read_persistence_intervals_in_dimension(argv[1]); - std::vector> diag2 = read_persistence_intervals_in_dimension(argv[2]); + std::vector> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]); + std::vector> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]); double tolerance = 0.; if (argc == 4) { diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp index 8517e7f6..d38808c7 100644 --- a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp @@ -57,7 +57,7 @@ int main(int argc, char * argv[]) { program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); - Distance_matrix distances = read_lower_triangular_matrix_from_csv_file(csv_matrix_file); + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file(csv_matrix_file); Rips_complex rips_complex_from_file(distances, threshold); // Construct the Rips complex in a Simplex Tree diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp index 7ae8126f..9e182f1e 100644 --- a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp +++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp @@ -32,7 +32,7 @@ int main(int argc, char **argv) { // Init of a Rips complex from a distance matrix in a csv file // Default separator is ';' // ---------------------------------------------------------------------------- - Distance_matrix distances = read_lower_triangular_matrix_from_csv_file(csv_file_name); + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file(csv_file_name); Rips_complex rips_complex_from_file(distances, threshold); std::streambuf* streambufffer; diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp index fc2179f2..fc83f5f7 100644 --- a/src/Rips_complex/test/test_rips_complex.cpp +++ b/src/Rips_complex/test/test_rips_complex.cpp @@ -244,7 +244,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) { std::cout << "========== CSV FILE NAME = " << csv_file_name << " - Rips threshold=" << rips_threshold << "==========" << std::endl; - Distance_matrix distances = read_lower_triangular_matrix_from_csv_file(csv_file_name); + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file(csv_file_name); Rips_complex rips_complex_from_file(distances, rips_threshold); const int DIMENSION_1 = 1; diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index f1684d78..8e99acfc 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -37,6 +37,8 @@ #include #include // for pair +namespace Gudhi { + // Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented. // It is required for global functions and variables. @@ -331,7 +333,7 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu } } } -} // read_persistence_diagram_from_file +} // read_persistence_diagram_from_file /** Reads a file containing persistence intervals. @@ -347,7 +349,7 @@ inline std::map>> read_persistence_in filename, boost::make_function_output_iterator([&ret](std::tuple t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); })); return ret; -} // read_persistence_diagram_from_file +} // read_persistence_diagram_from_file /** @@ -367,6 +369,8 @@ inline std::vector> read_persistence_intervals_in_dime filename, boost::make_function_output_iterator([&ret](std::tuple t) { ret.emplace_back(get<1>(t), get<2>(t)); })); return ret; -} // read_persistence_diagram_from_file +} // read_persistence_diagram_from_file + +} // namespace Gudhi #endif // READER_UTILS_H_ diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp index 95a73bd9..656e6f2e 100644 --- a/src/common/test/test_distance_matrix_reader.cpp +++ b/src/common/test/test_distance_matrix_reader.cpp @@ -36,7 +36,7 @@ BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix ) { Distance_matrix from_lower_triangular; // Read lower_triangular_distance_matrix.csv file where the separator is a ',' - from_lower_triangular = read_lower_triangular_matrix_from_csv_file("lower_triangular_distance_matrix.csv", + from_lower_triangular = Gudhi::read_lower_triangular_matrix_from_csv_file("lower_triangular_distance_matrix.csv", ','); for (auto& i : from_lower_triangular) { for (auto j : i) { @@ -69,7 +69,7 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix ) { Distance_matrix from_full_square; // Read full_square_distance_matrix.csv file where the separator is the default one ';' - from_full_square = read_lower_triangular_matrix_from_csv_file("full_square_distance_matrix.csv"); + from_full_square = Gudhi::read_lower_triangular_matrix_from_csv_file("full_square_distance_matrix.csv"); for (auto& i : from_full_square) { for (auto j : i) { std::cout << j << " "; diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index a984633e..70ff6001 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -5,7 +5,7 @@ import numpy as np (Geometric Understanding in Higher Dimensions) is a generic C++ library for computational topology. - Author(s): Vincent Rouvreau + Author(s): Vincent Rouvreau, Bertrand Michel Copyright (C) 2016 INRIA @@ -27,11 +27,13 @@ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 INRIA" __license__ = "GPL v3" -def __min_birth_max_death(persistence): +def __min_birth_max_death(persistence, band_boot=0.): """This function returns (min_birth, max_death) from the persistence. :param persistence: The persistence to plot. :type persistence: list of tuples(dimension, tuple(birth, death)). + :param band_boot: bootstrap band + :type band_boot: float. :returns: (float, float) -- (min_birth, max_death). """ # Look for minimum birth date and maximum death date for plot optimisation @@ -45,6 +47,8 @@ def __min_birth_max_death(persistence): max_death = float(interval[1][0]) if float(interval[1][0]) < min_birth: min_birth = float(interval[1][0]) + if band_boot > 0.: + max_death += band_boot return (min_birth, max_death) """ @@ -108,16 +112,18 @@ def plot_persistence_barcode(persistence, alpha=0.6): plt.axis([axis_start, infinity, 0, ind]) plt.show() -def plot_persistence_diagram(persistence, alpha=0.6): - """This function plots the persistence diagram. +def plot_persistence_diagram(persistence, alpha=0.6, band_boot=0.): + """This function plots the persistence diagram with confidence band. :param persistence: The persistence to plot. :type persistence: list of tuples(dimension, tuple(birth, death)). :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6). :type alpha: float. - :returns: plot -- An diagram plot of persistence. + :param band_boot: bootstrap band + :type band_boot: float. + :returns: plot -- A diagram plot of persistence. """ - (min_birth, max_death) = __min_birth_max_death(persistence) + (min_birth, max_death) = __min_birth_max_death(persistence, band_boot) ind = 0 delta = ((max_death - min_birth) / 10.0) # Replace infinity values with max_death + delta for diagram to be more @@ -131,6 +137,9 @@ def plot_persistence_diagram(persistence, alpha=0.6): plt.plot(x, x, color='k', linewidth=1.0) plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha) plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha) + # bootstrap band + if band_boot > 0.: + plt.fill_between(x, x, x+band_boot, alpha=alpha, facecolor='red') # Draw points in loop for interval in reversed(persistence): @@ -149,4 +158,4 @@ def plot_persistence_diagram(persistence, alpha=0.6): plt.ylabel('Death') # Ends plot on infinity value and starts a little bit before min_birth plt.axis([axis_start, infinity, axis_start, infinity + delta]) - plt.show() + return plt diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index cae18323..bc731f12 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -51,16 +51,18 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0) + rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13) + pplot.show() .. plot:: import gudhi - rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0) + rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13) + pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index 4c21b98e..5951eedf 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -39,6 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-e", "--max_edge_length", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) +parser.add_argument("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -64,7 +65,8 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") -- cgit v1.2.3 From 4832d865981bb74c8afc7240e953adc8f54c52b0 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 6 Jul 2017 15:38:44 +0000 Subject: Plot functions now returns a plot that can be modified before to be shown Add confidence band in plot_persistence_diagram Cythonization of read_lower_triangular_matrix_from_csv_file and read_persistence_intervals functions Add Python tests of read functions git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2590 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 522ec31e9ad3a9a688875612d246114704b8c74e --- src/common/include/gudhi/reader_utils.h | 2 +- src/cython/CMakeLists.txt | 2 +- src/cython/cython/persistence_graphical_tools.py | 4 +- src/cython/cython/reader_utils.pyx | 95 ++++++++++++++++++++++ src/cython/doc/pyplots/barcode_persistence.py | 2 +- src/cython/doc/pyplots/diagram_persistence.py | 8 +- ...ex_diagram_persistence_from_off_file_example.py | 4 +- ...ex_diagram_persistence_from_off_file_example.py | 5 +- ...ex_diagram_persistence_from_off_file_example.py | 5 +- .../example/gudhi_graphical_tools_example.py | 9 +- ...ersistence_from_distance_matrix_file_example.py | 4 +- src/cython/example/rips_persistence_diagram.py | 3 +- ...complex_plain_homology_from_off_file_example.py | 4 +- src/cython/gudhi.pyx.in | 1 + src/cython/include/Reader_utils_interface.h | 54 ++++++++++++ src/cython/include/Rips_complex_interface.h | 2 +- src/cython/test/test_reader_utils.py | 81 ++++++++++++++++++ 17 files changed, 267 insertions(+), 18 deletions(-) create mode 100644 src/cython/cython/reader_utils.pyx create mode 100644 src/cython/include/Reader_utils_interface.h create mode 100755 src/cython/test/test_reader_utils.py (limited to 'src/cython') diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 8e99acfc..f16ae61d 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -359,7 +359,7 @@ If `only_this_dim` = -1, dimension is ignored and all lines are returned. If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` (or where dimension is not specified) are returned. The return value is an `std::vector>` -where `dim` is an `int`, `birth` a `double`, and `death` a `double`. +where `birth` a `double`, and `death` a `double`. Note: the function does not check that birth <= death. **/ inline std::vector> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) { diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 99badffb..f427b3c5 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -100,7 +100,7 @@ if(CYTHON_FOUND) file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") # Persistence graphical tools examples file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") + file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") if (NOT CGAL_VERSION VERSION_LESS 4.8.1) # If CGAL_VERSION >= 4.8.1, include subsampling diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 70ff6001..da709b8a 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -113,13 +113,13 @@ def plot_persistence_barcode(persistence, alpha=0.6): plt.show() def plot_persistence_diagram(persistence, alpha=0.6, band_boot=0.): - """This function plots the persistence diagram with confidence band. + """This function plots the persistence diagram with an optional confidence band. :param persistence: The persistence to plot. :type persistence: list of tuples(dimension, tuple(birth, death)). :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6). :type alpha: float. - :param band_boot: bootstrap band + :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.) :type band_boot: float. :returns: plot -- A diagram plot of persistence. """ diff --git a/src/cython/cython/reader_utils.pyx b/src/cython/cython/reader_utils.pyx new file mode 100644 index 00000000..14976167 --- /dev/null +++ b/src/cython/cython/reader_utils.pyx @@ -0,0 +1,95 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.string cimport string +from libcpp.map cimport map +from libcpp.pair cimport pair +import os + +"""This file is part of the Gudhi Library. The Gudhi library + (Geometric Understanding in Higher Dimensions) is a generic C++ + library for computational topology. + + Author(s): Vincent Rouvreau + + Copyright (C) 2017 INRIA + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2017 INRIA" +__license__ = "GPL v3" + +cdef extern from "Reader_utils_interface.h" namespace "Gudhi": + vector[vector[double]] read_matrix_from_csv_file(string off_file, char separator) + map[int, vector[pair[double, double]]] read_pers_intervals_grouped_by_dimension(string filename) + vector[pair[double, double]] read_pers_intervals_in_dimension(string filename, int only_this_dim) + +def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): + """Read lower triangular matrix from a CSV style file. + + :param csv_file: A CSV file style name. + :type csv_file: string + :param separator: The value separator in the CSV file. Default value is ';' + :type separator: char + + :returns: The lower triangular matrix. + :rtype: vector[vector[double]] + """ + if csv_file is not '': + if os.path.isfile(csv_file): + return read_matrix_from_csv_file(str.encode(csv_file), str.encode(separator)[0]) + print("file " + csv_file + " not set or not found.") + return [] + +def read_persistence_intervals_grouped_by_dimension(persistence_file=''): + """Reads a file containing persistence intervals. + Each line might contain 2, 3 or 4 values: [[field] dimension] birth death + The return value is an `map[dim, vector[pair[birth, death]]]` + where `dim` is an `int`, `birth` a `double`, and `death` a `double`. + Note: the function does not check that birth <= death. + + :param persistence_file: A persistence file style name. + :type persistence_file: string + + :returns: The persistence pairs grouped by dimension. + :rtype: map[int, vector[pair[double, double]]] + """ + if persistence_file is not '': + if os.path.isfile(persistence_file): + return read_pers_intervals_grouped_by_dimension(str.encode(persistence_file)) + print("file " + persistence_file + " not set or not found.") + return [] + +def read_persistence_intervals_in_dimension(persistence_file='', only_this_dim=-1): + """Reads a file containing persistence intervals. + Each line might contain 2, 3 or 4 values: [[field] dimension] birth death + If `only_this_dim` = -1, dimension is ignored and all lines are returned. + If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` + (or where dimension is not specified) are returned. + The return value is an `vector[pair[birth, death]]` + where `birth` a `double`, and `death` a `double`. + Note: the function does not check that birth <= death. + + :param persistence_file: A persistence file style name. + :type persistence_file: string + + :returns: The persistence pairs grouped by dimension. + :rtype: map[int, vector[pair[double, double]]] + """ + if persistence_file is not '': + if os.path.isfile(persistence_file): + return read_pers_intervals_in_dimension(str.encode(persistence_file), only_this_dim) + print("file " + persistence_file + " not set or not found.") + return [] diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py index c06ac5a7..b021049f 100755 --- a/src/cython/doc/pyplots/barcode_persistence.py +++ b/src/cython/doc/pyplots/barcode_persistence.py @@ -1,5 +1,5 @@ import gudhi -periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt') +periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') diag = periodic_cc.persistence() gudhi.plot_persistence_barcode(diag) diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py index b4714fe3..56d6c50f 100755 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -1,5 +1,7 @@ import gudhi -alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off') -diag = alpha_complex.persistence() -gudhi.plot_persistence_diagram(diag) +rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) +simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) +diag = simplex_tree.persistence() +pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13) +pplot.show() diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py index adedc7d2..b4487be4 100755 --- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -38,6 +38,7 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from ' 'points from the given OFF file.') parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5) +parser.add_argument("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -63,7 +64,8 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index 2371c36c..e3f362dc 100755 --- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -40,6 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, required=True) parser.add_argument("-n", "--number_of_landmarks", type=int, required=True) parser.add_argument("-d", "--limit_dimension", type=int, required=True) +parser.add_argument("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -70,8 +71,8 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) - + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 5748aa8a..c236d992 100755 --- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -40,6 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, required=True) parser.add_argument("-n", "--number_of_landmarks", type=int, required=True) parser.add_argument("-d", "--limit_dimension", type=int, required=True) +parser.add_argument("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -70,8 +71,8 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) - + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py index bc3b16ec..ed87806b 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -44,4 +44,11 @@ gudhi.plot_persistence_barcode(persistence) print("#####################################################################") print("Show diagram persistence example") -gudhi.plot_persistence_diagram(persistence) +pplot = gudhi.plot_persistence_diagram(persistence) +pplot.show() + +print("#####################################################################") +print("Show diagram persistence example with a confidence band") + +pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2) +pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 984dbf1b..3baebd17 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -39,6 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-e", "--max_edge_length", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) +parser.add_argument("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -61,4 +62,5 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py index 4e5cd2c8..9bfea41c 100755 --- a/src/cython/example/rips_persistence_diagram.py +++ b/src/cython/example/rips_persistence_diagram.py @@ -39,4 +39,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1) diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0) print("diag=", diag) -gudhi.plot_persistence_diagram(diag) +pplot = gudhi.plot_persistence_diagram(diag) +pplot.show() diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py index 4845eb47..6145e7f2 100755 --- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py @@ -37,6 +37,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from ' '- Constructs a tangential complex with the ' 'points from the given OFF file') parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -59,7 +60,8 @@ with open(args.file, 'r') as f: print(st.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in index 34d7c3b5..ed2d28cc 100644 --- a/src/cython/gudhi.pyx.in +++ b/src/cython/gudhi.pyx.in @@ -30,6 +30,7 @@ include "cython/rips_complex.pyx" include "cython/cubical_complex.pyx" include "cython/periodic_cubical_complex.pyx" include "cython/persistence_graphical_tools.py" +include "cython/reader_utils.pyx" include "cython/witness_complex.pyx" include "cython/strong_witness_complex.pyx" @GUDHI_CYTHON_ALPHA_COMPLEX@ diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h new file mode 100644 index 00000000..b87b6cca --- /dev/null +++ b/src/cython/include/Reader_utils_interface.h @@ -0,0 +1,54 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2017 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#ifndef INCLUDE_READER_UTILS_INTERFACE_H_ +#define INCLUDE_READER_UTILS_INTERFACE_H_ + +#include + +#include +#include +#include + +namespace Gudhi { + +// Redefine functions with a different name in order the original name can be used in the Python version. +std::vector> read_matrix_from_csv_file(const std::string& filename, + const char separator = ';') { + return read_lower_triangular_matrix_from_csv_file(filename, separator); +} + +inline std::map>> + read_pers_intervals_grouped_by_dimension(std::string const& filename) { + return read_persistence_intervals_grouped_by_dimension(filename); +} + +inline std::vector> + read_pers_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) { + return read_persistence_intervals_in_dimension(filename, only_this_dim); +} + + +} // namespace Gudhi + + +#endif // INCLUDE_READER_UTILS_INTERFACE_H_ diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h index 6d813f4a..d06ee4bd 100644 --- a/src/cython/include/Rips_complex_interface.h +++ b/src/cython/include/Rips_complex_interface.h @@ -66,7 +66,7 @@ class Rips_complex_interface { } else { // Rips construction where values is a distance matrix Distance_matrix distances = - read_lower_triangular_matrix_from_csv_file::Filtration_value>(file_name); + Gudhi::read_lower_triangular_matrix_from_csv_file::Filtration_value>(file_name); rips_complex_ = new Rips_complex::Filtration_value>(distances, threshold); } } diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py new file mode 100755 index 00000000..517bf109 --- /dev/null +++ b/src/cython/test/test_reader_utils.py @@ -0,0 +1,81 @@ +import gudhi + +"""This file is part of the Gudhi Library. The Gudhi library + (Geometric Understanding in Higher Dimensions) is a generic C++ + library for computational topology. + + Author(s): Vincent Rouvreau + + Copyright (C) 2017 INRIA + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2017 INRIA" +__license__ = "GPL v3" + + +def test_non_existing_csv_file(): + # Try to open a non existing file + matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file='pouetpouettralala.toubiloubabdou') + assert matrix == [] + +def test_full_square_distance_matrix_csv_file(): + # Create test file + test_file = open('full_square_distance_matrix.csv', 'w') + test_file.write('0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;') + test_file.close() + matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="full_square_distance_matrix.csv") + assert matrix == [[], [1.0], [2.0, 4.0], [3.0, 5.0, 6.0]] + +def test_lower_triangular_distance_matrix_csv_file(): + # Create test file + test_file = open('lower_triangular_distance_matrix.csv', 'w') + test_file.write('\n1,\n2,3,\n4,5,6,\n7,8,9,10,') + test_file.close() + matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="lower_triangular_distance_matrix.csv", separator=",") + assert matrix == [[], [1.0], [2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0, 10.0]] + +def test_non_existing_persistence_file(): + # Try to open a non existing file + persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='pouetpouettralala.toubiloubabdou') + assert persistence == [] + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='pouetpouettralala.toubiloubabdou', only_this_dim=1) + assert persistence == [] + +def test_read_persistence_intervals_without_dimension(): + # Create test file + test_file = open('persistence_intervals_without_dimension.pers', 'w') + test_file.write('# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf') + test_file.close() + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers') + assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]] + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=15) + assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]] + persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers') + assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]} + +def test_read_persistence_intervals_with_dimension(): + # Create test file + test_file = open('persistence_intervals_with_dimension.pers', 'w') + test_file.write('# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf') + test_file.close() + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers') + assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]] + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1) + # BUG !!! + assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]] + persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers') + assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]} -- cgit v1.2.3 From 2c353d0c3db1c5c8fc11cb28ea65c90c559766a1 Mon Sep 17 00:00:00 2001 From: glisse Date: Mon, 10 Jul 2017 15:05:46 +0000 Subject: Cubical: use +inf instead of UINT_MAX as filtration value for non-simplices. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2595 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c578be16d9559b6d271cdb63be3a58a015735ab7 --- .../include/gudhi/Bitmap_cubical_complex.h | 27 +++++++++++----------- src/cython/test/test_cubical_complex.py | 4 ++-- 2 files changed, 16 insertions(+), 15 deletions(-) (limited to 'src/cython') diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h index 5a87b9b8..f395de65 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h @@ -97,7 +97,7 @@ class Bitmap_cubical_complex : public T { * with filtration on top dimensional cells. **/ Bitmap_cubical_complex(const std::vector& dimensions, - const std::vector& top_dimensional_cells) : + const std::vector& top_dimensional_cells) : T(dimensions, top_dimensional_cells), key_associated_to_simplex(this->total_number_of_cells + 1) { for (size_t i = 0; i != this->total_number_of_cells; ++i) { @@ -111,13 +111,13 @@ class Bitmap_cubical_complex : public T { /** * Constructor that requires vector of elements of type unsigned, which gives number of top dimensional cells - * in the following directions and vector of element of a type T::filtration_type + * in the following directions and vector of element of a type Filtration_value * with filtration on top dimensional cells. The last parameter of the constructor is a vector of boolean of a length * equal to the dimension of cubical complex. * If the position i on this vector is true, then we impose periodic boundary conditions in this direction. **/ Bitmap_cubical_complex(const std::vector& dimensions, - const std::vector& top_dimensional_cells, + const std::vector& top_dimensional_cells, std::vector< bool > directions_in_which_periodic_b_cond_are_to_be_imposed) : T(dimensions, top_dimensional_cells, directions_in_which_periodic_b_cond_are_to_be_imposed), key_associated_to_simplex(this->total_number_of_cells + 1) { @@ -170,20 +170,20 @@ class Bitmap_cubical_complex : public T { if (globalDbg) { std::cerr << "unsigned dimension(const Simplex_handle& sh)\n"; } - if (sh != std::numeric_limits::max()) return this->get_dimension_of_a_cell(sh); + if (sh != null_simplex()) return this->get_dimension_of_a_cell(sh); return -1; } /** * Return the filtration of a cell pointed by the Simplex_handle. **/ - typename T::filtration_type filtration(Simplex_handle sh) { + Filtration_value filtration(Simplex_handle sh) { if (globalDbg) { - std::cerr << "T::filtration_type filtration(const Simplex_handle& sh)\n"; + std::cerr << "Filtration_value filtration(const Simplex_handle& sh)\n"; } // Returns the filtration value of a simplex. - if (sh != std::numeric_limits::max()) return this->data[sh]; - return std::numeric_limits::max(); + if (sh != null_simplex()) return this->data[sh]; + return std::numeric_limits::infinity(); } /** @@ -203,7 +203,7 @@ class Bitmap_cubical_complex : public T { if (globalDbg) { std::cerr << "Simplex_key key(const Simplex_handle& sh)\n"; } - if (sh != std::numeric_limits::max()) { + if (sh != null_simplex()) { return this->key_associated_to_simplex[sh]; } return this->null_key(); @@ -216,7 +216,7 @@ class Bitmap_cubical_complex : public T { if (globalDbg) { std::cerr << "Simplex_handle simplex(Simplex_key key)\n"; } - if (key != std::numeric_limits::max()) { + if (key != null_key()) { return this->simplex_associated_to_key[ key ]; } return null_simplex(); @@ -229,7 +229,7 @@ class Bitmap_cubical_complex : public T { if (globalDbg) { std::cerr << "void assign_key(Simplex_handle& sh, Simplex_key key)\n"; } - if (key == std::numeric_limits::max()) return; + if (key == null_key()) return; this->key_associated_to_simplex[sh] = key; this->simplex_associated_to_key[key] = sh; } @@ -566,8 +566,9 @@ class is_before_in_filtration { bool operator()(const typename Bitmap_cubical_complex::Simplex_handle& sh1, const typename Bitmap_cubical_complex::Simplex_handle& sh2) const { // Not using st_->filtration(sh1) because it uselessly tests for null_simplex. - typename T::filtration_type fil1 = CC_->data[sh1]; - typename T::filtration_type fil2 = CC_->data[sh2]; + typedef typename T::filtration_type Filtration_value; + Filtration_value fil1 = CC_->data[sh1]; + Filtration_value fil2 = CC_->data[sh2]; if (fil1 != fil2) { return fil1 < fil2; } diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py index 2e281ee4..9a365823 100755 --- a/src/cython/test/test_cubical_complex.py +++ b/src/cython/test/test_cubical_complex.py @@ -67,7 +67,7 @@ def test_dimension_constructor(): top_dimensional_cells = [1,2,3,4,5,6,7,8,9]) assert cub.__is_defined() == True assert cub.__is_persistence_defined() == False - assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))] + assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))] assert cub.__is_persistence_defined() == True assert cub.betti_numbers() == [1, 0] assert cub.persistent_betti_numbers(0, 1000) == [0, 0] @@ -80,7 +80,7 @@ def test_dimension_constructor(): cub = CubicalComplex(perseus_file='CubicalOneSphere.txt') assert cub.__is_defined() == True assert cub.__is_persistence_defined() == False - assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))] + assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))] assert cub.__is_persistence_defined() == True assert cub.betti_numbers() == [1, 0, 0] assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0] -- cgit v1.2.3 From b8fdc4c7f6c30df5e7a28a0a23e697640f9d67cc Mon Sep 17 00:00:00 2001 From: glisse Date: Mon, 10 Jul 2017 18:58:12 +0000 Subject: simplex / complex confusion git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2596 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 77c093029d3e2518260ce59705110df3fbfe11e3 --- src/cython/cython/simplex_tree.pyx | 48 ++++++++++++++--------------- src/cython/include/Simplex_tree_interface.h | 8 ++--- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 9d40a8b5..2acdac3c 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -183,10 +183,10 @@ cdef class SimplexTree: :returns: true if the simplex was found, false otherwise. :rtype: bool """ - cdef vector[int] complex + cdef vector[int] csimplex for i in simplex: - complex.push_back(i) - return self.thisptr.find_simplex(complex) + csimplex.push_back(i) + return self.thisptr.find_simplex(csimplex) def insert(self, simplex, filtration=0.0): """This function inserts the given N-simplex and its subfaces with the @@ -200,10 +200,10 @@ cdef class SimplexTree: :returns: true if the simplex was found, false otherwise. :rtype: bool """ - cdef vector[int] complex + cdef vector[int] csimplex for i in simplex: - complex.push_back(i) - return self.thisptr.insert_simplex_and_subfaces(complex, + csimplex.push_back(i) + return self.thisptr.insert_simplex_and_subfaces(csimplex, filtration) def get_filtration(self): @@ -232,35 +232,35 @@ cdef class SimplexTree: :returns: The (simplices of the) skeleton of a maximum dimension. :rtype: list of tuples(simplex, filtration) """ - cdef vector[pair[vector[int], double]] skeletons \ + cdef vector[pair[vector[int], double]] skeleton \ = self.thisptr.get_skeleton(dimension) ct = [] - for filtered_complex in skeletons: + for filtered_simplex in skeleton: v = [] - for vertex in filtered_complex.first: + for vertex in filtered_simplex.first: v.append(vertex) - ct.append((v, filtered_complex.second)) + ct.append((v, filtered_simplex.second)) return ct def get_star(self, simplex): - """This function returns the stars of a given N-simplex. + """This function returns the star of a given N-simplex. :param simplex: The N-simplex, represented by a list of vertex. :type simplex: list of int. :returns: The (simplices of the) star of a simplex. :rtype: list of tuples(simplex, filtration) """ - cdef vector[int] complex + cdef vector[int] csimplex for i in simplex: - complex.push_back(i) - cdef vector[pair[vector[int], double]] stars \ - = self.thisptr.get_star(complex) + csimplex.push_back(i) + cdef vector[pair[vector[int], double]] star \ + = self.thisptr.get_star(csimplex) ct = [] - for filtered_complex in stars: + for filtered_simplex in star: v = [] - for vertex in filtered_complex.first: + for vertex in filtered_simplex.first: v.append(vertex) - ct.append((v, filtered_complex.second)) + ct.append((v, filtered_simplex.second)) return ct def get_cofaces(self, simplex, codimension): @@ -275,17 +275,17 @@ cdef class SimplexTree: :returns: The (simplices of the) cofaces of a simplex :rtype: list of tuples(simplex, filtration) """ - cdef vector[int] complex + cdef vector[int] csimplex for i in simplex: - complex.push_back(i) + csimplex.push_back(i) cdef vector[pair[vector[int], double]] cofaces \ - = self.thisptr.get_cofaces(complex, codimension) + = self.thisptr.get_cofaces(csimplex, codimension) ct = [] - for filtered_complex in cofaces: + for filtered_simplex in cofaces: v = [] - for vertex in filtered_complex.first: + for vertex in filtered_simplex.first: v.append(vertex) - ct.append((v, filtered_complex.second)) + ct.append((v, filtered_simplex.second)) return ct def remove_maximal_simplex(self, simplex): diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h index 45ce1916..09e7e992 100644 --- a/src/cython/include/Simplex_tree_interface.h +++ b/src/cython/include/Simplex_tree_interface.h @@ -70,14 +70,14 @@ class Simplex_tree_interface : public Simplex_tree { } // Do not interface this function, only used in strong witness interface for complex creation - bool insert_simplex(const std::vector& complex, Filtration_value filtration = 0) { - Insertion_result result = Base::insert_simplex(complex, filtration); + bool insert_simplex(const std::vector& simplex, Filtration_value filtration = 0) { + Insertion_result result = Base::insert_simplex(simplex, filtration); return (result.second); } // Do not interface this function, only used in strong witness interface for complex creation - bool insert_simplex_and_subfaces(const std::vector& complex, Filtration_value filtration = 0) { - Insertion_result result = Base::insert_simplex_and_subfaces(complex, filtration); + bool insert_simplex_and_subfaces(const std::vector& simplex, Filtration_value filtration = 0) { + Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration); return (result.second); } -- cgit v1.2.3 From 0f8c2b9623fcfd8b346944b637681144b4c58318 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 7 Aug 2017 13:27:32 +0000 Subject: Fix test reader utils git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2600 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 24bcf652d5374d158c6b4e90dd2233af7e153c49 --- src/cython/test/test_reader_utils.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'src/cython') diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py index 517bf109..79dc9064 100755 --- a/src/cython/test/test_reader_utils.py +++ b/src/cython/test/test_reader_utils.py @@ -61,9 +61,9 @@ def test_read_persistence_intervals_without_dimension(): test_file.write('# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf') test_file.close() persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers') - assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]] + assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))] persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=15) - assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]] + assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))] persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers') assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]} @@ -73,9 +73,9 @@ def test_read_persistence_intervals_with_dimension(): test_file.write('# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf') test_file.close() persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers') - assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]] + assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))] persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1) # BUG !!! - assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]] + assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))] persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers') assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]} -- cgit v1.2.3 From 295d60787357806ae9aac1bfab98f3fefcd759a0 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 8 Aug 2017 13:15:33 +0000 Subject: Fix persistence files reader unitary tests git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2603 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1b3ab678420a63b6607d15f350697eccc42b56f7 --- src/cython/test/test_reader_utils.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) (limited to 'src/cython') diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py index 79dc9064..25591fb3 100755 --- a/src/cython/test/test_reader_utils.py +++ b/src/cython/test/test_reader_utils.py @@ -62,8 +62,10 @@ def test_read_persistence_intervals_without_dimension(): test_file.close() persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers') assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))] - persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=15) - assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))] + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=0) + assert persistence == [] + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=1) + assert persistence == [] persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers') assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]} @@ -74,8 +76,13 @@ def test_read_persistence_intervals_with_dimension(): test_file.close() persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers') assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))] + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=0) + assert persistence == [(2.7, 3.7)] persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1) - # BUG !!! - assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))] + assert persistence == [(9.6, 14.), (3., float('Inf'))] + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=2) + assert persistence == [] + persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=3) + assert persistence == [(34.2, 34.974)] persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers') assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]} -- cgit v1.2.3 From c7da4a2e7f8cb26c63ebc5c226c0cfefb5290755 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 10 Aug 2017 08:50:04 +0000 Subject: Fix Python2 compatibility git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2607 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b8744511b527f7117d3432c559dcb68b59253e53 --- src/cython/cython/reader_utils.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/cython/reader_utils.pyx b/src/cython/cython/reader_utils.pyx index 14976167..3a17c5a0 100644 --- a/src/cython/cython/reader_utils.pyx +++ b/src/cython/cython/reader_utils.pyx @@ -49,7 +49,7 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): """ if csv_file is not '': if os.path.isfile(csv_file): - return read_matrix_from_csv_file(str.encode(csv_file), str.encode(separator)[0]) + return read_matrix_from_csv_file(str.encode(csv_file), ord(separator[0])) print("file " + csv_file + " not set or not found.") return [] -- cgit v1.2.3 From 2fc118133e76f05fc55d86cf32883223191fe473 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 17 Aug 2017 16:10:46 +0000 Subject: Add file formats for Python. Binding for persistence write files Launch py.test with the command "python -m pytest" (shall work everywhere) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2611 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9443a7eb5b580ece7708ff57949ad08339c1c5c3 --- .../include/gudhi/Persistent_cohomology.h | 13 +++++++--- .../modules/GUDHI_third_party_libraries.cmake | 2 -- src/common/doc/file_formats.h | 6 ++++- src/cython/CMakeLists.txt | 14 +++++----- src/cython/cython/simplex_tree.pyx | 22 +++++++++++++++- src/cython/doc/_templates/layout.html | 1 + src/cython/doc/fileformats.rst | 30 ++++++++++++++++++++++ src/cython/doc/reader_utils_ref.rst | 11 ++++++++ 8 files changed, 84 insertions(+), 15 deletions(-) create mode 100644 src/cython/doc/fileformats.rst create mode 100644 src/cython/doc/reader_utils_ref.rst (limited to 'src/cython') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index 672fda48..e0a147b3 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -591,10 +591,17 @@ class Persistent_cohomology { std::ofstream diagram_out(diagram_name.c_str()); cmp_intervals_by_length cmp(cpx_); std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp); + bool has_infinity = std::numeric_limits::has_infinity; for (auto pair : persistent_pairs_) { - diagram_out << cpx_->dimension(get<0>(pair)) << " " - << cpx_->filtration(get<0>(pair)) << " " - << cpx_->filtration(get<1>(pair)) << std::endl; + // Special case on windows, inf is "1.#INF" + if (has_infinity && cpx_->filtration(get<1>(pair)) == std::numeric_limits::infinity()) { + diagram_out << cpx_->dimension(get<0>(pair)) << " " + << cpx_->filtration(get<0>(pair)) << " inf" << std::endl; + } else { + diagram_out << cpx_->dimension(get<0>(pair)) << " " + << cpx_->filtration(get<0>(pair)) << " " + << cpx_->filtration(get<1>(pair)) << std::endl; + } } } diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 8f486118..e29ba40c 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -117,8 +117,6 @@ if(NOT GUDHI_CYTHON_PATH) endif(NOT GUDHI_CYTHON_PATH) if(PYTHONINTERP_FOUND AND CYTHON_FOUND) - # Unitary tests are available through py.test - find_program( PYTEST_PATH py.test ) # Default found version 2 if(PYTHON_VERSION_MAJOR EQUAL 2) # Documentation generation is available through sphinx diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h index 9d0415b1..d715aa4d 100644 --- a/src/common/doc/file_formats.h +++ b/src/common/doc/file_formats.h @@ -26,7 +26,7 @@ namespace Gudhi { /*! \page fileformats File formats - + \tableofcontents \section FileFormatsPers Persistence Diagram @@ -49,6 +49,10 @@ namespace Gudhi { \endverbatim Other sample files can be found in the `data/persistence_diagram` folder. + + Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with + `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or + `Gudhi::read_persistence_intervals_in_dimension()`. */ } // namespace Gudhi diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index f427b3c5..a06be008 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -16,7 +16,7 @@ function( add_gudhi_cython_lib THE_LIB ) endfunction( add_gudhi_cython_lib ) if(CYTHON_FOUND) - message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}") + message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") @@ -305,13 +305,11 @@ if(CYTHON_FOUND) set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") # Unitary tests are available through py.test - if(PYTEST_PATH) - add_test( - NAME gudhi_cython_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${PYTEST_PATH}") - set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - endif(PYTEST_PATH) + add_test( + NAME gudhi_cython_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest) + set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") # Documentation generation is available through sphinx if(SPHINX_PATH) diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 2acdac3c..9e3b2345 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -61,6 +61,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": vector[int] betti_numbers() vector[int] persistent_betti_numbers(double from_value, double to_value) vector[pair[double,double]] intervals_in_dimension(int dimension) + void write_output_diagram(string diagram_file_name) # SimplexTree python interface cdef class SimplexTree: @@ -385,7 +386,7 @@ cdef class SimplexTree: complex in a specific dimension. :param dimension: The specific dimension. - :type from_value: int. + :type dimension: int. :returns: The persistence intervals. :rtype: list of pair of float @@ -399,3 +400,22 @@ cdef class SimplexTree: print("intervals_in_dim function requires persistence function" " to be launched first.") return intervals_result + + def write_persistence_diagram(self, persistence_file=''): + """This function writes the persistence intervals of the simplicial + complex in a user given file name. + + :param persistence_file: The specific dimension. + :type persistence_file: string. + + :note: intervals_in_dim function requires persistence function to be + launched first. + """ + if self.pcohptr != NULL: + if persistence_file != '': + self.pcohptr.write_output_diagram(str.encode(persistence_file)) + else: + print("persistence_file must be specified") + else: + print("intervals_in_dim function requires persistence function" + " to be launched first.") diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html index b11c1236..243f33c6 100644 --- a/src/cython/doc/_templates/layout.html +++ b/src/cython/doc/_templates/layout.html @@ -65,6 +65,7 @@ {#- old style sidebars: using blocks -- should be deprecated #} {%- block sidebartoc %}

GUDHI

+

File formats

GUDHI installation

Acknowledging the GUDHI library

Index

diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst new file mode 100644 index 00000000..36225b6d --- /dev/null +++ b/src/cython/doc/fileformats.rst @@ -0,0 +1,30 @@ +File formats +############ + +To find the correct function to read the files, please refer to :doc:`reader_utils_ref` + +Persistence Diagram +******************* + +Such a file, whose extension is usually ``.pers``, contains a list of persistence intervals. + +Lines starting with ``#`` are ignored (comments). + +Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):: + + [[field] dimension] birth death + +Here is a simple sample file:: + + # Persistence diagram example + 2 2.7 3.7 + 2 9.6 14. + # Some comments + 3 34.2 34.974 + 4 3. inf + +Other sample files can be found in the data/persistence_diagram folder. + +Such files can be generated with :meth:`gudhi.SimplexTree.write_persistence_diagram` and read with +:meth:`gudhi.read_persistence_intervals_grouped_by_dimension`, or +:meth:`gudhi.read_persistence_intervals_in_dimension`. diff --git a/src/cython/doc/reader_utils_ref.rst b/src/cython/doc/reader_utils_ref.rst new file mode 100644 index 00000000..9c1ea6fc --- /dev/null +++ b/src/cython/doc/reader_utils_ref.rst @@ -0,0 +1,11 @@ +============================= +Reader utils reference manual +============================= + +.. autofunction:: gudhi.read_off + +.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file + +.. autofunction:: gudhi.read_persistence_intervals_grouped_by_dimension + +.. autofunction:: gudhi.read_persistence_intervals_in_dimension -- cgit v1.2.3 From 5b92662a7ed71546efb4a3697bc0b3e2b315fefc Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 18 Aug 2017 06:19:31 +0000 Subject: Add display function in file format doc git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2612 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b51ffdf8f7be07c6745ca2b6501c51a350deffd2 --- src/cython/doc/fileformats.rst | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) (limited to 'src/cython') diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst index 36225b6d..156ef4e4 100644 --- a/src/cython/doc/fileformats.rst +++ b/src/cython/doc/fileformats.rst @@ -1,16 +1,16 @@ File formats ############ -To find the correct function to read the files, please refer to :doc:`reader_utils_ref` - Persistence Diagram ******************* -Such a file, whose extension is usually ``.pers``, contains a list of persistence intervals. +Such a file, whose extension is usually ``.pers``, contains a list of +persistence intervals. Lines starting with ``#`` are ignored (comments). -Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):: +Other lines might contain 2, 3 or 4 values (the number of values on each line +must be the same for all lines):: [[field] dimension] birth death @@ -25,6 +25,9 @@ Here is a simple sample file:: Other sample files can be found in the data/persistence_diagram folder. -Such files can be generated with :meth:`gudhi.SimplexTree.write_persistence_diagram` and read with +Such files can be generated with +:meth:`gudhi.SimplexTree.write_persistence_diagram`, read with :meth:`gudhi.read_persistence_intervals_grouped_by_dimension`, or -:meth:`gudhi.read_persistence_intervals_in_dimension`. +:meth:`gudhi.read_persistence_intervals_in_dimension` and displayed with +:meth:`gudhi.plot_persistence_barcode` or +:meth:`gudhi.plot_persistence_diagram`. -- cgit v1.2.3 From ef36c8b63bc353ac9d4e6982b9bba6797d546e51 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 18 Aug 2017 09:40:19 +0000 Subject: Fix sphinx bug when python3 is not in /usr/bin git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2613 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 07f67d4cc1f3b558b191115e0979ce3ce0580206 --- src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +- src/cython/CMakeLists.txt | 1 + src/cython/doc/python3-sphinx-build | 11 ----------- src/cython/doc/python3-sphinx-build.in | 11 +++++++++++ 4 files changed, 13 insertions(+), 12 deletions(-) delete mode 100755 src/cython/doc/python3-sphinx-build create mode 100755 src/cython/doc/python3-sphinx-build.in (limited to 'src/cython') diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index e29ba40c..dbf2106a 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -123,7 +123,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND) find_program( SPHINX_PATH sphinx-build ) elseif(PYTHON_VERSION_MAJOR EQUAL 3) # No sphinx-build in Pyton3, just hack it - set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build") + set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build") else() message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.") endif(PYTHON_VERSION_MAJOR EQUAL 2) diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index a06be008..ab5ea9ef 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -194,6 +194,7 @@ if(CYTHON_FOUND) endif(UNIX) # set sphinx-build in make files + configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY) configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY) configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) diff --git a/src/cython/doc/python3-sphinx-build b/src/cython/doc/python3-sphinx-build deleted file mode 100755 index 44b94169..00000000 --- a/src/cython/doc/python3-sphinx-build +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/python3 - -""" -Emulate sphinx-build for python3 -""" - -from sys import exit, argv -from sphinx import main - -if __name__ == '__main__': - exit(main(argv)) diff --git a/src/cython/doc/python3-sphinx-build.in b/src/cython/doc/python3-sphinx-build.in new file mode 100755 index 00000000..c97965f5 --- /dev/null +++ b/src/cython/doc/python3-sphinx-build.in @@ -0,0 +1,11 @@ +#!@PYTHON_EXECUTABLE@ + +""" +Emulate sphinx-build for python3 +""" + +from sys import exit, argv +from sphinx import main + +if __name__ == '__main__': + exit(main(argv)) -- cgit v1.2.3 From 962ed22cc9f8a3de681e8543f3558b37525a5681 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 22 Aug 2017 13:19:58 +0000 Subject: Version files modification for new release git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2616 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8296050aef9e6658cd98080075f4047487e21b68 --- CMakeGUDHIVersion.txt | 2 +- src/Doxyfile | 2 +- src/cython/doc/conf.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index 3d9add66..d5620218 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,6 @@ set (GUDHI_MAJOR_VERSION 2) set (GUDHI_MINOR_VERSION 0) -set (GUDHI_PATCH_VERSION 1.beta) +set (GUDHI_PATCH_VERSION 1-rc1) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") diff --git a/src/Doxyfile b/src/Doxyfile index 2fecf5fb..6c01aefc 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -38,7 +38,7 @@ PROJECT_NAME = "GUDHI" # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = "2.0.0" +PROJECT_NUMBER = "2.0.1-rc1" # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py index 42bfd59c..072f7a94 100755 --- a/src/cython/doc/conf.py +++ b/src/cython/doc/conf.py @@ -69,7 +69,7 @@ copyright = u'2016, GUDHI Editorial Board' # The short X.Y version. version = '2.0' # The full version, including alpha/beta/rc tags. -release = '2.0.0' +release = '2.0.1-rc1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. -- cgit v1.2.3 From ff75dab4aa40bcea9400f861bbdf1bd133f892d1 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 25 Aug 2017 06:31:41 +0000 Subject: bug in Python SimplexTree (needs string) Doc issue in alpha_complex user doc git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2629 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ab35f6f64af33414002d6899275170f781e9cfa8 --- src/cython/cython/simplex_tree.pyx | 1 + src/cython/doc/alpha_complex_user.rst | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 9e3b2345..47aa5311 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -2,6 +2,7 @@ from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair from libcpp cimport bool +from libcpp.string cimport string """This file is part of the Gudhi Library. The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index e8268ef1..ff62390b 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst @@ -142,7 +142,7 @@ Prune above given filtration value ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The simplex tree is pruned from the given maximum alpha squared value (cf. `Simplex_tree::prune_above_filtration()` -int he `C++ version `_). +in the `C++ version `_). In the following example, the value is given by the user as argument of the program. -- cgit v1.2.3 From 94bf43f9d92f546837f5120379ffdc08bf274302 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 5 Sep 2017 15:47:24 +0000 Subject: Tests and compilation are now from sources (even if doc and examples are copied) This modification does not fix it for the doc git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2645 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0fa4850747d3f18cd54e0622ef1831d5d5c5a0df --- src/cython/CMakeLists.txt | 123 ++++++++++++++++++++++++++++++++++------------ src/cython/gudhi.pyx.in | 18 +++---- src/cython/setup.py.in | 2 +- 3 files changed, 102 insertions(+), 41 deletions(-) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index ab5ea9ef..a12b6029 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -73,13 +73,11 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") endif (EIGEN3_FOUND) - # Copy recursively include, cython, example, doc and test repositories before packages finding + # Copy recursively example and doc repositories before packages finding # Some tests and doc files are removed in case some packages are not found - file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + # Developper version for doc images file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png") file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") @@ -104,9 +102,9 @@ if(CYTHON_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) # If CGAL_VERSION >= 4.8.1, include subsampling - set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'") - set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'") - set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'") + set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") + set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") + set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") else (NOT CGAL_VERSION VERSION_LESS 4.8.1) # Remove subsampling unitary tests file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py) @@ -125,7 +123,7 @@ if(CYTHON_FOUND) endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_VERSION VERSION_LESS 4.7.0) # If CGAL_VERSION >= 4.7.0, include alpha - set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'") + set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'") else (NOT CGAL_VERSION VERSION_LESS 4.7.0) # Remove alpha complex unitary tests file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py) @@ -136,9 +134,9 @@ if(CYTHON_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.6.0) # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX - "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n") + "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n") else (NOT CGAL_VERSION VERSION_LESS 4.6.0) - # Remove alpha complex unitary tests + # Remove euclidean witness complex unitary tests file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py) file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst") file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst") @@ -177,6 +175,7 @@ if(CYTHON_FOUND) # Loop on INCLUDE_DIRECTORIES PROPERTY get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) + message(" --- ${GUDHI_INCLUDE_DIRECTORY} ---") set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") endforeach() set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") @@ -220,97 +219,159 @@ if(CYTHON_FOUND) # Test examples if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + # Bottleneck add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME bottleneck_basic_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py") + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test( + NAME test_bottleneck_distance_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py) + set_tests_properties(test_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + # Tangential add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test( + NAME test_tangential_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py) + set_tests_properties(test_tangential_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + # Euclidean witness add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + add_test( + NAME test_euclidean_witness_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py) + set_tests_properties(test_euclidean_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + # Alpha add_test(NAME alpha_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py") + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) + add_test( + NAME test_alpha_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py) + set_tests_properties(test_alpha_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) + # Cubical add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME random_cubical_complex_persistence_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/random_cubical_complex_persistence_example.py" + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" 10 10 10) set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test( + NAME test_cubical_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py) + set_tests_properties(test_cubical_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + # Rips add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_from_points_example.py) + COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test( + NAME test_rips_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py) + set_tests_properties(test_rips_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + # Simplex tree add_test(NAME simplex_tree_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py) + COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test( + NAME test_simplex_tree_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py) + set_tests_properties(test_simplex_tree_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + # Witness add_test(NAME witness_complex_from_nearest_landmark_table_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py) + COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - # Unitary tests are available through py.test add_test( - NAME gudhi_cython_py_test + NAME test_witness_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py) + set_tests_properties(test_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + # Reader utils + add_test( + NAME test_reader_utils_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py) + set_tests_properties(test_reader_utils_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + + # Subsampling + add_test( + NAME test_subsampling_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest) - set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py) + set_tests_properties(test_subsampling_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") # Documentation generation is available through sphinx if(SPHINX_PATH) diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in index ed2d28cc..1141673a 100644 --- a/src/cython/gudhi.pyx.in +++ b/src/cython/gudhi.pyx.in @@ -24,15 +24,15 @@ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 INRIA" __license__ = "GPL v3" -include "cython/off_reader.pyx" -include "cython/simplex_tree.pyx" -include "cython/rips_complex.pyx" -include "cython/cubical_complex.pyx" -include "cython/periodic_cubical_complex.pyx" -include "cython/persistence_graphical_tools.py" -include "cython/reader_utils.pyx" -include "cython/witness_complex.pyx" -include "cython/strong_witness_complex.pyx" +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/rips_complex.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/cubical_complex.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/periodic_cubical_complex.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/persistence_graphical_tools.py' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/reader_utils.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/witness_complex.pyx' +include '@CMAKE_CURRENT_SOURCE_DIR@/cython/strong_witness_complex.pyx' @GUDHI_CYTHON_ALPHA_COMPLEX@ @GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@ @GUDHI_CYTHON_SUBSAMPLING@ diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in index c1a1717a..fefa36bb 100644 --- a/src/cython/setup.py.in +++ b/src/cython/setup.py.in @@ -29,7 +29,7 @@ __license__ = "GPL v3" gudhi = Extension( "gudhi", - sources = ['gudhi.pyx',], + sources = ['@CMAKE_CURRENT_BINARY_DIR@/gudhi.pyx',], language = 'c++', extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@], extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@], -- cgit v1.2.3 From c15a3570fa54e837c27f0e5b862e7bb5c16302d7 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 7 Sep 2017 13:17:19 +0000 Subject: Python documentation is now built from sources to the build directory. Missing bibtex and images to be "as before" git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2649 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0deda91875e34ce534c88a601cfb167d9c7dfa01 --- src/cython/CMakeLists.txt | 200 ++++++++------------- src/cython/doc/Makefile.in | 44 ----- src/cython/doc/alpha_complex_user.rst | 3 +- src/cython/doc/conf.py | 90 +--------- src/cython/doc/cubical_complex_user.rst | 10 +- src/cython/doc/examples.rst | 19 +- src/cython/doc/generate_examples.py | 43 ----- src/cython/doc/make.bat.in | 67 ------- .../doc/persistence_graphical_tools_user.rst | 13 +- src/cython/doc/pyplots/barcode_persistence.py | 3 +- src/cython/doc/pyplots/diagram_persistence.py | 3 +- src/cython/doc/rips_complex_user.rst | 6 +- src/cython/doc/tangential_complex_user.rst | 3 +- src/cython/gudhi.pyx.in | 3 + 14 files changed, 131 insertions(+), 376 deletions(-) delete mode 100644 src/cython/doc/Makefile.in delete mode 100755 src/cython/doc/generate_examples.py delete mode 100644 src/cython/doc/make.bat.in (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index a12b6029..6c8232ea 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -73,33 +73,6 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") endif (EIGEN3_FOUND) - # Copy recursively example and doc repositories before packages finding - # Some tests and doc files are removed in case some packages are not found - file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - - # Developper version for doc images - file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png") - file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg") - file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - # User version for doc images - file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png") - file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg") - file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - # Biblio - file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib") - file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - # Cubical complex perseus doc example - file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt") - file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - # Persistence graphical tools examples - file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) # If CGAL_VERSION >= 4.8.1, include subsampling set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") @@ -192,11 +165,6 @@ if(CYTHON_FOUND) set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") endif(UNIX) - # set sphinx-build in make files - configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY) - configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY) - configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) - # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY) # Generate gudhi.pyx - Gudhi cython file @@ -222,52 +190,46 @@ if(CYTHON_FOUND) # Bottleneck add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME bottleneck_basic_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") - set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") - add_test( - NAME test_bottleneck_distance_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py) - set_tests_properties(test_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_bottleneck_distance_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py) # Tangential add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - add_test( - NAME test_tangential_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py) - set_tests_properties(test_tangential_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_tangential_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py) # Euclidean witness add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - add_test( - NAME test_euclidean_witness_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py) - set_tests_properties(test_euclidean_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_euclidean_witness_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py) endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) @@ -275,115 +237,105 @@ if(CYTHON_FOUND) # Alpha add_test(NAME alpha_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") - set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) - set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - add_test( - NAME test_alpha_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py) - set_tests_properties(test_alpha_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_alpha_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py) endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) # Cubical add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME random_cubical_complex_persistence_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" 10 10 10) - set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - add_test( - NAME test_cubical_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py) - set_tests_properties(test_cubical_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_cubical_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py) # Rips add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) - set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) - set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) - add_test( - NAME test_rips_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py) - set_tests_properties(test_rips_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_rips_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py) # Simplex tree add_test(NAME simplex_tree_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) - set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) - add_test( - NAME test_simplex_tree_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py) - set_tests_properties(test_simplex_tree_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_simplex_tree_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py) # Witness add_test(NAME witness_complex_from_nearest_landmark_table_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) - set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) - add_test( - NAME test_witness_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py) - set_tests_properties(test_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_witness_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py) # Reader utils - add_test( - NAME test_reader_utils_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py) - set_tests_properties(test_reader_utils_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME test_reader_utils_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py) # Subsampling - add_test( - NAME test_subsampling_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py) - set_tests_properties(test_subsampling_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - - # Documentation generation is available through sphinx - if(SPHINX_PATH) - if (UNIX) - add_custom_target(sphinx - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc - DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" - COMMAND make html doctest) - else (UNIX) - add_custom_target(sphinx - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc - COMMAND make.bat html doctest) - endif (UNIX) - endif(SPHINX_PATH) + add_test(NAME test_subsampling_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py) + + # Documentation generation is available through sphinx - requires all modules + if(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1) + # set sphinx-build in make files + configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY) + + add_custom_target(sphinx + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${SPHINX_PATH} -b html . "${CMAKE_CURRENT_BINARY_DIR}/sphinx" + DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so") + + add_test(NAME sphinx_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx") + + endif(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1) endif(CYTHON_FOUND) diff --git a/src/cython/doc/Makefile.in b/src/cython/doc/Makefile.in deleted file mode 100644 index 526350b3..00000000 --- a/src/cython/doc/Makefile.in +++ /dev/null @@ -1,44 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = @SPHINX_PATH@ -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - rm -f examples.inc - rm -rf $(BUILDDIR)/* - -# GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean) - -html: - ./generate_examples.py - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index e8268ef1..e541e6d3 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst @@ -158,7 +158,8 @@ Then, it is asked to display information about the alpha complex: .. testcode:: import gudhi - alpha_complex = gudhi.AlphaComplex(off_file='alphacomplexdoc.off') + alpha_complex = gudhi.AlphaComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off') simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=59.0) result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py index 072f7a94..19a880d4 100755 --- a/src/cython/doc/conf.py +++ b/src/cython/doc/conf.py @@ -21,7 +21,7 @@ import os #sys.path.insert(0, os.path.abspath('.')) # Path to Gudhi.so from source path -sys.path.insert(0, os.path.abspath('..')) +sys.path.insert(0, os.path.abspath('.')) # -- General configuration ------------------------------------------------ @@ -58,18 +58,20 @@ source_suffix = '.rst' # The master toctree document. master_doc = 'index' +import gudhi + # General information about the project. -project = u'GUDHI' -copyright = u'2016, GUDHI Editorial Board' +project = gudhi.__name__ +copyright = gudhi.__copyright__ # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. -version = '2.0' +version = gudhi.__version__ # The full version, including alpha/beta/rc tags. -release = '2.0.1-rc1' +#release = '2.0.1-rc1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. @@ -198,81 +200,3 @@ html_static_path = ['_static'] # Output file base name for HTML help builder. htmlhelp_basename = 'GUDHIdoc' - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - ('index', 'GUDHI.tex', u'GUDHI Documentation', - u'Vincent Rouvreau', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'gudhi', u'GUDHI Documentation', - [u'Vincent Rouvreau'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ('index', 'GUDHI', u'GUDHI Documentation', - u'Vincent Rouvreau', 'GUDHI', 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 344b9554..8c9a3ed6 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -97,12 +97,13 @@ The input file for the following complex is: .. literalinclude:: cubicalcomplexdoc.txt -.. centered:: cubicalcomplexdoc.txt +.. centered:: data/bitmap/cubicalcomplexdoc.txt .. testcode:: import gudhi - cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt') + cubical_complex = gudhi.CubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/cubicalcomplexdoc.txt') result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \ repr(cubical_complex.num_simplices()) + ' simplices.' print(result_str) @@ -129,14 +130,15 @@ For instance: .. literalinclude:: periodiccubicalcomplexdoc.txt -.. centered:: periodiccubicalcomplexdoc.txt +.. centered:: data/bitmap/periodiccubicalcomplexdoc.txt Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. .. testcode:: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='periodiccubicalcomplexdoc.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/periodiccubicalcomplexdoc.txt') result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \ repr(periodic_cc.num_simplices()) + ' simplices.' print(result_str) diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst index a89e0596..1e596e18 100644 --- a/src/cython/doc/examples.rst +++ b/src/cython/doc/examples.rst @@ -1,4 +1,21 @@ Examples ######## -.. include:: examples.inc +.. only:: builder_html + + * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_example.py>` + * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>` + * :download:`simplex_tree_example.py <../example/simplex_tree_example.py>` + * :download:`alpha_rips_persistence_bottleneck_distance.py <../example/alpha_rips_persistence_bottleneck_distance.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` + * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` + * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` + * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>` + * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>` + * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` + * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>` diff --git a/src/cython/doc/generate_examples.py b/src/cython/doc/generate_examples.py deleted file mode 100755 index d64d506c..00000000 --- a/src/cython/doc/generate_examples.py +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env python - -from os import listdir - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2017 INRIA - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" -__license__ = "GPL v3" - -""" -generate_examples.py generates examples.inc to be included in examples.rst. -Refer to Makefile and make.bat to see if it is correctly launched. -""" - -output_file = open('examples.inc','w') - -output_file.write('.. only:: builder_html\n\n') - -for file in listdir('../example/'): - output_file.write(" * :download:`" + file + " <../example/" + file + ">`\n") - -output_file.close() diff --git a/src/cython/doc/make.bat.in b/src/cython/doc/make.bat.in deleted file mode 100644 index ff1a6d56..00000000 --- a/src/cython/doc/make.bat.in +++ /dev/null @@ -1,67 +0,0 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=@SPHINX_PATH@ -) -set BUILDDIR=_build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . -set I18NSPHINXOPTS=%SPHINXOPTS% . -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^` where ^ is one of - echo. html to make standalone HTML files - echo. doctest to run all doctests embedded in the documentation if enabled - goto end -) - -if "%1" == "clean" ( - del examples.inc - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - - -%SPHINXBUILD% 2> nul -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -:: GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean) - -if "%1" == "html" ( - generate_examples.py - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -:end diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 13198162..9033331f 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -32,7 +32,8 @@ This function can display the persistence result as a barcode: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/3d_torus.txt') diag = periodic_cc.persistence() plt = gudhi.plot_persistence_barcode(diag) plt.show() @@ -41,8 +42,10 @@ This function can display the persistence result as a barcode: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/3d_torus.txt') diag = periodic_cc.persistence() + print("diag = ", diag) plt = gudhi.plot_persistence_barcode(diag) plt.show() @@ -55,7 +58,8 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) @@ -65,7 +69,8 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py index 9cd3149d..de33d506 100755 --- a/src/cython/doc/pyplots/barcode_persistence.py +++ b/src/cython/doc/pyplots/barcode_persistence.py @@ -1,6 +1,7 @@ import gudhi -periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') +periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/3d_torus.txt') diag = periodic_cc.persistence() plt = gudhi.plot_persistence_barcode(diag) plt.show() diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py index 30661965..c2fbf801 100755 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -1,6 +1,7 @@ import gudhi -rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) +rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index f9760976..6b48422b 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -101,7 +101,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(off_file='alphacomplexdoc.off', max_edge_length=12.0) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off', max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ @@ -205,7 +206,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(csv_file='full_square_distance_matrix.csv', max_edge_length=12.0) + rips_complex = gudhi.RipsComplex(csv_file=gudhi.__root_source_dir__ + \ + '/data/distance_matrix/full_square_distance_matrix.csv', max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst index 03f9fea6..d670cfdb 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/cython/doc/tangential_complex_user.rst @@ -122,7 +122,8 @@ This example builds the Tangential complex of point set read in an OFF file. .. testcode:: import gudhi - tc = gudhi.TangentialComplex(off_file='alphacomplexdoc.off') + tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off') result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \ ' simplices - ' + repr(tc.num_vertices()) + ' vertices.' print(result_str) diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in index 1141673a..a8dd9f80 100644 --- a/src/cython/gudhi.pyx.in +++ b/src/cython/gudhi.pyx.in @@ -23,6 +23,9 @@ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 INRIA" __license__ = "GPL v3" +__version__ = "@GUDHI_VERSION@" +# This variable is used by doctest to find files +__root_source_dir__ = "@CMAKE_SOURCE_DIR@" include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx' include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx' -- cgit v1.2.3 From ef8a5bca22be47df00f61d660e84948f1f45f9ba Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 7 Sep 2017 16:07:41 +0000 Subject: Fix doc for user_version git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2650 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 18aebd67968fd48ccfcfcfbff75c614496f4424e --- src/cython/doc/alpha_complex_sum.rst | 2 +- src/cython/doc/alpha_complex_user.rst | 6 +++--- src/cython/doc/bottleneck_distance_sum.rst | 2 +- src/cython/doc/cubical_complex_sum.rst | 22 +++++++++++----------- src/cython/doc/cubical_complex_user.rst | 2 +- src/cython/doc/index.rst | 8 +++++--- src/cython/doc/persistent_cohomology_sum.rst | 2 +- src/cython/doc/persistent_cohomology_user.rst | 2 +- src/cython/doc/rips_complex_sum.rst | 2 +- src/cython/doc/rips_complex_user.rst | 2 +- src/cython/doc/simplex_tree_sum.rst | 2 +- src/cython/doc/tangential_complex_sum.rst | 4 ++-- src/cython/doc/tangential_complex_user.rst | 14 +++++++------- src/cython/doc/witness_complex_sum.rst | 26 ++++++++++++++------------ src/cython/doc/witness_complex_user.rst | 4 ++-- 15 files changed, 52 insertions(+), 48 deletions(-) (limited to 'src/cython') diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst index a5f6420a..1680a712 100644 --- a/src/cython/doc/alpha_complex_sum.rst +++ b/src/cython/doc/alpha_complex_sum.rst @@ -5,7 +5,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | Alpha_complex is a simplicial complex constructed from the finite | -| img/alpha_complex_representation.png | cells of a Delaunay Triangulation. | +| ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | | :alt: Alpha complex representation | | | :figclass: align-center | The filtration value of each simplex is computed as the square of the | | | circumradius of the simplex if the circumsphere is empty (the simplex | diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index e541e6d3..c3a13bef 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst @@ -75,7 +75,7 @@ In order to build the alpha complex, first, a Simplex tree is built from the cel (The filtration value is set to NaN, which stands for unknown value): .. figure:: - img/alpha_complex_doc.png + ../../doc/Alpha_complex/alpha_complex_doc.png :figclass: align-center :alt: Simplex tree structure construction example @@ -112,7 +112,7 @@ computes the filtration value of the triangle, and then propagates the filtratio here: .. figure:: - img/alpha_complex_doc_420.png + ../../doc/Alpha_complex/alpha_complex_doc_420.png :figclass: align-center :alt: Filtration value propagation example @@ -201,6 +201,6 @@ the program output is: CGAL citations ============== -.. bibliography:: how_to_cite_cgal.bib +.. bibliography:: ../../biblio/how_to_cite_cgal.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst index 5c475d0d..030fad9e 100644 --- a/src/cython/doc/bottleneck_distance_sum.rst +++ b/src/cython/doc/bottleneck_distance_sum.rst @@ -5,7 +5,7 @@ +-----------------------------------------------------------------+----------------------------------------------------------------------+ | .. figure:: | Bottleneck distance measures the similarity between two persistence | -| img/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | +| ../../doc/Bottleneck_distance/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | | :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | | | diagonal points) such that any couple of matched points are at | | Bottleneck distance is the length of | distance at most b. | diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst index 3ddf6375..280ad0e0 100644 --- a/src/cython/doc/cubical_complex_sum.rst +++ b/src/cython/doc/cubical_complex_sum.rst @@ -2,14 +2,14 @@ :Author: Pawel Dlotko :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 ================================================================= =================================== =================================== -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| .. figure:: | The cubical complex is an example of a structured complex useful in | -| img/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image | -| :alt: Cubical complex representation | analysis. | -| :figclass: align-center | | -| | | -| Cubical complex representation | | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | -| | * :doc:`periodic_cubical_complex_ref` | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ +| .. figure:: | The cubical complex is an example of a structured complex useful in | +| ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image | +| :alt: Cubical complex representation | analysis. | +| :figclass: align-center | | +| | | +| Cubical complex representation | | ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ +| :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | +| | * :doc:`periodic_cubical_complex_ref` | ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 8c9a3ed6..36fa3ba9 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -157,6 +157,6 @@ End user programs are available in cython/example/ folder. Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst index f6d10567..3945d72a 100644 --- a/src/cython/doc/index.rst +++ b/src/cython/doc/index.rst @@ -1,8 +1,10 @@ GUDHI Python module documentation ################################# -.. image:: img/Gudhi_banner.png - :align: center +.. figure:: + ../../doc/common/Gudhi_banner.png + :alt: Gudhi banner + :figclass: align-center Introduction ************ @@ -81,6 +83,6 @@ Persistence graphical tools Bibliography ************ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst index d1f79cb4..a26df1dc 100644 --- a/src/cython/doc/persistent_cohomology_sum.rst +++ b/src/cython/doc/persistent_cohomology_sum.rst @@ -4,7 +4,7 @@ +-----------------------------------------------------------------+-----------------------------------------------------------------------+ | .. figure:: | The theory of homology consists in attaching to a topological space | -| img/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | +| ../../doc/Persistent_cohomology/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | | :figclass: align-center | features like connected components, holes, cavities, etc. Persistent | | | homology studies the evolution -- birth, life and death -- of these | | Rips Persistent Cohomology on a 3D | features when the topological space is changing. Consequently, the | diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst index 72f1a7f7..bf90c163 100644 --- a/src/cython/doc/persistent_cohomology_user.rst +++ b/src/cython/doc/persistent_cohomology_user.rst @@ -109,6 +109,6 @@ We provide several example files: run these examples with -h for details on thei Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst index 2b65fc19..5616bfa9 100644 --- a/src/cython/doc/rips_complex_sum.rst +++ b/src/cython/doc/rips_complex_sum.rst @@ -4,7 +4,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton | -| img/rips_complex_representation.png | graph. | +| ../../doc/Rips_complex/rips_complex_representation.png | graph. | | :figclass: align-center | | | | The filtration value of each edge is computed from a user-given | | Rips complex representation | distance function and is inserted until a user-given threshold | diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 6b48422b..96ba9944 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -26,7 +26,7 @@ structure, and then expands the simplicial complex when required. Vertex name correspond to the index of the point in the given range (aka. the point cloud). .. figure:: - img/rips_complex_representation.png + ../../doc/Rips_complex/rips_complex_representation.png :align: center Rips-complex one skeleton graph representation diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst index 3174fb62..fb0e54c1 100644 --- a/src/cython/doc/simplex_tree_sum.rst +++ b/src/cython/doc/simplex_tree_sum.rst @@ -4,7 +4,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | The simplex tree is an efficient and flexible data structure for | -| img/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | +| ../../doc/Simplex_tree/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | | :alt: Simplex tree representation | | | :figclass: align-center | The data structure is described in | | | :cite:`boissonnatmariasimplextreealgorithmica` | diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst index 2b05bc10..72b4d7ba 100644 --- a/src/cython/doc/tangential_complex_sum.rst +++ b/src/cython/doc/tangential_complex_sum.rst @@ -5,10 +5,10 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to | -| img/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | +| ../../doc/Tangential_complex/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | | :figclass: align-center | dimensional Euclidean space. The input is a point sample coming from | | | an unknown manifold. The running time depends only linearly on the | -| **Tangential complex representation** | extrinsic dimension :math:`d` and exponentially on the intrinsic | +| Tangential complex representation | extrinsic dimension :math:`d` and exponentially on the intrinsic | | | dimension :math:`k`. | +----------------------------------------------------------------+------------------------------------------------------------------------+ | :doc:`tangential_complex_user` | :doc:`tangential_complex_ref` | diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst index d670cfdb..efa6d7ce 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/cython/doc/tangential_complex_user.rst @@ -22,7 +22,7 @@ Let us start with the description of the Tangential complex of a simple example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points :math:`P` located on a curve embedded in 2D. -.. figure:: img/tc_example_01.png +.. figure:: ../../doc/Tangential_complex/tc_example_01.png :alt: The input :figclass: align-center @@ -31,7 +31,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g. using PCA). -.. figure:: img/tc_example_02.png +.. figure:: ../../doc/Tangential_complex/tc_example_02.png :alt: The estimated normals :figclass: align-center @@ -42,7 +42,7 @@ Let us add the Voronoi diagram of the points in orange. For each point :math:`p`, construct its star in the Delaunay triangulation of :math:`P` restricted to :math:`T_p`. -.. figure:: img/tc_example_03.png +.. figure:: ../../doc/Tangential_complex/tc_example_03.png :alt: The Voronoi diagram :figclass: align-center @@ -62,7 +62,7 @@ simplex is not in the star of all its vertices. Let us take the same example. -.. figure:: img/tc_example_07_before.png +.. figure:: ../../doc/Tangential_complex/tc_example_07_before.png :alt: Before :figclass: align-center @@ -70,7 +70,7 @@ Let us take the same example. Let us slightly move the tangent subspace :math:`T_q` -.. figure:: img/tc_example_07_after.png +.. figure:: ../../doc/Tangential_complex/tc_example_07_after.png :alt: After :figclass: align-center @@ -79,7 +79,7 @@ Let us slightly move the tangent subspace :math:`T_q` Now, the star of :math:`Q` contains :math:`QP`, but the star of :math:`P` does not contain :math:`QP`. We have an inconsistency. -.. figure:: img/tc_example_08.png +.. figure:: ../../doc/Tangential_complex/tc_example_08.png :alt: After :figclass: align-center @@ -191,6 +191,6 @@ The output is: Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst index b65522ba..a8a126a0 100644 --- a/src/cython/doc/witness_complex_sum.rst +++ b/src/cython/doc/witness_complex_sum.rst @@ -3,15 +3,17 @@ :Euclidean version requires: CGAL :math:`\geq` 4.6.0 Eigen3 ================================================================= =================================== =================================== -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| .. image:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | -| img/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | -| | | -| | The data structure is described in | -| | :cite:`boissonnatmariasimplextreealgorithmica`. | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | -| | * :doc:`strong_witness_complex_ref` | -| | * :doc:`euclidean_witness_complex_ref` | -| | * :doc:`euclidean_strong_witness_complex_ref` | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ ++-------------------------------------------------------------------+----------------------------------------------------------------------+ +| .. figure:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | +| ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | +| :alt: Witness complex representation | | +| :figclass: align-center | The data structure is described in | +| | :cite:`boissonnatmariasimplextreealgorithmica`. | +| | | +| Witness complex representation | | ++-------------------------------------------------------------------+----------------------------------------------------------------------+ +| :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | +| | * :doc:`strong_witness_complex_ref` | +| | * :doc:`euclidean_witness_complex_ref` | +| | * :doc:`euclidean_strong_witness_complex_ref` | ++-------------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst index aa9cbb2c..29413269 100644 --- a/src/cython/doc/witness_complex_user.rst +++ b/src/cython/doc/witness_complex_user.rst @@ -33,7 +33,7 @@ Both definitions can be relaxed by a real value :math:`\alpha`: which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and **strong relaxed witness complex** respectively. -.. figure:: img/swit.svg +.. figure:: ../../doc/Witness_complex/swit.svg :alt: Strongly witnessed simplex :figclass: align-center @@ -126,6 +126,6 @@ Here is an example of constructing a strong witness complex filtration and compu Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt -- cgit v1.2.3 From df9030e6c1df5fb735914eadd44cf27b86fce239 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 11 Sep 2017 15:12:01 +0000 Subject: Add comment for the dependency git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2655 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ab03b16bc884fe3291e3308e4a975b7c6232a861 --- src/cython/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 6c8232ea..ea6e840a 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -326,6 +326,7 @@ if(CYTHON_FOUND) # set sphinx-build in make files configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY) + # sphinx target requires gudhi.so, because conf.py reads gudhi version from it add_custom_target(sphinx WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" -- cgit v1.2.3 From 03bb8ee15f7c8b71fd922a27ed02bca4c98825d9 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 11 Sep 2017 15:16:39 +0000 Subject: remove debug traces git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2656 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4ea039d0564268458ca64950113fbffdc86c10b3 --- src/cython/CMakeLists.txt | 1 - 1 file changed, 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index ea6e840a..7cf31a03 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -148,7 +148,6 @@ if(CYTHON_FOUND) # Loop on INCLUDE_DIRECTORIES PROPERTY get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) - message(" --- ${GUDHI_INCLUDE_DIRECTORY} ---") set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") endforeach() set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") -- cgit v1.2.3 From 04fe614e8a859257b57aadfdb5aa14fc3d78babb Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 12 Sep 2017 08:30:31 +0000 Subject: Euclidean witness requires CGAL 4.6.0 Subsampling requires CGAL 4.8.1 All modules requiring CGAL requires also Eigen3 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2662 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: df4c03882b8c5eb91f12939b460b3c9b85cbb870 --- src/cython/CMakeLists.txt | 96 +++++++++++++++++------------------------------ 1 file changed, 35 insertions(+), 61 deletions(-) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 7cf31a03..db23d42b 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -73,47 +73,18 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") endif (EIGEN3_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - # If CGAL_VERSION >= 4.8.1, include subsampling + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") - else (NOT CGAL_VERSION VERSION_LESS 4.8.1) - # Remove subsampling unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst") - # Remove tangential complex and bottleneck unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py) - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst") - endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - # If CGAL_VERSION >= 4.7.0, include alpha + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'") - else (NOT CGAL_VERSION VERSION_LESS 4.7.0) - # Remove alpha complex unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst") - endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n") - else (NOT CGAL_VERSION VERSION_LESS 4.6.0) - # Remove euclidean witness complex unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst") - endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) if(CGAL_FOUND) # Add CGAL compilation args @@ -185,7 +156,7 @@ if(CYTHON_FOUND) PATTERN "*.pyd") # Test examples - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) # Bottleneck add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} @@ -213,26 +184,14 @@ if(CYTHON_FOUND) WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py) - # Euclidean witness - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - - add_test(NAME test_euclidean_witness_complex_py_test + # Subsampling + add_test(NAME test_subsampling_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py) + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py) - endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) # Alpha add_test(NAME alpha_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} @@ -249,7 +208,27 @@ if(CYTHON_FOUND) WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py) - endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + # Euclidean witness + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + + add_test(NAME test_euclidean_witness_complex_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) # Cubical add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test @@ -315,13 +294,8 @@ if(CYTHON_FOUND) WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py) - # Subsampling - add_test(NAME test_subsampling_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py) - # Documentation generation is available through sphinx - requires all modules - if(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1) + if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) # set sphinx-build in make files configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY) @@ -337,5 +311,5 @@ if(CYTHON_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx") - endif(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1) + endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) endif(CYTHON_FOUND) -- cgit v1.2.3 From 9a3df180af4976242fb45d7dcd49c3632e65f04c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 12 Sep 2017 20:36:58 +0000 Subject: Bottleneck does not require Eigen3 (C++ and Python) Doc issue about examples requiring Eigen3 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2666 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5e127d4e8137a44ee3bd688c32653acfb4a55007 --- src/Bottleneck_distance/benchmark/CMakeLists.txt | 4 ++-- src/Bottleneck_distance/example/CMakeLists.txt | 26 ++++++++++++++++-------- src/Bottleneck_distance/test/CMakeLists.txt | 4 ++-- src/common/doc/main_page.h | 20 ++++++++++++++++-- src/cython/CMakeLists.txt | 26 ++++++++++++++---------- 5 files changed, 54 insertions(+), 26 deletions(-) (limited to 'src/cython') diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt index 170081ce..20a4e47b 100644 --- a/src/Bottleneck_distance/benchmark/CMakeLists.txt +++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt @@ -1,9 +1,9 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_benchmark) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) if (TBB_FOUND) target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES}) endif(TBB_FOUND) -endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +endif(NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index dc1da31c..eac617db 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -1,30 +1,38 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) - add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES}) target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES}) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Bottleneck_distance_example_basic COMMAND $) - add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck - COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") - add_test(NAME Bottleneck_read_file_example COMMAND $ "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers") install(TARGETS bottleneck_read_file_example DESTINATION bin) install(TARGETS bottleneck_basic_example DESTINATION bin) - install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin) +endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) + +# Eigen3 and CGAL > 4.7.0 is required for alpha complex +# CGAL > 4.8.1 is required for bottleneck distance => +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") + + install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin) + if (TBB_FOUND) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) + endif(TBB_FOUND) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index a165d472..2676b82c 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -1,7 +1,7 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_tests) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) include(GUDHI_test_coverage) add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp ) @@ -12,4 +12,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) gudhi_add_coverage_test(Bottleneck_distance_test_unit) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index bd4615f5..1a7994a5 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -160,7 +160,7 @@ Author: François Godi
Introduced in: GUDHI 2.0.0
Copyright: GPL v3
- Requires: \ref cgal ≥ 4.8.1 and \ref eigen3 + Requires: \ref cgal ≥ 4.8.1 Bottleneck distance measures the similarity between two persistence diagrams. @@ -329,13 +329,29 @@ make doxygen * Alpha_complex/Alpha_complex_from_off.cpp * \li * Alpha_complex/Alpha_complex_from_points.cpp + * \li + * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp * \li * Persistent_cohomology/alpha_complex_persistence.cpp * \li * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp - * + * \li + * Spatial_searching/example_spatial_searching.cpp + * \li + * Subsampling/example_choose_n_farthest_points.cpp + * \li + * Subsampling/example_custom_kernel.cpp + * \li + * Subsampling/example_pick_n_random_points.cpp + * \li + * Subsampling/example_sparsify_point_set.cpp + * \li + * Tangential_complex/example_basic.cpp + * \li + * Tangential_complex/example_with_perturb.cpp + * * \subsection tbb Threading Building Blocks * Intel® TBB lets you easily write parallel * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index db23d42b..baeeb203 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -73,10 +73,12 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") endif (EIGEN3_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") - set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'") @@ -157,22 +159,13 @@ if(CYTHON_FOUND) # Test examples if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - # Bottleneck + # Bottleneck and Alpha add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - add_test(NAME bottleneck_basic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") - - add_test(NAME test_bottleneck_distance_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py) - # Tangential add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} @@ -190,6 +183,17 @@ if(CYTHON_FOUND) COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + # Bottleneck + add_test(NAME bottleneck_basic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") + + add_test(NAME test_bottleneck_distance_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py) + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) # Alpha -- cgit v1.2.3 From 8a22b7c6111b41e91766cdd53c0116b845e068b5 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 12 Sep 2017 21:47:19 +0000 Subject: Fix sphinx build for python3 on Ubuntu git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2667 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c720b8be2919344e06f3d71cefdd7693439f63f0 --- src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +- src/cython/CMakeLists.txt | 9 +++------ src/cython/doc/python3-sphinx-build.in | 11 ----------- src/cython/doc/python3-sphinx-build.py | 11 +++++++++++ 4 files changed, 15 insertions(+), 18 deletions(-) delete mode 100755 src/cython/doc/python3-sphinx-build.in create mode 100755 src/cython/doc/python3-sphinx-build.py (limited to 'src/cython') diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index dbf2106a..f2bbafdc 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -123,7 +123,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND) find_program( SPHINX_PATH sphinx-build ) elseif(PYTHON_VERSION_MAJOR EQUAL 3) # No sphinx-build in Pyton3, just hack it - set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build") + set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build.py") else() message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.") endif(PYTHON_VERSION_MAJOR EQUAL 2) diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index baeeb203..d1761f47 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -75,7 +75,7 @@ if(CYTHON_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") @@ -300,20 +300,17 @@ if(CYTHON_FOUND) # Documentation generation is available through sphinx - requires all modules if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - # set sphinx-build in make files - configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY) - # sphinx target requires gudhi.so, because conf.py reads gudhi version from it add_custom_target(sphinx WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${SPHINX_PATH} -b html . "${CMAKE_CURRENT_BINARY_DIR}/sphinx" + ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc sphinx DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so") add_test(NAME sphinx_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx") + ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc doctest) endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) endif(CYTHON_FOUND) diff --git a/src/cython/doc/python3-sphinx-build.in b/src/cython/doc/python3-sphinx-build.in deleted file mode 100755 index c97965f5..00000000 --- a/src/cython/doc/python3-sphinx-build.in +++ /dev/null @@ -1,11 +0,0 @@ -#!@PYTHON_EXECUTABLE@ - -""" -Emulate sphinx-build for python3 -""" - -from sys import exit, argv -from sphinx import main - -if __name__ == '__main__': - exit(main(argv)) diff --git a/src/cython/doc/python3-sphinx-build.py b/src/cython/doc/python3-sphinx-build.py new file mode 100755 index 00000000..44b94169 --- /dev/null +++ b/src/cython/doc/python3-sphinx-build.py @@ -0,0 +1,11 @@ +#!/usr/bin/python3 + +""" +Emulate sphinx-build for python3 +""" + +from sys import exit, argv +from sphinx import main + +if __name__ == '__main__': + exit(main(argv)) -- cgit v1.2.3 From bc62d9afbb151279a9da1e082a53788d3fd0d242 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 18 Sep 2017 09:37:20 +0000 Subject: Add warning for developper version that sphinx is configured for user version Removes GudhUI ERROR mesages (just warnings git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2677 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0111272d9f6d6dc10e370360b2242eff4828611b --- src/GudhUI/CMakeLists.txt | 34 +++------------------------------- src/cython/CMakeLists.txt | 13 ++++++++++--- 2 files changed, 13 insertions(+), 34 deletions(-) (limited to 'src/cython') diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index 57861946..374195d0 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -5,28 +5,6 @@ find_package(Qt5 COMPONENTS Widgets Xml OpenGL) find_package(QGLViewer) find_package(OpenGL) -if (CGAL_VERSION VERSION_EQUAL 4.8.0) - message(ERROR " GudhUI does not compile with CGAL 4.8.0. 4.8.1, 4.8.2 and 4.9 are OK.") -endif() - -if (NOT CGAL_FOUND) - message(ERROR " GudhUI requires CGAL and will not be compiled.") -endif() - -if (NOT Qt5_FOUND) - message(ERROR " GudhUI requires Qt5 and will not be compiled.") -endif() - -if (NOT OPENGL_FOUND) - message(ERROR " GudhUI requires OpenGL and will not be compiled.") -endif() - -if (NOT QGLVIEWER_FOUND) - message(ERROR " GudhUI requires QGLViewer and will not be compiled.") -endif() - - - if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0) set(CMAKE_AUTOMOC ON) @@ -37,8 +15,6 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_ SET(Boost_USE_MULTITHREAD OFF) include_directories (${QGLVIEWER_INCLUDE_DIR}) - ##################################################################### - add_executable ( GudhUI gui/gudhui.cpp gui/MainWindow.cpp @@ -52,14 +28,10 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_ target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL ) target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} ) target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ) -if (TBB_FOUND) - target_link_libraries( GudhUI ${TBB_LIBRARIES}) -endif() + if (TBB_FOUND) + target_link_libraries( GudhUI ${TBB_LIBRARIES}) + endif() install(TARGETS GudhUI DESTINATION bin) -############################################################################### - -else() - message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt5, and will not be compiled.") endif() diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index d1761f47..ed0aace1 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -300,17 +300,24 @@ if(CYTHON_FOUND) # Documentation generation is available through sphinx - requires all modules if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") + # User warning - Sphinx is a static pages generator, and configured to work fine with user_version + # Images and biblio warnings because not found on developper version + if (GUDHI_CYTHON_PATH STREQUAL "src/cython") + set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss") + endif() # sphinx target requires gudhi.so, because conf.py reads gudhi version from it add_custom_target(sphinx WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc sphinx - DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so") + ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx + DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM) add_test(NAME sphinx_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc doctest) + ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest) endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) endif(CYTHON_FOUND) -- cgit v1.2.3 From 7f7aac2010f5cda05dfd1057827d8deaea186cf5 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 18 Sep 2017 12:58:10 +0000 Subject: Add a function to launch py.test as required for no cache files in sources git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2678 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 92ca1aabcbe276198fa29ea75f763fb0aa3c504f --- src/cython/CMakeLists.txt | 50 +++++++++++++++++++---------------------------- 1 file changed, 20 insertions(+), 30 deletions(-) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index ed0aace1..ec8589f0 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -15,6 +15,16 @@ function( add_gudhi_cython_lib THE_LIB ) endif(EXISTS ${THE_LIB}) endfunction( add_gudhi_cython_lib ) +# THE_TEST is the python test file name (without .py extension) containing tests functions +function( add_gudhi_py_test THE_TEST ) + # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python + # use py.test no cache provider, otherwise a .cache file is created in sources by py.test + add_test(NAME ${THE_TEST}_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py) +endfunction( add_gudhi_py_test ) + + if(CYTHON_FOUND) message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}") @@ -173,14 +183,10 @@ if(CYTHON_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - add_test(NAME test_tangential_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py) + add_gudhi_py_test(test_tangential_complex) # Subsampling - add_test(NAME test_subsampling_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py) + add_gudhi_py_test(test_subsampling) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) @@ -190,9 +196,7 @@ if(CYTHON_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") - add_test(NAME test_bottleneck_distance_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py) + add_gudhi_py_test(test_bottleneck_distance) endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) @@ -208,9 +212,7 @@ if(CYTHON_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) - add_test(NAME test_alpha_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py) + add_gudhi_py_test(test_alpha_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) @@ -228,9 +230,7 @@ if(CYTHON_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - add_test(NAME test_euclidean_witness_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py) + add_gudhi_py_test(test_euclidean_witness_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) @@ -247,9 +247,7 @@ if(CYTHON_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" 10 10 10) - add_test(NAME test_cubical_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py) + add_gudhi_py_test(test_cubical_complex) # Rips add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test @@ -269,9 +267,7 @@ if(CYTHON_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) - add_test(NAME test_rips_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py) + add_gudhi_py_test(test_rips_complex) # Simplex tree add_test(NAME simplex_tree_example_py_test @@ -279,9 +275,7 @@ if(CYTHON_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) - add_test(NAME test_simplex_tree_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py) + add_gudhi_py_test(test_simplex_tree) # Witness add_test(NAME witness_complex_from_nearest_landmark_table_py_test @@ -289,14 +283,10 @@ if(CYTHON_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) - add_test(NAME test_witness_complex_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py) + add_gudhi_py_test(test_witness_complex) # Reader utils - add_test(NAME test_reader_utils_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py) + add_gudhi_py_test(test_reader_utils) # Documentation generation is available through sphinx - requires all modules if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) -- cgit v1.2.3 From 18c1daaba21430c54647f4823eec9c7ed52c2878 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 19 Sep 2017 12:09:27 +0000 Subject: Fix memory leak git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_memory_leak_fix@2686 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a8fd65accb5be293e9d3f5fe411225745cb76b0b --- src/cython/include/Rips_complex_interface.h | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'src/cython') diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h index d06ee4bd..02985727 100644 --- a/src/cython/include/Rips_complex_interface.h +++ b/src/cython/include/Rips_complex_interface.h @@ -71,6 +71,10 @@ class Rips_complex_interface { } } + ~Rips_complex_interface() { + delete rips_complex_; + } + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) { rips_complex_->create_complex(*simplex_tree, dim_max); simplex_tree->initialize_filtration(); -- cgit v1.2.3 From c9f8ebc4d43d4a861aab1dabc2d31f2f6ed640d2 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 20 Sep 2017 10:45:50 +0000 Subject: Merge modifications for simplex_tree automatic dimension set git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2689 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c18c6316d51f476a795b59c8b870db1aaf0b4591 --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 2 - src/Alpha_complex/test/Alpha_complex_unit_test.cpp | 4 +- .../example/alpha_complex_3d_persistence.cpp | 1 - .../example/exact_alpha_complex_3d_persistence.cpp | 1 - .../periodic_alpha_complex_3d_persistence.cpp | 1 - .../persistence_from_simple_simplex_tree.cpp | 1 - .../example/plain_homology.cpp | 2 - .../example/rips_persistence_step_by_step.cpp | 5 +- .../weighted_alpha_complex_3d_persistence.cpp | 1 - .../test/betti_numbers_unit_test.cpp | 4 - .../test/persistent_cohomology_unit_test.cpp | 2 - src/Simplex_tree/include/gudhi/Simplex_tree.h | 47 ++- src/Simplex_tree/test/CMakeLists.txt | 14 +- src/Simplex_tree/test/README | 2 +- .../test/simplex_tree_remove_unit_test.cpp | 346 +++++++++++++++++++++ src/Simplex_tree/test/simplex_tree_unit_test.cpp | 289 +---------------- .../include/gudhi/Strong_witness_complex.h | 1 - .../include/gudhi/Witness_complex.h | 1 - src/cython/include/Tangential_complex_interface.h | 2 - src/cython/test/test_simplex_tree.py | 11 +- 20 files changed, 421 insertions(+), 316 deletions(-) create mode 100644 src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp (limited to 'src/cython') diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 1ff95c3d..5f7d7622 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -268,8 +268,6 @@ class Alpha_complex { return false; // ----- >> } - complex.set_dimension(triangulation_->maximal_dimension()); - // -------------------------------------------------------------------------------------------- // Simplex_tree construction from loop on triangulation finite full cells list if (triangulation_->number_of_vertices() > 0) { diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp index 7380547f..166373fe 100644 --- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -159,7 +159,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { BOOST_CHECK(simplex_tree.num_simplices() == 15); std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl; - BOOST_CHECK(simplex_tree.dimension() == 4); + BOOST_CHECK(simplex_tree.dimension() == 3); std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl; BOOST_CHECK(simplex_tree.num_vertices() == 4); @@ -232,7 +232,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { BOOST_CHECK(simplex_tree.num_simplices() == 10); std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl; - BOOST_CHECK(simplex_tree.dimension() == 4); + BOOST_CHECK(simplex_tree.dimension() == 1); std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl; BOOST_CHECK(simplex_tree.num_vertices() == 4); diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index fd227b82..40eb3576 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -203,7 +203,6 @@ int main(int argc, char * const argv[]) { std::cout << "This shall not happen" << std::endl; } simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp index 8a335075..9881debf 100644 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -205,7 +205,6 @@ int main(int argc, char * const argv[]) { std::cout << "This shall not happen" << std::endl; } simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp index 8928cfc2..71faebd7 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -222,7 +222,6 @@ int main(int argc, char * const argv[]) { std::cout << "This shall not happen" << std::endl; } simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp index 7ca9410a..7809d5ff 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -142,7 +142,6 @@ int main(int argc, char * const argv[]) { /* An edge [11,6] */ /* An edge [10,12,2] */ - st.set_dimension(2); st.set_filtration(0.4); std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp index 50f692f2..a5ae09c8 100644 --- a/src/Persistent_cohomology/example/plain_homology.cpp +++ b/src/Persistent_cohomology/example/plain_homology.cpp @@ -64,8 +64,6 @@ int main() { st.insert_simplex_and_subfaces(edge03); st.insert_simplex(edge13); st.insert_simplex(vertex4); - // FIXME: Remove this line - st.set_dimension(2); // Sort the simplices in the order of the filtration st.initialize_filtration(); diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp index 554eeba6..75580aac 100644 --- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp @@ -88,6 +88,9 @@ int main(int argc, char * argv[]) { Simplex_tree st; // insert the proximity graph in the simplex tree st.insert_graph(prox_graph); + std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << st.dimension() << " \n"; +/* // expand the graph until dimension dim_max st.expansion(dim_max); @@ -112,7 +115,7 @@ int main(int argc, char * argv[]) { pcoh.output_diagram(out); out.close(); } - +*/ return 0; } diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp index 34b90933..968db753 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -223,7 +223,6 @@ int main(int argc, char * const argv[]) { std::cout << "This shall not happen" << std::endl; } simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp index da418034..0a08d200 100644 --- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp +++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp @@ -62,8 +62,6 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) st.insert_simplex_and_subfaces(edge04); st.insert_simplex(edge14); st.insert_simplex(vertex5); - // FIXME: Remove this line - st.set_dimension(3); // Sort the simplices in the order of the filtration st.initialize_filtration(); @@ -170,8 +168,6 @@ BOOST_AUTO_TEST_CASE( betti_numbers ) st.insert_simplex_and_subfaces(edge04, 2.0); st.insert_simplex(edge14, 2.0); st.insert_simplex(vertex5, 1.0); - // FIXME: Remove this line - st.set_dimension(3); // Sort the simplices in the order of the filtration st.initialize_filtration(); diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp index f8174020..887aa25f 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -197,8 +197,6 @@ BOOST_AUTO_TEST_CASE( persistence_constructor_exception ) // To make number of simplices = 255 const short simplex_0[] = {0, 1, 2, 3, 4, 5, 6, 7}; st.insert_simplex_and_subfaces(simplex_0); - // FIXME: Remove this line - st.set_dimension(8); // Sort the simplices in the order of the filtration st.initialize_filtration(); diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 317bce23..478ed80f 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -601,7 +601,11 @@ class Simplex_tree { // if filtration value unchanged return std::pair(null_simplex(), false); } - // otherwise the insertion has succeeded + // otherwise the insertion has succeeded - size is a size_type + if (static_cast(simplex.size()) - 1 > dimension_) { + // Update dimension if needed + dimension_ = static_cast(simplex.size()) - 1; + } return res_insert; } @@ -1159,7 +1163,11 @@ class Simplex_tree { * complex has changed , please call `initialize_filtration()` to recompute it. */ bool prune_above_filtration(Filtration_value filtration) { - return rec_prune_above_filtration(root(), filtration); + bool modified = rec_prune_above_filtration(root(), filtration); + if (modified) { + auto_dimension_set(dimension()); + } + return modified; } private: @@ -1187,6 +1195,33 @@ class Simplex_tree { return modified; } + private: + /** \brief Resets the Simplex_tree dimension. + * @param[in] old_dimension The former dimension value until the loop stopped when it is reached. + * @return The dimension modification information. + * \pre Please check the simplex has not a too low dimension value. + * This cannot happen if set_dimension has not been performed. + */ + bool auto_dimension_set(int old_dimension) { + int new_dimension = -1; + for (Simplex_handle sh : skeleton_simplex_range(old_dimension)) { +#ifdef DEBUG_TRACES + for (auto vertex : simplex_vertex_range(sh)) { + std::cout << " " << vertex; + } + std::cout << std::endl; +#endif // DEBUG_TRACES + + int sh_dimension = dimension(sh); + if (sh_dimension >= old_dimension) + return false; + new_dimension = std::max(new_dimension, sh_dimension); + } + set_dimension(new_dimension); + return true; + } + + public: /** \brief Remove a maximal simplex. * @param[in] sh Simplex handle on the maximal simplex to remove. @@ -1207,9 +1242,17 @@ class Simplex_tree { // Special case when child is the root of the simplex tree, just remove it from members child->erase(sh); } else { + // Keep information before remove action + int sh_dim = dimension(sh); + // Sibling is emptied : must be deleted, and its parent must point on his own Sibling child->oncles()->members().at(child->parent()).assign_children(child->oncles()); delete child; + + // No need to reset dimension in case maximal simplex is not the maximal dimension one + if (sh_dim >= dimension()) { + auto_dimension_set(sh_dim); + } } } diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index 81999de6..1c169ff7 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -3,13 +3,21 @@ project(Simplex_tree_tests) include(GUDHI_test_coverage) +# Do not forget to copy test files in current binary dir +file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_executable ( Simplex_tree_test_unit simplex_tree_unit_test.cpp ) target_link_libraries(Simplex_tree_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Simplex_tree_test_unit ${TBB_LIBRARIES}) endif() -# Do not forget to copy test files in current binary dir -file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - gudhi_add_coverage_test(Simplex_tree_test_unit) + +add_executable ( Simplex_tree_remove_test_unit simplex_tree_remove_unit_test.cpp ) +target_link_libraries(Simplex_tree_remove_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Simplex_tree_remove_test_unit ${TBB_LIBRARIES}) +endif() + +gudhi_add_coverage_test(Simplex_tree_remove_test_unit) diff --git a/src/Simplex_tree/test/README b/src/Simplex_tree/test/README index 21c3d871..df2ab89a 100644 --- a/src/Simplex_tree/test/README +++ b/src/Simplex_tree/test/README @@ -9,6 +9,6 @@ make To launch with details: *********************** -./SimplexTreeUT --report_level=detailed --log_level=all +./Simplex_tree_test_unit --report_level=detailed --log_level=all ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp new file mode 100644 index 00000000..ad71fed3 --- /dev/null +++ b/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp @@ -0,0 +1,346 @@ +#include + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "simplex_tree_remove" +#include +#include + +// ^ +// /!\ Nothing else from Simplex_tree shall be included to test includes are well defined. +#include "gudhi/Simplex_tree.h" + +using namespace Gudhi; + +struct MyOptions : Simplex_tree_options_full_featured { + // Not doing persistence, so we don't need those + static const bool store_key = false; + static const bool store_filtration = false; + // I have few vertices + typedef short Vertex_handle; +}; + +using Mini_stree = Simplex_tree; +using Stree = Simplex_tree<>; + +BOOST_AUTO_TEST_CASE(remove_maximal_simplex) { + std::cout << "********************************************************************" << std::endl; + std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl; + + Mini_stree st; + + st.insert_simplex_and_subfaces({0, 1, 6, 7}); + st.insert_simplex_and_subfaces({3, 4, 5}); + + // Constructs a copy at this state for further test purpose + Mini_stree st_pruned = st; + + st.insert_simplex_and_subfaces({3, 0}); + st.insert_simplex_and_subfaces({2, 1, 0}); + + // Constructs a copy at this state for further test purpose + Mini_stree st_complete = st; + // st_complete and st: + // 1 6 + // o---o + // /X\7/ + // o---o---o---o + // 2 0 3\X/4 + // o + // 5 + // st_pruned: + // 1 6 + // o---o + // \7/ + // o o---o + // 0 3\X/4 + // o + // 5 + +#ifdef GUDHI_DEBUG + std::cout << "Check exception throw in debug mode" << std::endl; + // throw excpt because sh has children + BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({0, 1, 6})), std::invalid_argument); + BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({3})), std::invalid_argument); + BOOST_CHECK(st == st_complete); +#endif + std::cout << "st.remove_maximal_simplex({0, 2})" << std::endl; + st.remove_maximal_simplex(st.find({0, 2})); + std::cout << "st.remove_maximal_simplex({0, 1, 2})" << std::endl; + st.remove_maximal_simplex(st.find({0, 1, 2})); + std::cout << "st.remove_maximal_simplex({1, 2})" << std::endl; + st.remove_maximal_simplex(st.find({1, 2})); + std::cout << "st.remove_maximal_simplex({2})" << std::endl; + st.remove_maximal_simplex(st.find({2})); + std::cout << "st.remove_maximal_simplex({3})" << std::endl; + st.remove_maximal_simplex(st.find({0, 3})); + + BOOST_CHECK(st == st_pruned); + // Remove all, but as the simplex tree is not storing filtration, there is no modification + st.prune_above_filtration(0.0); + BOOST_CHECK(st == st_pruned); + + Mini_stree st_wo_seven; + + st_wo_seven.insert_simplex_and_subfaces({0, 1, 6}); + st_wo_seven.insert_simplex_and_subfaces({3, 4, 5}); + // st_wo_seven: + // 1 6 + // o---o + // \X/ + // o o---o + // 0 3\X/4 + // o + // 5 + + // Remove all 7 to test the both remove_maximal_simplex cases (when _members is empty or not) + std::cout << "st.remove_maximal_simplex({0, 1, 6, 7})" << std::endl; + st.remove_maximal_simplex(st.find({0, 1, 6, 7})); + std::cout << "st.remove_maximal_simplex({0, 1, 7})" << std::endl; + st.remove_maximal_simplex(st.find({0, 1, 7})); + std::cout << "st.remove_maximal_simplex({0, 6, 7})" << std::endl; + st.remove_maximal_simplex(st.find({0, 6, 7})); + std::cout << "st.remove_maximal_simplex({0, 7})" << std::endl; + st.remove_maximal_simplex(st.find({0, 7})); + std::cout << "st.remove_maximal_simplex({1, 6, 7})" << std::endl; + st.remove_maximal_simplex(st.find({1, 6, 7})); + std::cout << "st.remove_maximal_simplex({1, 7})" << std::endl; + st.remove_maximal_simplex(st.find({1, 7})); + std::cout << "st.remove_maximal_simplex({6, 7})" << std::endl; + st.remove_maximal_simplex(st.find({6, 7})); + std::cout << "st.remove_maximal_simplex({7})" << std::endl; + st.remove_maximal_simplex(st.find({7})); + + std::cout << "st.dimension()=" << st.dimension() << " | st_wo_seven.dimension()=" << st_wo_seven.dimension() << std::endl; + BOOST_CHECK(st == st_wo_seven); +} + +BOOST_AUTO_TEST_CASE(auto_dimension_set) { + std::cout << "********************************************************************" << std::endl; + std::cout << "DIMENSION ON REMOVE MAXIMAL SIMPLEX" << std::endl; + + Mini_stree st; + + st.insert_simplex_and_subfaces({0, 1, 2}); + st.insert_simplex_and_subfaces({0, 1, 3}); + st.insert_simplex_and_subfaces({1, 2, 3, 4}); + st.insert_simplex_and_subfaces({1, 2, 3, 5}); + st.insert_simplex_and_subfaces({6, 7, 8, 9}); + st.insert_simplex_and_subfaces({6, 7, 8, 10}); + + BOOST_CHECK(st.dimension() == 3); + + std::cout << "st.remove_maximal_simplex({6, 7, 8, 10})" << std::endl; + st.remove_maximal_simplex(st.find({6, 7, 8, 10})); + BOOST_CHECK(st.dimension() == 3); + + std::cout << "st.remove_maximal_simplex({6, 7, 8, 9})" << std::endl; + st.remove_maximal_simplex(st.find({6, 7, 8, 9})); + BOOST_CHECK(st.dimension() == 3); + + std::cout << "st.remove_maximal_simplex({1, 2, 3, 4})" << std::endl; + st.remove_maximal_simplex(st.find({1, 2, 3, 4})); + BOOST_CHECK(st.dimension() == 3); + + std::cout << "st.remove_maximal_simplex({1, 2, 3, 5})" << std::endl; + st.remove_maximal_simplex(st.find({1, 2, 3, 5})); + BOOST_CHECK(st.dimension() == 2); + + std::cout << "st.insert_simplex_and_subfaces({1, 2, 3, 5})" << std::endl; + st.insert_simplex_and_subfaces({1, 2, 3, 5}); + BOOST_CHECK(st.dimension() == 3); + + std::cout << "st.insert_simplex_and_subfaces({1, 2, 3, 4})" << std::endl; + st.insert_simplex_and_subfaces({1, 2, 3, 4}); + BOOST_CHECK(st.dimension() == 3); + + std::cout << "st.remove_maximal_simplex({1, 2, 3, 5})" << std::endl; + st.remove_maximal_simplex(st.find({1, 2, 3, 5})); + BOOST_CHECK(st.dimension() == 3); + + std::cout << "st.remove_maximal_simplex({1, 2, 3, 4})" << std::endl; + st.remove_maximal_simplex(st.find({1, 2, 3, 4})); + BOOST_CHECK(st.dimension() == 2); + + std::cout << "st.insert_simplex_and_subfaces({0, 1, 3, 4})" << std::endl; + st.insert_simplex_and_subfaces({0, 1, 3, 4}); + BOOST_CHECK(st.dimension() == 3); + + std::cout << "st.remove_maximal_simplex({0, 1, 3, 4})" << std::endl; + st.remove_maximal_simplex(st.find({0, 1, 3, 4})); + BOOST_CHECK(st.dimension() == 2); + + std::cout << "st.insert_simplex_and_subfaces({0, 1, 2, 3, 4, 5, 6})" << std::endl; + st.insert_simplex_and_subfaces({0, 1, 2, 3, 4, 5, 6}); + BOOST_CHECK(st.dimension() == 6); + + std::cout << "st.remove_maximal_simplex({0, 1, 2, 3, 4, 5, 6})" << std::endl; + st.remove_maximal_simplex(st.find({0, 1, 2, 3, 4, 5, 6})); + BOOST_CHECK(st.dimension() == 5); + +} + +BOOST_AUTO_TEST_CASE(prune_above_filtration) { + std::cout << "********************************************************************" << std::endl; + std::cout << "PRUNE ABOVE FILTRATION" << std::endl; + + Stree st; + + st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0); + st.insert_simplex_and_subfaces({3, 4, 5}, 2.0); + + // Constructs a copy at this state for further test purpose + Stree st_pruned = st; + st_pruned.initialize_filtration(); // reset + + st.insert_simplex_and_subfaces({3, 0}, 3.0); + st.insert_simplex_and_subfaces({2, 1, 0}, 4.0); + + // Constructs a copy at this state for further test purpose + Stree st_complete = st; + // st_complete and st: + // 1 6 + // o---o + // /X\7/ + // o---o---o---o + // 2 0 3\X/4 + // o + // 5 + // st_pruned: + // 1 6 + // o---o + // \7/ + // o o---o + // 0 3\X/4 + // o + // 5 + + bool simplex_is_changed = false; + // Check the no action cases + // greater than initial filtration value + simplex_is_changed = st.prune_above_filtration(10.0); + if (simplex_is_changed) + st.initialize_filtration(); + BOOST_CHECK(st == st_complete); + BOOST_CHECK(!simplex_is_changed); + // equal to initial filtration value + simplex_is_changed = st.prune_above_filtration(6.0); + if (simplex_is_changed) + st.initialize_filtration(); + BOOST_CHECK(st == st_complete); + BOOST_CHECK(!simplex_is_changed); + // lower than initial filtration value, but still greater than the maximum filtration value + simplex_is_changed = st.prune_above_filtration(5.0); + if (simplex_is_changed) + st.initialize_filtration(); + BOOST_CHECK(st == st_complete); + BOOST_CHECK(!simplex_is_changed); + + // Display the Simplex_tree + std::cout << "The complex contains " << st.num_simplices() << " simplices"; + std::cout << " - dimension " << st.dimension() << std::endl; + std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << " " << "[" << st.filtration(f_simplex) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << (int) vertex << " "; + } + std::cout << std::endl; + } + + // Check the pruned cases + simplex_is_changed = st.prune_above_filtration(2.5); + if (simplex_is_changed) + st.initialize_filtration(); + BOOST_CHECK(st == st_pruned); + BOOST_CHECK(simplex_is_changed); + + // Display the Simplex_tree + std::cout << "The complex pruned at 2.5 contains " << st.num_simplices() << " simplices"; + std::cout << " - dimension " << st.dimension() << std::endl; + + simplex_is_changed = st.prune_above_filtration(2.0); + if (simplex_is_changed) + st.initialize_filtration(); + + std::cout << "The complex pruned at 2.0 contains " << st.num_simplices() << " simplices"; + std::cout << " - dimension " << st.dimension() << std::endl; + + BOOST_CHECK(st == st_pruned); + BOOST_CHECK(!simplex_is_changed); + + Stree st_empty; + simplex_is_changed = st.prune_above_filtration(0.0); + if (simplex_is_changed) + st.initialize_filtration(); + + // Display the Simplex_tree + std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices"; + std::cout << " - dimension " << st.dimension() << std::endl; + + BOOST_CHECK(st == st_empty); + BOOST_CHECK(simplex_is_changed); + + // Test case to the limit + simplex_is_changed = st.prune_above_filtration(-1.0); + if (simplex_is_changed) + st.initialize_filtration(); + BOOST_CHECK(st == st_empty); + BOOST_CHECK(!simplex_is_changed); +} + +BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) { + std::cout << "********************************************************************" << std::endl; + std::cout << "MINI PRUNE ABOVE FILTRATION" << std::endl; + + Mini_stree st; + + st.insert_simplex_and_subfaces({0, 1, 6, 7}); + st.insert_simplex_and_subfaces({3, 4, 5}); + st.insert_simplex_and_subfaces({3, 0}); + st.insert_simplex_and_subfaces({2, 1, 0}); + + // st: + // 1 6 + // o---o + // /X\7/ + // o---o---o---o + // 2 0 3\X/4 + // o + // 5 + + st.initialize_filtration(); + + // Display the Simplex_tree + std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; + BOOST_CHECK(st.num_simplices() == 27); + + // Test case to the limit - With these options, there is no filtration, which means filtration is 0 + bool simplex_is_changed = st.prune_above_filtration(1.0); + if (simplex_is_changed) + st.initialize_filtration(); + // Display the Simplex_tree + std::cout << "The complex pruned at 1.0 contains " << st.num_simplices() << " simplices" << std::endl; + BOOST_CHECK(!simplex_is_changed); + BOOST_CHECK(st.num_simplices() == 27); + + simplex_is_changed = st.prune_above_filtration(0.0); + if (simplex_is_changed) + st.initialize_filtration(); + // Display the Simplex_tree + std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices" << std::endl; + BOOST_CHECK(!simplex_is_changed); + BOOST_CHECK(st.num_simplices() == 27); + + // Test case to the limit + simplex_is_changed = st.prune_above_filtration(-1.0); + if (simplex_is_changed) + st.initialize_filtration(); + // Display the Simplex_tree + std::cout << "The complex pruned at -1.0 contains " << st.num_simplices() << " simplices" << std::endl; + BOOST_CHECK(simplex_is_changed); + BOOST_CHECK(st.num_simplices() == 0); + + // Display the Simplex_tree + std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; + +} diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index b06d7ec9..7323aa6c 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -148,16 +148,9 @@ void test_simplex_tree_insert_returns_true(const typePairSimplexBool& returnValu // Global variables double max_fil = 0.0; -int dim_max = -1; template void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, const Filtration_value& fil) { - if (vectorSize > dim_max + 1) { - dim_max = vectorSize - 1; - simplexTree.set_dimension(dim_max); - std::cout << " set_and_test_simplex_tree_dim_fil - dim_max=" << dim_max - << std::endl; - } if (fil > max_fil) { max_fil = fil; simplexTree.set_filtration(max_fil); @@ -165,7 +158,7 @@ void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, cons << std::endl; } - BOOST_CHECK(simplexTree.dimension() == dim_max); + BOOST_CHECK(simplexTree.dimension() >= vectorSize - 1); BOOST_CHECK(AreAlmostTheSame(simplexTree.filtration(), max_fil)); // Another way to count simplices: @@ -189,7 +182,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var const Filtration_value THIRD_FILTRATION_VALUE = 0.3; const Filtration_value FOURTH_FILTRATION_VALUE = 0.4; // reset since we run the test several times - dim_max = -1; max_fil = 0.0; // TEST OF INSERTION @@ -308,8 +300,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var // Simplex_handle = boost::container::flat_map< typeST::Vertex_handle, Node >::iterator typename typeST::Simplex_handle shReturned = returnValue.first; BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr)); + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !! - BOOST_CHECK(st.dimension() == dim_max); BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil)); // ++ ELEVENTH @@ -324,7 +316,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var shReturned = returnValue.first; BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr)); BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !! - BOOST_CHECK(st.dimension() == dim_max); + std::cout << " - INSERT (2,1,0) (already inserted)" << std::endl; + BOOST_CHECK(st.dimension() == 2); BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil)); /* Inserted simplex: */ @@ -630,9 +623,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(coface_on_simplex_tree, typeST, list_of_tested_var /* o */ /* 5 */ - // FIXME - st.set_dimension(3); - std::vector simplex_result; std::vector result; std::cout << "First test - Star of (3):" << std::endl; @@ -729,9 +719,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(copy_move_on_simplex_tree, typeST, list_of_tested_ /* o */ /* 5 */ - // FIXME - st.set_dimension(3); - std::cout << "Printing st - address = " << &st << std::endl; // Copy constructor @@ -882,271 +869,3 @@ BOOST_AUTO_TEST_CASE(make_filtration_non_decreasing) { BOOST_CHECK(st == st_other_copy); } - -struct MyOptions : Simplex_tree_options_full_featured { - // Not doing persistence, so we don't need those - static const bool store_key = false; - static const bool store_filtration = false; - // I have few vertices - typedef short Vertex_handle; -}; - -BOOST_AUTO_TEST_CASE(remove_maximal_simplex) { - std::cout << "********************************************************************" << std::endl; - std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl; - - - typedef Simplex_tree miniST; - miniST st; - - // FIXME - st.set_dimension(3); - - st.insert_simplex_and_subfaces({0, 1, 6, 7}); - st.insert_simplex_and_subfaces({3, 4, 5}); - - // Constructs a copy at this state for further test purpose - miniST st_pruned = st; - - st.insert_simplex_and_subfaces({3, 0}); - st.insert_simplex_and_subfaces({2, 1, 0}); - - // Constructs a copy at this state for further test purpose - miniST st_complete = st; - // st_complete and st: - // 1 6 - // o---o - // /X\7/ - // o---o---o---o - // 2 0 3\X/4 - // o - // 5 - // st_pruned: - // 1 6 - // o---o - // \7/ - // o o---o - // 0 3\X/4 - // o - // 5 - -#ifdef GUDHI_DEBUG - std::cout << "Check exception throw in debug mode" << std::endl; - // throw excpt because sh has children - BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({0, 1, 6})), std::invalid_argument); - BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({3})), std::invalid_argument); - BOOST_CHECK(st == st_complete); -#endif - - st.remove_maximal_simplex(st.find({0, 2})); - st.remove_maximal_simplex(st.find({0, 1, 2})); - st.remove_maximal_simplex(st.find({1, 2})); - st.remove_maximal_simplex(st.find({2})); - st.remove_maximal_simplex(st.find({0, 3})); - - BOOST_CHECK(st == st_pruned); - // Remove all, but as the simplex tree is not storing filtration, there is no modification - st.prune_above_filtration(0.0); - BOOST_CHECK(st == st_pruned); - - miniST st_wo_seven; - // FIXME - st_wo_seven.set_dimension(3); - - st_wo_seven.insert_simplex_and_subfaces({0, 1, 6}); - st_wo_seven.insert_simplex_and_subfaces({3, 4, 5}); - // st_wo_seven: - // 1 6 - // o---o - // \X/ - // o o---o - // 0 3\X/4 - // o - // 5 - - // Remove all 7 to test the both remove_maximal_simplex cases (when _members is empty or not) - st.remove_maximal_simplex(st.find({0, 1, 6, 7})); - st.remove_maximal_simplex(st.find({0, 1, 7})); - st.remove_maximal_simplex(st.find({0, 6, 7})); - st.remove_maximal_simplex(st.find({0, 7})); - st.remove_maximal_simplex(st.find({1, 6, 7})); - st.remove_maximal_simplex(st.find({1, 7})); - st.remove_maximal_simplex(st.find({6, 7})); - st.remove_maximal_simplex(st.find({7})); - - BOOST_CHECK(st == st_wo_seven); -} - -BOOST_AUTO_TEST_CASE(prune_above_filtration) { - std::cout << "********************************************************************" << std::endl; - std::cout << "PRUNE ABOVE FILTRATION" << std::endl; - typedef Simplex_tree<> typeST; - typeST st; - - // FIXME - st.set_dimension(3); - - st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0); - st.insert_simplex_and_subfaces({3, 4, 5}, 2.0); - - // Constructs a copy at this state for further test purpose - typeST st_pruned = st; - st_pruned.initialize_filtration(); // reset - - st.insert_simplex_and_subfaces({3, 0}, 3.0); - st.insert_simplex_and_subfaces({2, 1, 0}, 4.0); - - // Constructs a copy at this state for further test purpose - typeST st_complete = st; - // st_complete and st: - // 1 6 - // o---o - // /X\7/ - // o---o---o---o - // 2 0 3\X/4 - // o - // 5 - // st_pruned: - // 1 6 - // o---o - // \7/ - // o o---o - // 0 3\X/4 - // o - // 5 - - bool simplex_is_changed = false; - // Check the no action cases - // greater than initial filtration value - simplex_is_changed = st.prune_above_filtration(10.0); - if (simplex_is_changed) - st.initialize_filtration(); - BOOST_CHECK(st == st_complete); - BOOST_CHECK(!simplex_is_changed); - // equal to initial filtration value - simplex_is_changed = st.prune_above_filtration(6.0); - if (simplex_is_changed) - st.initialize_filtration(); - BOOST_CHECK(st == st_complete); - BOOST_CHECK(!simplex_is_changed); - // lower than initial filtration value, but still greater than the maximum filtration value - simplex_is_changed = st.prune_above_filtration(5.0); - if (simplex_is_changed) - st.initialize_filtration(); - BOOST_CHECK(st == st_complete); - BOOST_CHECK(!simplex_is_changed); - - // Display the Simplex_tree - std::cout << "The complex contains " << st.num_simplices() << " simplices"; - std::cout << " - dimension " << st.dimension() << std::endl; - std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; - for (auto f_simplex : st.filtration_simplex_range()) { - std::cout << " " << "[" << st.filtration(f_simplex) << "] "; - for (auto vertex : st.simplex_vertex_range(f_simplex)) { - std::cout << (int) vertex << " "; - } - std::cout << std::endl; - } - - // Check the pruned cases - simplex_is_changed = st.prune_above_filtration(2.5); - if (simplex_is_changed) - st.initialize_filtration(); - BOOST_CHECK(st == st_pruned); - BOOST_CHECK(simplex_is_changed); - - // Display the Simplex_tree - std::cout << "The complex pruned at 2.5 contains " << st.num_simplices() << " simplices"; - std::cout << " - dimension " << st.dimension() << std::endl; - - simplex_is_changed = st.prune_above_filtration(2.0); - if (simplex_is_changed) - st.initialize_filtration(); - - std::cout << "The complex pruned at 2.0 contains " << st.num_simplices() << " simplices"; - std::cout << " - dimension " << st.dimension() << std::endl; - - BOOST_CHECK(st == st_pruned); - BOOST_CHECK(!simplex_is_changed); - - typeST st_empty; - // FIXME - st_empty.set_dimension(3); - simplex_is_changed = st.prune_above_filtration(0.0); - if (simplex_is_changed) - st.initialize_filtration(); - - // Display the Simplex_tree - std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices"; - std::cout << " - dimension " << st.dimension() << std::endl; - - BOOST_CHECK(st == st_empty); - BOOST_CHECK(simplex_is_changed); - - // Test case to the limit - simplex_is_changed = st.prune_above_filtration(-1.0); - if (simplex_is_changed) - st.initialize_filtration(); - BOOST_CHECK(st == st_empty); - BOOST_CHECK(!simplex_is_changed); -} - -BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) { - std::cout << "********************************************************************" << std::endl; - std::cout << "MINI PRUNE ABOVE FILTRATION" << std::endl; - typedef Simplex_tree typeST; - typeST st; - - // FIXME - st.set_dimension(3); - - st.insert_simplex_and_subfaces({0, 1, 6, 7}); - st.insert_simplex_and_subfaces({3, 4, 5}); - st.insert_simplex_and_subfaces({3, 0}); - st.insert_simplex_and_subfaces({2, 1, 0}); - - // st: - // 1 6 - // o---o - // /X\7/ - // o---o---o---o - // 2 0 3\X/4 - // o - // 5 - - st.initialize_filtration(); - - // Display the Simplex_tree - std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; - BOOST_CHECK(st.num_simplices() == 27); - - // Test case to the limit - With these options, there is no filtration, which means filtration is 0 - bool simplex_is_changed = st.prune_above_filtration(1.0); - if (simplex_is_changed) - st.initialize_filtration(); - // Display the Simplex_tree - std::cout << "The complex pruned at 1.0 contains " << st.num_simplices() << " simplices" << std::endl; - BOOST_CHECK(!simplex_is_changed); - BOOST_CHECK(st.num_simplices() == 27); - - simplex_is_changed = st.prune_above_filtration(0.0); - if (simplex_is_changed) - st.initialize_filtration(); - // Display the Simplex_tree - std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices" << std::endl; - BOOST_CHECK(!simplex_is_changed); - BOOST_CHECK(st.num_simplices() == 27); - - // Test case to the limit - simplex_is_changed = st.prune_above_filtration(-1.0); - if (simplex_is_changed) - st.initialize_filtration(); - // Display the Simplex_tree - std::cout << "The complex pruned at -1.0 contains " << st.num_simplices() << " simplices" << std::endl; - BOOST_CHECK(simplex_is_changed); - BOOST_CHECK(st.num_simplices() == 0); - - // Display the Simplex_tree - std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; - -} \ No newline at end of file diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index 6f4bcf60..c18335d3 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -127,7 +127,6 @@ class Strong_witness_complex { if ((Landmark_id)simplex.size() - 1 > complex_dim) complex_dim = simplex.size() - 1; } - complex.set_dimension(complex_dim); return true; } diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index bcfe8484..53c38520 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -130,7 +130,6 @@ class Witness_complex { } k++; } - complex.set_dimension(k-1); return true; } diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h index 5e9dc0e4..ecf014b3 100644 --- a/src/cython/include/Tangential_complex_interface.h +++ b/src/cython/include/Tangential_complex_interface.h @@ -106,8 +106,6 @@ class Tangential_complex_interface { void create_simplex_tree(Simplex_tree<>* simplex_tree) { int max_dim = tangential_complex_->create_complex>(*simplex_tree); - // FIXME - simplex_tree->set_dimension(max_dim); simplex_tree->initialize_filtration(); } diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index 3ae537e3..a6d6a9f3 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -34,9 +34,13 @@ def test_insertion(): # insert test assert st.insert([0, 1]) == True + + assert st.dimension() == 1 + assert st.insert([0, 1, 2], filtration=4.0) == True - # FIXME: Remove this line - st.set_dimension(2) + + assert st.dimension() == 2 + assert st.num_simplices() == 7 assert st.num_vertices() == 3 @@ -87,8 +91,9 @@ def test_insertion(): assert st.find([2]) == True st.initialize_filtration() - assert st.persistence() == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))] + assert st.persistence(persistence_dim_max = True) == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))] assert st.__is_persistence_defined() == True + assert st.betti_numbers() == [1, 1] assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0] assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0] -- cgit v1.2.3 From 346ba542c13db7e49e6d81412144ed21ac46bd83 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 21 Sep 2017 06:41:40 +0000 Subject: Remove set_dimension from examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2698 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cde0919e6bb53ad8ace21f1c6894708468449276 --- src/Simplex_tree/example/mini_simplex_tree.cpp | 2 -- src/Simplex_tree/example/simple_simplex_tree.cpp | 1 - src/cython/example/simplex_tree_example.py | 2 -- 3 files changed, 5 deletions(-) (limited to 'src/cython') diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp index ad99df23..19e45361 100644 --- a/src/Simplex_tree/example/mini_simplex_tree.cpp +++ b/src/Simplex_tree/example/mini_simplex_tree.cpp @@ -52,8 +52,6 @@ int main() { auto edge03 = {0, 3}; st.insert_simplex_and_subfaces(triangle012); st.insert_simplex_and_subfaces(edge03); - // FIXME: Remove this line - st.set_dimension(2); auto edge02 = {0, 2}; ST::Simplex_handle e = st.find(edge02); diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index 60f9a35e..26d663fb 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -186,7 +186,6 @@ int main(int argc, char * const argv[]) { // ++ GENERAL VARIABLE SET simplexTree.set_filtration(FOURTH_FILTRATION_VALUE); // Max filtration value - simplexTree.set_dimension(2); // Max dimension = 2 -> (2,1,0) std::cout << "********************************************************************\n"; // Display the Simplex_tree - Can not be done in the middle of 2 inserts diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py index 3af20fcf..7e4b0b6c 100755 --- a/src/cython/example/simplex_tree_example.py +++ b/src/cython/example/simplex_tree_example.py @@ -48,8 +48,6 @@ if st.insert([0, 1, 2], filtration=4.0): else: print("Not inserted...") -# FIXME: Remove this line -st.set_dimension(3) print("dimension=", st.dimension()) st.set_filtration(4.0) -- cgit v1.2.3 From 3534c24fd805f8cf0ed8f1d5faea183513966b9f Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 22 Sep 2017 06:59:33 +0000 Subject: Remove global filtration attribute of te simplex tree (including getter and setter) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2705 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a6c179ae47e61d1ca12d1f54c4ae1fc0e3c1fde2 --- src/Hasse_complex/include/gudhi/Hasse_complex.h | 10 +--------- .../example/alpha_complex_3d_persistence.cpp | 2 -- .../example/exact_alpha_complex_3d_persistence.cpp | 2 -- .../periodic_alpha_complex_3d_persistence.cpp | 2 -- .../example/persistence_from_file.cpp | 3 +-- .../persistence_from_simple_simplex_tree.cpp | 3 +-- .../weighted_alpha_complex_3d_persistence.cpp | 2 -- .../test/persistent_cohomology_unit_test.cpp | 3 +-- ...persistent_cohomology_unit_test_multi_field.cpp | 3 +-- src/Simplex_tree/example/simple_simplex_tree.cpp | 3 +-- src/Simplex_tree/include/gudhi/Simplex_tree.h | 22 ---------------------- src/Simplex_tree/test/simplex_tree_unit_test.cpp | 22 ++++------------------ src/cython/cython/simplex_tree.pyx | 10 ---------- src/cython/example/simplex_tree_example.py | 1 - src/cython/test/test_simplex_tree.py | 1 - 15 files changed, 10 insertions(+), 79 deletions(-) (limited to 'src/cython') diff --git a/src/Hasse_complex/include/gudhi/Hasse_complex.h b/src/Hasse_complex/include/gudhi/Hasse_complex.h index 8b06b771..834201a5 100644 --- a/src/Hasse_complex/include/gudhi/Hasse_complex.h +++ b/src/Hasse_complex/include/gudhi/Hasse_complex.h @@ -104,7 +104,6 @@ class Hasse_complex { Hasse_complex(Complex_ds & cpx) : complex_(cpx.num_simplices()) , vertices_() - , threshold_(cpx.filtration()) , num_vertices_() , dim_max_(cpx.dimension()) { int size = complex_.size(); @@ -125,7 +124,6 @@ class Hasse_complex { Hasse_complex() : complex_() , vertices_() - , threshold_(0) , num_vertices_(0) , dim_max_(-1) { } @@ -157,15 +155,11 @@ class Hasse_complex { Filtration_value filtration(Simplex_handle sh) { if (sh == null_simplex()) { - return filtration(); + return INFINITY; } return complex_[sh].filtration_; } - Filtration_value filtration() { - return threshold_; - } - int dimension(Simplex_handle sh) { if (complex_[sh].boundary_.empty()) return 0; return complex_[sh].boundary_.size() - 1; @@ -206,7 +200,6 @@ class Hasse_complex { std::vector< Hasse_simp, Gudhi::no_init_allocator > complex_; std::vector vertices_; - Filtration_value threshold_; size_t num_vertices_; int dim_max_; }; @@ -245,7 +238,6 @@ std::istream& operator>>(std::istream & is } hcpx.dim_max_ = max_dim; - hcpx.threshold_ = max_fil; return is; } diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index fd227b82..53e50a69 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -202,7 +202,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -216,7 +215,6 @@ int main(int argc, char * const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp index 8a335075..acb34bcb 100644 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -204,7 +204,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -218,7 +217,6 @@ int main(int argc, char * const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp index 8928cfc2..f731d349 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -221,7 +221,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -235,7 +234,6 @@ int main(int argc, char * const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp index 67235467..eafa3fd5 100644 --- a/src/Persistent_cohomology/example/persistence_from_file.cpp +++ b/src/Persistent_cohomology/example/persistence_from_file.cpp @@ -61,8 +61,7 @@ int main(int argc, char * argv[]) { simplex_tree_stream >> simplex_tree; std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() - << std::endl; + std::cout << " - dimension " << simplex_tree.dimension() << std::endl; /* std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp index 7ca9410a..8214d66a 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -143,11 +143,10 @@ int main(int argc, char * const argv[]) { /* An edge [10,12,2] */ st.set_dimension(2); - st.set_filtration(0.4); std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; std::cout << "**************************************************************" << std::endl; diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp index 34b90933..9728f22d 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -222,7 +222,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -236,7 +235,6 @@ int main(int argc, char * const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp index f8174020..f53987b6 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -31,12 +31,11 @@ std::string test_rips_persistence(int coefficient, int min_persistence) { // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() - << " - filtration= " << st.filtration() << std::endl; + << std::endl; // Check BOOST_CHECK(st.num_simplices() == 98); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(st.filtration() == 1.89); // Sort the simplices in the order of the filtration st.initialize_filtration(); 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 3537cfa4..9e767943 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 @@ -31,12 +31,11 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, doub // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() - << " - filtration= " << st.filtration() << std::endl; + << std::endl; // Check BOOST_CHECK(st.num_simplices() == 58); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(st.filtration() == 0.4); // Sort the simplices in the order of the filtration st.initialize_filtration(); diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index 60f9a35e..d8318f03 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -185,13 +185,12 @@ int main(int argc, char * const argv[]) { } // ++ GENERAL VARIABLE SET - simplexTree.set_filtration(FOURTH_FILTRATION_VALUE); // Max filtration value simplexTree.set_dimension(2); // Max dimension = 2 -> (2,1,0) std::cout << "********************************************************************\n"; // Display the Simplex_tree - Can not be done in the middle of 2 inserts std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n"; - std::cout << " - dimension " << simplexTree.dimension() << " - filtration " << simplexTree.filtration() << "\n"; + std::cout << " - dimension " << simplexTree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : simplexTree.filtration_simplex_range()) { std::cout << " " << "[" << simplexTree.filtration(f_simplex) << "] "; diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 317bce23..8c91cc67 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -289,7 +289,6 @@ class Simplex_tree { /** \brief Constructs an empty simplex tree. */ Simplex_tree() : null_vertex_(-1), - threshold_(0), root_(nullptr, null_vertex_), filtration_vect_(), dimension_(-1) { } @@ -297,7 +296,6 @@ class Simplex_tree { /** \brief User-defined copy constructor reproduces the whole tree structure. */ Simplex_tree(const Simplex_tree& simplex_source) : null_vertex_(simplex_source.null_vertex_), - threshold_(simplex_source.threshold_), root_(nullptr, null_vertex_ , simplex_source.root_.members_), filtration_vect_(), dimension_(simplex_source.dimension_) { @@ -323,12 +321,10 @@ class Simplex_tree { /** \brief User-defined move constructor moves the whole tree structure. */ Simplex_tree(Simplex_tree && old) : null_vertex_(std::move(old.null_vertex_)), - threshold_(std::move(old.threshold_)), root_(std::move(old.root_)), filtration_vect_(std::move(old.filtration_vect_)), dimension_(std::move(old.dimension_)) { old.dimension_ = -1; - old.threshold_ = 0; old.root_ = Siblings(nullptr, null_vertex_); } @@ -356,7 +352,6 @@ class Simplex_tree { /** \brief Checks if two simplex trees are equal. */ bool operator==(Simplex_tree& st2) { if ((null_vertex_ != st2.null_vertex_) || - (threshold_ != st2.threshold_) || (dimension_ != st2.dimension_)) return false; return rec_equal(&root_, &st2.root_); @@ -427,11 +422,6 @@ class Simplex_tree { sh->second.assign_filtration(fv); } - /** \brief Returns an upper bound of the filtration values of the simplices. */ - Filtration_value filtration() const { - return threshold_; - } - /** \brief Returns a Simplex_handle different from all Simplex_handles * associated to the simplices in the simplicial complex. * @@ -757,11 +747,6 @@ class Simplex_tree { return &root_; } - /** Set an upper bound for the filtration values. */ - void set_filtration(Filtration_value fil) { - threshold_ = fil; - } - /** Set a dimension for the simplicial complex. */ void set_dimension(int dimension) { dimension_ = dimension; @@ -1215,8 +1200,6 @@ class Simplex_tree { private: Vertex_handle null_vertex_; - /** \brief Upper bound on the filtration values of the simplices.*/ - Filtration_value threshold_; /** \brief Total number of simplices in the complex, without the empty simplex.*/ /** \brief Set of simplex tree Nodes representing the vertices.*/ Siblings root_; @@ -1244,7 +1227,6 @@ std::istream& operator>>(std::istream & is, Simplex_tree & st) { typedef Simplex_tree ST; std::vector simplex; typename ST::Filtration_value fil; - typename ST::Filtration_value max_fil = 0; int max_dim = -1; while (read_simplex(is, simplex, fil)) { // read all simplices in the file as a list of vertices @@ -1253,15 +1235,11 @@ std::istream& operator>>(std::istream & is, Simplex_tree & st) { if (max_dim < dim) { max_dim = dim; } - if (max_fil < fil) { - max_fil = fil; - } // insert every simplex in the simplex tree st.insert_simplex(simplex, fil); simplex.clear(); } st.set_dimension(max_dim); - st.set_filtration(max_fil); return is; } diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index b06d7ec9..17ddc605 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -26,7 +26,6 @@ void test_empty_simplex_tree(typeST& tst) { typedef typename typeST::Vertex_handle Vertex_handle; const Vertex_handle DEFAULT_VERTEX_VALUE = Vertex_handle(- 1); BOOST_CHECK(tst.null_vertex() == DEFAULT_VERTEX_VALUE); - BOOST_CHECK(tst.filtration() == 0.0); BOOST_CHECK(tst.num_vertices() == (size_t) 0); BOOST_CHECK(tst.num_simplices() == (size_t) 0); typename typeST::Siblings* STRoot = tst.root(); @@ -98,12 +97,11 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_from_file, typeST, list_of_tested_var // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; // Check BOOST_CHECK(st.num_simplices() == 143353); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(AreAlmostTheSame(st.filtration(), 0.4)); int previous_size = 0; for (auto f_simplex : st.filtration_simplex_range()) { @@ -147,7 +145,6 @@ void test_simplex_tree_insert_returns_true(const typePairSimplexBool& returnValu } // Global variables -double max_fil = 0.0; int dim_max = -1; template @@ -158,15 +155,8 @@ void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, cons std::cout << " set_and_test_simplex_tree_dim_fil - dim_max=" << dim_max << std::endl; } - if (fil > max_fil) { - max_fil = fil; - simplexTree.set_filtration(max_fil); - std::cout << " set_and_test_simplex_tree_dim_fil - max_fil=" << max_fil - << std::endl; - } BOOST_CHECK(simplexTree.dimension() == dim_max); - BOOST_CHECK(AreAlmostTheSame(simplexTree.filtration(), max_fil)); // Another way to count simplices: size_t num_simp = 0; @@ -190,7 +180,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var const Filtration_value FOURTH_FILTRATION_VALUE = 0.4; // reset since we run the test several times dim_max = -1; - max_fil = 0.0; // TEST OF INSERTION std::cout << "********************************************************************" << std::endl; @@ -310,7 +299,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr)); BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !! BOOST_CHECK(st.dimension() == dim_max); - BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil)); // ++ ELEVENTH std::cout << " - INSERT (2,1,0) (already inserted)" << std::endl; @@ -325,7 +313,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr)); BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !! BOOST_CHECK(st.dimension() == dim_max); - BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil)); /* Inserted simplex: */ /* 1 */ @@ -365,7 +352,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var // Display the Simplex_tree - Can not be done in the middle of 2 inserts std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; for (auto f_simplex : st.filtration_simplex_range()) { std::cout << " " << "[" << st.filtration(f_simplex) << "] "; @@ -575,7 +562,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o // Display the Simplex_tree - Can not be done in the middle of 2 inserts std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; for (auto f_simplex : st.filtration_simplex_range()) { std::cout << " " << "[" << st.filtration(f_simplex) << "] "; @@ -756,7 +743,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(copy_move_on_simplex_tree, typeST, list_of_tested_ typeST st_empty; // Check st has been emptied by the move BOOST_CHECK(st == st_empty); - BOOST_CHECK(st.filtration() == 0); BOOST_CHECK(st.dimension() == -1); BOOST_CHECK(st.num_simplices() == 0); BOOST_CHECK(st.num_vertices() == (size_t)0); @@ -1149,4 +1135,4 @@ BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) { // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl; -} \ No newline at end of file +} diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 47aa5311..45487158 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -36,9 +36,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface": Simplex_tree() - double filtration() double simplex_filtration(vector[int] simplex) - void set_filtration(double filtration) void initialize_filtration() int num_vertices() int num_simplices() @@ -115,14 +113,6 @@ cdef class SimplexTree: """ return self.thisptr.simplex_filtration(simplex) - def set_filtration(self, filtration): - """This function sets the main simplicial complex filtration value. - - :param filtration: The filtration value. - :type filtration: float. - """ - self.thisptr.set_filtration( filtration) - def initialize_filtration(self): """This function initializes and sorts the simplicial complex filtration vector. diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py index 3af20fcf..831d9da8 100755 --- a/src/cython/example/simplex_tree_example.py +++ b/src/cython/example/simplex_tree_example.py @@ -52,7 +52,6 @@ else: st.set_dimension(3) print("dimension=", st.dimension()) -st.set_filtration(4.0) st.initialize_filtration() print("filtration=", st.get_filtration()) print("filtration[1, 2]=", st.filtration([1, 2])) diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index 3ae537e3..4d452d7d 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -53,7 +53,6 @@ def test_insertion(): assert st.find([2, 3]) == False # filtration test - st.set_filtration(5.0) st.initialize_filtration() assert st.filtration([0, 1, 2]) == 4.0 assert st.filtration([0, 2]) == 4.0 -- cgit v1.2.3 From 6965bcc31dfc44ba82524637b4184f8dfdd86e9c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 25 Sep 2017 15:44:28 +0000 Subject: Do not advertise nor use the exact bottleneck distance version git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2711 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e441b042d15bfbe727789803ca17b17711a48d9c --- .../example/bottleneck_read_file_example.cpp | 12 ++++++------ src/cython/doc/bottleneck_distance_user.rst | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) (limited to 'src/cython') diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp index 1408681a..24d73c57 100644 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp @@ -25,21 +25,21 @@ #include #include #include // for pair -#include -#include #include +#include // for numeric_limits int main(int argc, char** argv) { if (argc < 3) { - std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " << - "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" << - " distance (set by default to zero). The program will now terminate \n"; + std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" << + " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" << + " distance (set by default to the smallest positive double value). If you set the error bound to 0, be" << + " aware this version is exact but expensive. The program will now terminate \n"; return -1; } std::vector> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]); std::vector> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]); - double tolerance = 0.; + double tolerance = std::numeric_limits::min(); if (argc == 4) { tolerance = atof(argv[3]); } diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst index 0066992f..7692dce2 100644 --- a/src/cython/doc/bottleneck_distance_user.rst +++ b/src/cython/doc/bottleneck_distance_user.rst @@ -25,7 +25,7 @@ This example computes the bottleneck distance from 2 persistence diagrams: message = "Bottleneck distance approximation=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0.1) print(message) - message = "Bottleneck distance exact value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0) + message = "Bottleneck distance value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2) print(message) The output is: @@ -33,4 +33,4 @@ The output is: .. testoutput:: Bottleneck distance approximation=0.81 - Bottleneck distance exact value=0.75 + Bottleneck distance value=0.75 -- cgit v1.2.3 From 526625e6faa7b01430b481d5c21d7d7dfe16e290 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 27 Sep 2017 20:25:21 +0000 Subject: Fix some cpplints git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2721 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 76b127e54d9511b70294ab48336ca6dbd6fdb1d6 --- ...Bitmap_cubical_complex_periodic_boundary_conditions.cpp | 1 + src/Bottleneck_distance/include/gudhi/Neighbors_finder.h | 8 ++++---- src/Spatial_searching/include/gudhi/Kd_tree_search.h | 14 ++++++-------- src/common/utilities/off_file_from_shape_generator.cpp | 2 +- src/cython/include/Reader_utils_interface.h | 2 ++ 5 files changed, 14 insertions(+), 13 deletions(-) (limited to 'src/cython') diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp index f8754345..122160a2 100644 --- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp +++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp @@ -30,6 +30,7 @@ #include #include #include +#include int main(int argc, char** argv) { std::cout << "This program computes persistent homology, by using " << diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index bdc47578..a6b9b021 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -44,16 +44,16 @@ struct Square_query { typedef Internal_point Point_d; typedef double FT; bool contains(Point_d p) const { - return std::abs(p.x()-c.x())<=size && std::abs(p.y()-c.y())<=size; + return std::abs(p.x()-c.x()) <= size && std::abs(p.y()-c.y()) <= size; } - bool inner_range_intersects(CGAL::Kd_tree_rectangle const&r) const { + bool inner_range_intersects(CGAL::Kd_tree_rectangle const&r) const { return r.max_coord(0) >= c.x() - size && r.min_coord(0) <= c.x() + size && r.max_coord(1) >= c.y() - size && r.min_coord(1) <= c.y() + size; } - bool outer_range_contains(CGAL::Kd_tree_rectangle const&r) const { + bool outer_range_contains(CGAL::Kd_tree_rectangle const&r) const { return r.min_coord(0) >= c.x() - size && r.max_coord(0) <= c.x() + size && @@ -146,7 +146,7 @@ inline int Neighbors_finder::pull_near(int u_point_index) { // Is the query point near to a V point in the plane ? Internal_point u_point = g.get_u_point(u_point_index); auto neighbor = kd_t.search_any_point(Square_query{u_point, r}); - if(!neighbor) + if (!neighbor) return null_point_index(); tmp = neighbor->point_index; auto point = g.get_v_point(tmp); diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h index a4385c84..af04736b 100644 --- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h +++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h @@ -193,7 +193,7 @@ class Kd_tree_search { /// \brief Search incrementally for the nearest neighbors from a query point. /// @param[in] p The query point. /// @param[in] eps Approximation factor. - /// @return A range (whose `value_type` is `std::size_t`) containing the + /// @return A range (whose `value_type` is `std::size_t`) containing the /// neighbors sorted by their distance to p. /// All the neighbors are not computed by this function, but they will be /// computed incrementally when the iterator on the range is incremented. @@ -239,7 +239,7 @@ class Kd_tree_search { /// \brief Search incrementally for the farthest neighbors from a query point. /// @param[in] p The query point. /// @param[in] eps Approximation factor. - /// @return A range (whose `value_type` is `std::size_t`) + /// @return A range (whose `value_type` is `std::size_t`) /// containing the neighbors sorted by their distance to p. /// All the neighbors are not computed by this function, but they will be /// computed incrementally when the iterator on the range is incremented. @@ -264,12 +264,10 @@ class Kd_tree_search { /// Note: `it` is used this way: `*it++ = each_point`. /// @param[in] eps Approximation factor. template - void near_search( - Point const& p, - FT radius, - OutputIterator it, - FT eps = FT(0)) const { - + void near_search(Point const& p, + FT radius, + OutputIterator it, + FT eps = FT(0)) const { m_tree.search(it, Fuzzy_sphere(p, radius, eps, m_tree.traits())); } diff --git a/src/common/utilities/off_file_from_shape_generator.cpp b/src/common/utilities/off_file_from_shape_generator.cpp index 0f310a13..afcd558c 100644 --- a/src/common/utilities/off_file_from_shape_generator.cpp +++ b/src/common/utilities/off_file_from_shape_generator.cpp @@ -77,7 +77,7 @@ int main(int argc, char **argv) { usage(argv[0]); } - enum class Data_shape { sphere, cube, curve, torus, klein, undefined } ; + enum class Data_shape { sphere, cube, curve, torus, klein, undefined}; Data_shape shape = Data_shape::undefined; if (memcmp(argv[2], "sphere", sizeof("sphere")) == 0) { diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h index b87b6cca..8ec34f61 100644 --- a/src/cython/include/Reader_utils_interface.h +++ b/src/cython/include/Reader_utils_interface.h @@ -28,6 +28,8 @@ #include #include #include +#include +#include // for pair<> namespace Gudhi { -- cgit v1.2.3 From 36d71f6a62d0390c5a8193171c92e75a85889b4a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 29 Sep 2017 21:06:08 +0000 Subject: Doc issue fix git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2733 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ea0323fed1ca42ecee50d6fbf9db9fbfb3e64cc9 --- src/Persistent_cohomology/doc/Intro_persistent_cohomology.h | 11 ++++++----- src/cython/doc/cubical_complex_user.rst | 8 ++++---- 2 files changed, 10 insertions(+), 9 deletions(-) (limited to 'src/cython') diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index e17e5926..6400116b 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -189,10 +189,10 @@ and a weights file. \code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights 2 0.45 \endcode \code Simplex_tree dim: 3 -2 -0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 \endcode +2 0 -1 inf +2 1 -0.931784 0.000103311 +2 1 -0.906588 2.60165e-05 +2 2 -0.43556 0.0393798 \endcode \li Persistent_cohomology/alpha_complex_persistence.cpp computes the persistent homology with @@ -208,7 +208,8 @@ Simplex_tree dim: 3 \li Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. -\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 \endcode +\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off +../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 \endcode \code Periodic Delaunay computed. Simplex_tree dim: 3 3 0 0 inf diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 36fa3ba9..4f902d0a 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -59,7 +59,7 @@ directions, allows to determine, dimension, neighborhood, boundary and coboundar :math:`C \in \mathcal{K}`. .. figure:: - img/Cubical_complex_representation.png + ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png :alt: Cubical complex. :figclass: align-center @@ -87,7 +87,7 @@ in the example below). Next, in lexicographical order, the filtration of top dim 20 4 7 6 5 in the example below). .. figure:: - img/exampleBitmap.png + ../../doc/Bitmap_cubical_complex/exampleBitmap.png :alt: Example of a input data. :figclass: align-center @@ -97,7 +97,7 @@ The input file for the following complex is: .. literalinclude:: cubicalcomplexdoc.txt -.. centered:: data/bitmap/cubicalcomplexdoc.txt +.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt .. testcode:: @@ -130,7 +130,7 @@ For instance: .. literalinclude:: periodiccubicalcomplexdoc.txt -.. centered:: data/bitmap/periodiccubicalcomplexdoc.txt +.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. -- cgit v1.2.3 From 8868bb6e355a4aec8e084aaf73a1ed1cf47a8589 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 29 Sep 2017 21:43:01 +0000 Subject: Build doc issue git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2736 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 438179e355d47083f9db2c237d7ceb132c7b0168 --- src/cython/doc/cubical_complex_user.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src/cython') diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 4f902d0a..2bfac62a 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -95,7 +95,7 @@ in the example below). Next, in lexicographical order, the filtration of top dim The input file for the following complex is: -.. literalinclude:: cubicalcomplexdoc.txt +.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt .. centered:: ../../data/bitmap/cubicalcomplexdoc.txt @@ -128,7 +128,7 @@ complex with periodic boundary conditions. One can also use Perseus style input conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance: -.. literalinclude:: periodiccubicalcomplexdoc.txt +.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt .. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt -- cgit v1.2.3 From 8d21e4d56cc40e94b395a3a497757c149b4b9f1c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Sun, 1 Oct 2017 20:35:12 +0000 Subject: Euclidean Witness examples requires CGAL >= 4.8.1 because it is using subsampling (CMake and install doc) Bad link to Gudhi bibtex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2741 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8c1b84a4030029ec7d1470c49662e15836cf02de --- src/cython/CMakeLists.txt | 25 +++++++++++++------------ src/cython/doc/citation.rst | 2 +- src/cython/doc/installation.rst | 23 ++++++++++++----------- 3 files changed, 26 insertions(+), 24 deletions(-) (limited to 'src/cython') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index ec8589f0..afca9d60 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -185,6 +185,19 @@ if(CYTHON_FOUND) add_gudhi_py_test(test_tangential_complex) + # Witness complex AND Subsampling + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + # Subsampling add_gudhi_py_test(test_subsampling) @@ -218,18 +231,6 @@ if(CYTHON_FOUND) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) # Euclidean witness - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - add_gudhi_py_test(test_euclidean_witness_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst index 6cdfb7cc..f4fdf83b 100644 --- a/src/cython/doc/citation.rst +++ b/src/cython/doc/citation.rst @@ -12,4 +12,4 @@ Manual, as well as for publications directly related to the GUDHI library. GUDHI bibtex ************ -.. literalinclude:: how_to_cite_gudhi.bib +.. literalinclude:: ../../biblio/how_to_cite_gudhi.bib diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index f98a5039..c182f176 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -68,31 +68,32 @@ The :doc:`Alpha complex `, C++ library which provides easy access to efficient and reliable geometric algorithms. -Having CGAL version 4.6.0 or higher installed is recommended. The procedure to -install this library according to your operating system is detailed +Having CGAL, the Computational Geometry Algorithms Library, version 4.7.0 or +higher installed is recommended. The procedure to install this library +according to your operating system is detailed `here `_. -The following examples require the Computational Geometry Algorithms Library: - -.. only:: builder_html - - * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` - * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` - -The following example requires CGAL version ≥ 4.7.0: +The following examples requires CGAL version ≥ 4.7.0: .. only:: builder_html * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>` -The following example requires CGAL version ≥ 4.8.0: +The following examples requires CGAL version ≥ 4.8.0: .. only:: builder_html * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` +The following examples requires CGAL version ≥ 4.8.1: + +.. only:: builder_html + + * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` + Eigen3 ====== -- cgit v1.2.3 From 4e3cf64d56874353aea48ccc1820069bbf37671a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 19 Oct 2017 20:35:41 +0000 Subject: Code review : remove template specification for std::max Fix cython tests accordingly to the other modifications git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2794 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e1009a3304455fa26fbd368c4cce4451bc3d7784 --- src/Simplex_tree/include/gudhi/Simplex_tree.h | 4 ++-- src/cython/test/test_simplex_tree.py | 12 ++++++------ 2 files changed, 8 insertions(+), 8 deletions(-) (limited to 'src/cython') diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 8a827086..a2febe54 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1202,7 +1202,7 @@ class Simplex_tree { */ bool automatic_dimension_set() { int new_dimension = -1; - // Browse the tree from te left to the right as higher dimension cells are more likely on the left part of the tree + // Browse the tree from the left to the right as higher dimension cells are more likely on the left part of the tree for (Simplex_handle sh : skeleton_simplex_range(dimension_)) { #ifdef DEBUG_TRACES for (auto vertex : simplex_vertex_range(sh)) { @@ -1215,7 +1215,7 @@ class Simplex_tree { if (sh_dimension >= dimension_) // Stop browsing as soon as the dimension is reached, no need to go furter return false; - new_dimension = std::max(new_dimension, sh_dimension); + new_dimension = std::max(new_dimension, sh_dimension); } dimension_ = new_dimension; return true; diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index a6d6a9f3..177cfdad 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -94,12 +94,12 @@ def test_insertion(): assert st.persistence(persistence_dim_max = True) == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))] assert st.__is_persistence_defined() == True - assert st.betti_numbers() == [1, 1] - assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0] - assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0] - assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0] - assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1] - assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1] + assert st.betti_numbers() == [1, 1, 0] + assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0, 0] + assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0, 0] + assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0, 0] + assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1, 0] + assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1, 0] def test_expansion(): st = SimplexTree() -- cgit v1.2.3 From 8f7e5a1259287ee39595623e87149cb07ab2e293 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 26 Oct 2017 20:16:33 +0000 Subject: Code review: downgrade_dimension renamed lower_upper_bound_dimension and make it private. Automatically when dimension_to_be_lowered_ is set (on removal) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2810 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c764433bcc5357acc6454683d4f4182c7c960d6d --- src/Alpha_complex/test/Alpha_complex_unit_test.cpp | 2 +- src/Simplex_tree/include/gudhi/Simplex_tree.h | 34 ++++++-- .../test/simplex_tree_remove_unit_test.cpp | 98 ++++++++++++---------- src/cython/test/test_simplex_tree.py | 12 +-- 4 files changed, 87 insertions(+), 59 deletions(-) (limited to 'src/cython') diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp index e60089c4..166373fe 100644 --- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -232,7 +232,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { BOOST_CHECK(simplex_tree.num_simplices() == 10); std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl; - BOOST_CHECK(simplex_tree.dimension() == 3); + BOOST_CHECK(simplex_tree.dimension() == 1); std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl; BOOST_CHECK(simplex_tree.num_vertices() == 4); diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index ce0994da..54f5de13 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -492,7 +492,16 @@ class Simplex_tree { } /** \brief Returns an upper bound on the dimension of the simplicial complex. */ - int dimension() const { + int upper_bound_dimension() const { + return dimension_; + } + + /** \brief Returns the dimension of the simplicial complex. + \details This function is not constant time because it can trigger `lower_upper_bound_dimension()` if required. + */ + int dimension() { + if (dimension_to_be_lowered_) + lower_upper_bound_dimension(); return dimension_; } @@ -1162,8 +1171,8 @@ class Simplex_tree { * function is not launching `initialize_filtration()` but returns the filtration modification information. If the * complex has changed , please call `initialize_filtration()` to recompute it. * \post Note that the dimension of the simplicial complex may be lower after calling `prune_above_filtration()` - * than it was before. However, `Simplex_tree::dimension()` will return the old value, which remains a valid upper - * bound. If you care, you can call `downgrade_dimension()` to recompute the exact dimension. + * than it was before. However, `upper_bond_dimension()` will return the old value, which remains a valid upper + * bound. If you care, you can call `dimension()` to recompute the exact dimension. */ bool prune_above_filtration(Filtration_value filtration) { return rec_prune_above_filtration(root(), filtration); @@ -1175,6 +1184,8 @@ class Simplex_tree { auto last = std::remove_if(list.begin(), list.end(), [=](Dit_value_t& simplex) { if (simplex.second.filtration() <= filt) return false; if (has_children(&simplex)) rec_delete(simplex.second.children()); + // dimension may need to be lowered + dimension_to_be_lowered_ = true; return true; }); @@ -1183,6 +1194,8 @@ class Simplex_tree { // Removing the whole siblings, parent becomes a leaf. sib->oncles()->members()[sib->parent()].assign_children(sib->oncles()); delete sib; + // dimension may need to be lowered + dimension_to_be_lowered_ = true; return true; } else { // Keeping some elements of siblings. Remove the others, and recurse in the remaining ones. @@ -1194,13 +1207,15 @@ class Simplex_tree { return modified; } - public: + private: /** \brief Deep search simplex tree dimension recompute. * @return True if the dimension was modified, false otherwise. * \pre Be sure the simplex tree has not a too low dimension value as the deep search stops when the former dimension - * has been reached (cf. `dimension()` and `set_dimension()` methods). + * has been reached (cf. `upper_bound_dimension()` and `set_dimension()` methods). */ - bool downgrade_dimension() { + bool lower_upper_bound_dimension() { + // reset automatic detection to recompute + dimension_to_be_lowered_ = false; int new_dimension = -1; // Browse the tree from the left to the right as higher dimension cells are more likely on the left part of the tree for (Simplex_handle sh : complex_simplex_range()) { @@ -1229,8 +1244,8 @@ class Simplex_tree { * \exception std::invalid_argument In debug mode, if sh has children. * \post Be aware that removing is shifting data in a flat_map (`initialize_filtration()` to be done). * \post Note that the dimension of the simplicial complex may be lower after calling `remove_maximal_simplex()` - * than it was before. However, `Simplex_tree::dimension()` will return the old value, which remains a valid upper - * bound. If you care, you can call `downgrade_dimension()` to recompute the exact dimension. + * than it was before. However, `upper_bond_dimension()` will return the old value, which remains a valid upper + * bound. If you care, you can call `dimension()` to recompute the exact dimension. */ void remove_maximal_simplex(Simplex_handle sh) { // Guarantee the simplex has no children @@ -1248,6 +1263,8 @@ class Simplex_tree { // Sibling is emptied : must be deleted, and its parent must point on his own Sibling child->oncles()->members().at(child->parent()).assign_children(child->oncles()); delete child; + // dimension may need to be lowered + dimension_to_be_lowered_ = true; } } @@ -1262,6 +1279,7 @@ class Simplex_tree { std::vector filtration_vect_; /** \brief Upper bound on the dimension of the simplicial complex.*/ int dimension_; + bool dimension_to_be_lowered_ = false; }; // Print a Simplex_tree in os. diff --git a/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp index 747e7eeb..dc37375c 100644 --- a/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp @@ -109,11 +109,15 @@ BOOST_AUTO_TEST_CASE(remove_maximal_simplex) { std::cout << "st.remove_maximal_simplex({7})" << std::endl; st.remove_maximal_simplex(st.find({7})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; - BOOST_CHECK(st.dimension() == 3); + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); - st.downgrade_dimension(); + // Check dimension calls lower_upper_bound_dimension to recompute dimension + BOOST_CHECK(st.dimension() == 2); + BOOST_CHECK(st.upper_bound_dimension() == 2); + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() + << " | st_wo_seven.upper_bound_dimension()=" << st_wo_seven.upper_bound_dimension() << std::endl; std::cout << "st.dimension()=" << st.dimension() << " | st_wo_seven.dimension()=" << st_wo_seven.dimension() << std::endl; BOOST_CHECK(st == st_wo_seven); } @@ -131,116 +135,121 @@ BOOST_AUTO_TEST_CASE(auto_dimension_set) { st.insert_simplex_and_subfaces({6, 7, 8, 9}); st.insert_simplex_and_subfaces({6, 7, 8, 10}); + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); std::cout << "st.remove_maximal_simplex({6, 7, 8, 10})" << std::endl; st.remove_maximal_simplex(st.find({6, 7, 8, 10})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); std::cout << "st.remove_maximal_simplex({6, 7, 8, 9})" << std::endl; st.remove_maximal_simplex(st.find({6, 7, 8, 9})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); std::cout << "st.remove_maximal_simplex({1, 2, 3, 4})" << std::endl; st.remove_maximal_simplex(st.find({1, 2, 3, 4})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); std::cout << "st.remove_maximal_simplex({1, 2, 3, 5})" << std::endl; st.remove_maximal_simplex(st.find({1, 2, 3, 5})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; - BOOST_CHECK(st.dimension() == 3); - st.downgrade_dimension(); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 2); + std::cout << "st.dimension()=" << st.dimension() << std::endl; std::cout << "st.insert_simplex_and_subfaces({1, 2, 3, 5})" << std::endl; st.insert_simplex_and_subfaces({1, 2, 3, 5}); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); std::cout << "st.insert_simplex_and_subfaces({1, 2, 3, 4})" << std::endl; st.insert_simplex_and_subfaces({1, 2, 3, 4}); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); + std::cout << "st.remove_maximal_simplex({1, 2, 3, 5})" << std::endl; st.remove_maximal_simplex(st.find({1, 2, 3, 5})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); + std::cout << "st.remove_maximal_simplex({1, 2, 3, 4})" << std::endl; st.remove_maximal_simplex(st.find({1, 2, 3, 4})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; - BOOST_CHECK(st.dimension() == 3); - st.downgrade_dimension(); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 2); + std::cout << "st.dimension()=" << st.dimension() << std::endl; std::cout << "st.insert_simplex_and_subfaces({0, 1, 3, 4})" << std::endl; st.insert_simplex_and_subfaces({0, 1, 3, 4}); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); std::cout << "st.remove_maximal_simplex({0, 1, 3, 4})" << std::endl; st.remove_maximal_simplex(st.find({0, 1, 3, 4})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; - BOOST_CHECK(st.dimension() == 3); - st.downgrade_dimension(); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 2); + std::cout << "st.dimension()=" << st.dimension() << std::endl; std::cout << "st.insert_simplex_and_subfaces({1, 2, 3, 5})" << std::endl; st.insert_simplex_and_subfaces({1, 2, 3, 5}); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); std::cout << "st.insert_simplex_and_subfaces({1, 2, 3, 4})" << std::endl; st.insert_simplex_and_subfaces({1, 2, 3, 4}); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); // Check you can override the dimension // This is a limit test case - shall not happen st.set_dimension(1); - std::cout << "st.dimension()=" << st.dimension() << std::endl; - BOOST_CHECK(st.dimension() == 1); - st.downgrade_dimension(); - std::cout << "st.dimension()=" << st.dimension() << std::endl; - // check downgrade_dimension() is not giving the rigt answer because dimension is too low + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 1); + // check dimension() and lower_upper_bound_dimension() is not giving the right answer because dimension is too low BOOST_CHECK(st.dimension() == 1); // Check you can override the dimension // This is a limit test case - shall not happen st.set_dimension(6); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 6); + // check dimension() do not launch lower_upper_bound_dimension() BOOST_CHECK(st.dimension() == 6); - st.downgrade_dimension(); - std::cout << "st.dimension()=" << st.dimension() << std::endl; - // check downgrade_dimension() resets the correct dimension - BOOST_CHECK(st.dimension() == 3); // Reset with the correct value st.set_dimension(3); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); BOOST_CHECK(st.dimension() == 3); std::cout << "st.insert_simplex_and_subfaces({0, 1, 2, 3, 4, 5, 6})" << std::endl; st.insert_simplex_and_subfaces({0, 1, 2, 3, 4, 5, 6}); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 6); BOOST_CHECK(st.dimension() == 6); std::cout << "st.remove_maximal_simplex({0, 1, 2, 3, 4, 5, 6})" << std::endl; st.remove_maximal_simplex(st.find({0, 1, 2, 3, 4, 5, 6})); - std::cout << "st.dimension()=" << st.dimension() << std::endl; - BOOST_CHECK(st.dimension() == 6); - st.downgrade_dimension(); - std::cout << "st.dimension()=" << st.dimension() << std::endl; + std::cout << "st.upper_bound_dimension()=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 6); BOOST_CHECK(st.dimension() == 5); } @@ -336,17 +345,18 @@ BOOST_AUTO_TEST_CASE(prune_above_filtration) { Stree st_empty; simplex_is_changed = st.prune_above_filtration(0.0); + BOOST_CHECK(simplex_is_changed == true); if (simplex_is_changed) st.initialize_filtration(); // Display the Simplex_tree std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices"; - std::cout << " - dimension " << st.dimension() << std::endl; - BOOST_CHECK(st.dimension() == 3); + std::cout << " - upper_bound_dimension " << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == 3); - st.downgrade_dimension(); - std::cout << "dimension=" << st.dimension() << std::endl; BOOST_CHECK(st.dimension() == -1); + std::cout << "upper_bound_dimension=" << st.upper_bound_dimension() << std::endl; + BOOST_CHECK(st.upper_bound_dimension() == -1); BOOST_CHECK(st == st_empty); BOOST_CHECK(simplex_is_changed); diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index 177cfdad..a6d6a9f3 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -94,12 +94,12 @@ def test_insertion(): assert st.persistence(persistence_dim_max = True) == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))] assert st.__is_persistence_defined() == True - assert st.betti_numbers() == [1, 1, 0] - assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0, 0] - assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0, 0] - assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0, 0] - assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1, 0] - assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1, 0] + assert st.betti_numbers() == [1, 1] + assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0] + assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0] + assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0] + assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1] + assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1] def test_expansion(): st = SimplexTree() -- cgit v1.2.3