diff options
202 files changed, 30463 insertions, 1479 deletions
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index a00ae1b2..bd0c57ac 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,6 @@ -set (GUDHI_MAJOR_VERSION 1) -set (GUDHI_MINOR_VERSION 3) -set (GUDHI_PATCH_VERSION 1) +set (GUDHI_MAJOR_VERSION 2) +set (GUDHI_MINOR_VERSION 0) +set (GUDHI_PATCH_VERSION 0) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") diff --git a/CMakeLists.txt b/CMakeLists.txt index 1346f5d9..18cd0ca2 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -5,172 +5,88 @@ include(CMakeGUDHIVersion.txt) # Generate GUDHI official version file configure_file(GUDHIVersion.cmake.in "${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake" @ONLY) -find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread REQUIRED) - -if(NOT Boost_FOUND) - message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") +set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") +set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") +message("CMAKE_PREFIX_PATH = ${CMAKE_PREFIX_PATH}") +message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}") + +enable_testing() + +# For "make user_version" +include("${CMAKE_MODULE_PATH}/GUDHI_user_version_target.txt") +# For "make doxygen" +include("${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt") +# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH +include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt") + +if(MSVC) + # Turn off some VC++ warnings + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic") +endif() - set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") - set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") - message("CMAKE_PREFIX_PATH = ${CMAKE_PREFIX_PATH}") - message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}") - - enable_testing() - - # For "make user_version" - include(${CMAKE_MODULE_PATH}/GUDHI_user_version_target.txt) - # For "make doxygen" - include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt) - - find_package(GMP) - if(GMP_FOUND) - message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}") - INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR}) - find_package(GMPXX) - if(GMPXX_FOUND) - message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") - INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR}) - endif() - endif() - - # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten. - # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 - # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11". - # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html - # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html - # but it implies to use cmake version 3.1 at least. - find_package(CGAL) - # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL - if (CGAL_VERSION VERSION_LESS 4.4.0) - message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.") - unset(CGAL_FOUND) - endif() - if(CGAL_FOUND) - message(STATUS "CGAL version: ${CGAL_VERSION}.") - include( ${CGAL_USE_FILE} ) - - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - include_directories(BEFORE "src/common/include/gudhi_patches") - endif() - endif() - - if(MSVC) - # Turn off some VC++ warnings - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") - else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic") - endif() - - if(CMAKE_BUILD_TYPE MATCHES Debug) - message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") - else() - message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") - endif() - - set(Boost_USE_STATIC_LIBS ON) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) - - # Find TBB package for parallel sort - not mandatory, just optional. - set(TBB_FIND_QUIETLY ON) - find_package(TBB) - if (TBB_FOUND) - include(${TBB_USE_FILE}) - message("TBB found in ${TBB_LIBRARY_DIRS}") - add_definitions(-DGUDHI_USE_TBB) - endif() - - find_package(Eigen3 3.1.0) - if (EIGEN3_FOUND) - message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") - include( ${EIGEN3_USE_FILE} ) - #include_directories (BEFORE "../../include") - endif (EIGEN3_FOUND) - - # Required programs for unitary tests purpose - FIND_PROGRAM( GCOVR_PATH gcovr ) - if (GCOVR_PATH) - message("gcovr found in ${GCOVR_PATH}") - endif() - # Required programs for unitary tests purpose - FIND_PROGRAM( GPROF_PATH gprof ) - if (GPROF_PATH) - message("gprof found in ${GPROF_PATH}") - endif() - FIND_PROGRAM( DIFF_PATH diff ) - if (DIFF_PATH) - message("diff found in ${DIFF_PATH}") - endif() - - # BOOST ISSUE result_of vs C++11 - add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) - # BOOST ISSUE with Libraries name resolution under Windows - add_definitions(-DBOOST_ALL_NO_LIB) - - INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) - LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) - - message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS}) - message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) - - if (DEBUG_TRACES) - # For programs to be more verbose - message(STATUS "DEBUG_TRACES are activated") - add_definitions(-DDEBUG_TRACES) - endif() - - include_directories(src/common/include/) - include_directories(src/Alpha_complex/include/) - include_directories(src/Bitmap_cubical_complex/include/) - include_directories(src/Bottleneck_distance/include/) - include_directories(src/Contraction/include/) - include_directories(src/Hasse_complex/include/) - include_directories(src/Persistent_cohomology/include/) - include_directories(src/Rips_complex/include/) - include_directories(src/Simplex_tree/include/) - include_directories(src/Skeleton_blocker/include/) - include_directories(src/Spatial_searching/include/) - include_directories(src/Subsampling/include/) - include_directories(src/Tangential_complex/include/) - include_directories(src/Witness_complex/include/) - - add_subdirectory(src/common/example) - add_subdirectory(src/common/test) - add_subdirectory(src/Simplex_tree/test) - add_subdirectory(src/Simplex_tree/example) - add_subdirectory(src/Persistent_cohomology/test) - add_subdirectory(src/Persistent_cohomology/example) - add_subdirectory(src/Persistent_cohomology/benchmark) - add_subdirectory(src/Skeleton_blocker/test) - add_subdirectory(src/Skeleton_blocker/example) - add_subdirectory(src/Contraction/example) - add_subdirectory(src/Witness_complex/test) - add_subdirectory(src/Witness_complex/example) - add_subdirectory(src/Bitmap_cubical_complex/test) - add_subdirectory(src/Bitmap_cubical_complex/example) - add_subdirectory(src/Alpha_complex/example) - add_subdirectory(src/Alpha_complex/test) - add_subdirectory(src/Spatial_searching/example) - add_subdirectory(src/Spatial_searching/test) - add_subdirectory(src/Subsampling/example) - add_subdirectory(src/Subsampling/test) - add_subdirectory(src/Tangential_complex/example) - add_subdirectory(src/Tangential_complex/test) - add_subdirectory(src/Tangential_complex/benchmark) - add_subdirectory(src/Bottleneck_distance/example) - add_subdirectory(src/Bottleneck_distance/test) - add_subdirectory(src/Bottleneck_distance/benchmark) - add_subdirectory(src/Rips_complex/example) - add_subdirectory(src/Rips_complex/test) - - # data points generator - add_subdirectory(data/points/generator) - - # Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS - # GudhUI - add_subdirectory(src/GudhUI) - -endif() - - +if(CMAKE_BUILD_TYPE MATCHES Debug) + message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") +else() + message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") +endif() + +if (DEBUG_TRACES) + # For programs to be more verbose + message(STATUS "DEBUG_TRACES are activated") + add_definitions(-DDEBUG_TRACES) +endif() + +include_directories(src/common/include/) +include_directories(src/Alpha_complex/include/) +include_directories(src/Bitmap_cubical_complex/include/) +include_directories(src/Bottleneck_distance/include/) +include_directories(src/Contraction/include/) +include_directories(src/Hasse_complex/include/) +include_directories(src/Persistent_cohomology/include/) +include_directories(src/Rips_complex/include/) +include_directories(src/Simplex_tree/include/) +include_directories(src/Skeleton_blocker/include/) +include_directories(src/Spatial_searching/include/) +include_directories(src/Subsampling/include/) +include_directories(src/Tangential_complex/include/) +include_directories(src/Witness_complex/include/) + +add_subdirectory(src/common/example) +add_subdirectory(src/common/test) +add_subdirectory(src/Simplex_tree/test) +add_subdirectory(src/Simplex_tree/example) +add_subdirectory(src/Persistent_cohomology/test) +add_subdirectory(src/Persistent_cohomology/example) +add_subdirectory(src/Persistent_cohomology/benchmark) +add_subdirectory(src/Skeleton_blocker/test) +add_subdirectory(src/Skeleton_blocker/example) +add_subdirectory(src/Contraction/example) +add_subdirectory(src/Witness_complex/test) +add_subdirectory(src/Witness_complex/example) +add_subdirectory(src/Bitmap_cubical_complex/test) +add_subdirectory(src/Bitmap_cubical_complex/example) +add_subdirectory(src/Alpha_complex/example) +add_subdirectory(src/Alpha_complex/test) +add_subdirectory(src/Spatial_searching/example) +add_subdirectory(src/Spatial_searching/test) +add_subdirectory(src/Subsampling/example) +add_subdirectory(src/Subsampling/test) +add_subdirectory(src/Tangential_complex/example) +add_subdirectory(src/Tangential_complex/test) +add_subdirectory(src/Tangential_complex/benchmark) +add_subdirectory(src/Bottleneck_distance/example) +add_subdirectory(src/Bottleneck_distance/test) +add_subdirectory(src/Bottleneck_distance/benchmark) +add_subdirectory(src/Rips_complex/example) +add_subdirectory(src/Rips_complex/test) + +# data points generator +add_subdirectory(data/points/generator) + +add_subdirectory(src/GudhUI) + +# This variable is used by Cython CMakeLists.txt to know its path +set(GUDHI_CYTHON_PATH "src/cython") +add_subdirectory(${GUDHI_CYTHON_PATH}) diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 4940ec78..9d53a628 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -25,7 +25,8 @@ year={2014}, issn={0178-4617}, journal={Algorithmica}, doi={10.1007/s00453-014-9887-3}, -title={\href{http://dx.doi.org/10.1007/s00453-014-9887-3}{The Simplex Tree: An Efficient Data Structure for General Simplicial Complexes}}, +title={The Simplex Tree: An Efficient Data Structure for General Simplicial Complexes}, +url={http://dx.doi.org/10.1007/s00453-014-9887-3}, publisher={Springer US}, keywords={Simplicial complexes; Data structure; Computational topology; Flag complexes; Witness complexes}, author={Boissonnat, Jean-Daniel and Maria, Cl\'ement}, @@ -74,8 +75,9 @@ language={English}, author = {Jean-Daniel Boissonnat and Tamal K. Dey and Cl{\'e}ment Maria}, - title = {\href{http://dx.doi.org/10.1007/978-3-642-40450-4_59}{The Compressed Annotation Matrix: An Efficient Data Structure - for Computing Persistent Cohomology}}, + title = {The Compressed Annotation Matrix: An Efficient Data Structure for Computing Persistent Cohomology}, + url = {http://dx.doi.org/10.1007/978-3-642-40450-4_59}, + doi = {10.1007/978-3-642-40450-4_59}, booktitle = {ESA}, year = {2013}, pages = {695-706}, @@ -93,8 +95,9 @@ language={English}, @inproceedings{DBLP:conf/esa/BoissonnatM12, author = {Jean-Daniel Boissonnat and Cl{\'e}ment Maria}, - title = {\href{http://dx.doi.org/10.1007/978-3-642-33090-2_63}{The Simplex Tree: An Efficient Data Structure for General - Simplicial Complexes}}, + title = {The Simplex Tree: An Efficient Data Structure for General Simplicial Complexes}, + url = {http://dx.doi.org/10.1007/978-3-642-33090-2_63}, + doi = {10.1007/978-3-642-33090-2_63}, booktitle = {ESA}, year = {2012}, pages = {731-742}, @@ -176,7 +179,7 @@ language={English}, @article{RS62, author={J. B. Rosser and L. Schoenfeld}, title={Approximate Formulas for some Functions of Prime Numbers}, - journal= ijm, + journal= {ijm}, volume= 6, year= 1962, pages={64-94}, @@ -954,7 +957,7 @@ misc{jplex_cite, publisher={Springer New York} } -@ARTICLE{peikert2012topological, +@inbook{peikert2012topological, year={2012}, isbn={978-3-642-23174-2}, booktitle={Topological Methods in Data Analysis and Visualization II}, @@ -969,3 +972,10 @@ pages={91-106}, language={English} } +@article{de2004topological, + title={Topological estimation using witness complexes}, + author={De Silva, Vin and Carlsson, Gunnar}, + journal={Proc. Sympos. Point-Based Graphics}, + pages={157-166}, + year={2004} +} diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib index fde1d9b1..79b1ddd6 100644 --- a/biblio/how_to_cite_gudhi.bib +++ b/biblio/how_to_cite_gudhi.bib @@ -112,4 +112,13 @@ , booktitle = "{GUDHI} User and Reference Manual" , url = "http://gudhi.gforge.inria.fr/doc/latest/group__bottleneck__distance.html" , year = 2016 -}
\ No newline at end of file +} + +@incollection{gudhi:cython +, author = "Vincent Rouvreau" +, title = "Cython interface" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/cython/latest/" +, year = 2016 +} diff --git a/data/bitmap/cubicalcomplexdoc.txt b/data/bitmap/cubicalcomplexdoc.txt new file mode 100644 index 00000000..a87ad775 --- /dev/null +++ b/data/bitmap/cubicalcomplexdoc.txt @@ -0,0 +1,12 @@ +2 +3 +3 +1 +4 +6 +8 +20 +4 +7 +6 +5 diff --git a/data/bitmap/periodiccubicalcomplexdoc.txt b/data/bitmap/periodiccubicalcomplexdoc.txt new file mode 100644 index 00000000..e93cb2b3 --- /dev/null +++ b/data/bitmap/periodiccubicalcomplexdoc.txt @@ -0,0 +1,12 @@ +2 +-3 +3 +1 +4 +6 +8 +20 +4 +7 +6 +5 diff --git a/data/meshes/min_cube3D_8.off b/data/meshes/min_cube3D_8.off deleted file mode 100644 index 7398eaea..00000000 --- a/data/meshes/min_cube3D_8.off +++ /dev/null @@ -1,16 +0,0 @@ -OFF -8 6 0 --0.500000 -0.500000 0.500000 - 0.500000 -0.500000 0.500000 --0.500000 0.500000 0.500000 - 0.500000 0.500000 0.500000 --0.500000 0.500000 -0.500000 - 0.500000 0.500000 -0.500000 --0.500000 -0.500000 -0.500000 - 0.500000 -0.500000 -0.500000 -4 0 1 3 2 -4 2 3 5 4 -4 4 5 7 6 -4 6 7 1 0 -4 1 7 5 3 -4 6 0 2 4 diff --git a/data/points/README b/data/points/README deleted file mode 100644 index 943bb2ec..00000000 --- a/data/points/README +++ /dev/null @@ -1,2 +0,0 @@ -The bunny pointset comes from the Stanford Computer Graphics Laboratory. -http://graphics.stanford.edu/data/3Dscanrep/ diff --git a/data/points/SO3.COPYRIGHT b/data/points/SO3.COPYRIGHT index 36618c9c..26bbb0ad 100644 --- a/data/points/SO3.COPYRIGHT +++ b/data/points/SO3.COPYRIGHT @@ -1,6 +1,6 @@ The SO3 points clouds have been generated from the ISOI software available at this webpage : -http://www.mitchell-lab.org/rots.php +https://mitchell-lab.biochem.wisc.edu/soi/index.php This software is an implementation of the two following papers: diff --git a/data/points/bunny.COPYRIGHT b/data/points/bunny.COPYRIGHT new file mode 100644 index 00000000..310ca5b5 --- /dev/null +++ b/data/points/bunny.COPYRIGHT @@ -0,0 +1,6 @@ +The bunny pointset comes from the Stanford Computer Graphics Laboratory. +http://graphics.stanford.edu/data/3Dscanrep/ + +Please acknowledge... + +Please be sure to acknowledge the source of the bunny data set. You are welcome to use the bunny data and models for research purposes. You are also welcome to mirror or redistribute them for free. Finally, you may publish images made using these models, or the images on this web site, in a scholarly article or book - as long as credit is given to the Stanford Computer Graphics Laboratory. However, such models or images are not to be used for commercial purposes, nor should they appear in a product for sale (with the exception of scholarly journals or books), without our permission. diff --git a/data/points/generator/CMakeLists.txt b/data/points/generator/CMakeLists.txt index f559610c..9a7f7bce 100644 --- a/data/points/generator/CMakeLists.txt +++ b/data/points/generator/CMakeLists.txt @@ -1,18 +1,14 @@ cmake_minimum_required(VERSION 2.6) project(Data_points_generator) -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - if (EIGEN3_FOUND) - add_executable ( hypergenerator hypergenerator.cpp ) - target_link_libraries(hypergenerator ${Boost_SYSTEM_LIBRARY}) - add_test(hypergenerator_on_sphere_3000_10_5.0 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 3000 10 5.0) - add_test(hypergenerator_on_sphere_10000_3 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 10000 3) - add_test(hypergenerator_in_sphere_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 7000 12 10.8) - add_test(hypergenerator_in_sphere_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 50000 2) - # on cube is not available in CGAL - add_test(hypergenerator_in_cube_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 7000 12 10.8) - add_test(hypergenerator_in_cube_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 50000 3) - endif(EIGEN3_FOUND) - endif(NOT CGAL_VERSION VERSION_LESS 4.6.0) -endif(CGAL_FOUND) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + add_executable ( hypergenerator hypergenerator.cpp ) + target_link_libraries(hypergenerator ${Boost_SYSTEM_LIBRARY}) + add_test(hypergenerator_on_sphere_3000_10_5.0 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 3000 10 5.0) + add_test(hypergenerator_on_sphere_10000_3 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 10000 3) + add_test(hypergenerator_in_sphere_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 7000 12 10.8) + add_test(hypergenerator_in_sphere_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 50000 2) + # on cube is not available in CGAL + add_test(hypergenerator_in_cube_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 7000 12 10.8) + add_test(hypergenerator_in_cube_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 50000 3) +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/data/points/sphere3D_pts_on_grid.off b/data/points/sphere3D_pts_on_grid.off new file mode 100644 index 00000000..7f562559 --- /dev/null +++ b/data/points/sphere3D_pts_on_grid.off @@ -0,0 +1,17286 @@ +OFF +17284 0 0 +0.44 0.38 0.02 +0.46 0.38 0.02 +0.48 0.38 0.02 +0.5 0.38 0.02 +0.52 0.38 0.02 +0.54 0.38 0.02 +0.56 0.38 0.02 +0.42 0.4 0.02 +0.44 0.4 0.02 +0.46 0.4 0.02 +0.48 0.4 0.02 +0.5 0.4 0.02 +0.52 0.4 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+1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh index bf30f101..f999c6c4 100755 --- a/scripts/generate_version.sh +++ b/scripts/generate_version.sh @@ -66,7 +66,7 @@ do if [ -d "$ROOT_DIR/src/$package" ] && [ $package != "Bottleneck" ] then echo $package - if [ "$package" == "cmake" ] || [ "$package" == "debian" ] + if [ "$package" == "cmake" ] then # SPECIFIC FOR CMAKE MODULES cp -R $ROOT_DIR/src/$package $VERSION_DIR @@ -74,6 +74,10 @@ do then # SPECIFIC FOR GUDHI USER INTERFACE cp -R $ROOT_DIR/src/$package $VERSION_DIR + elif [ "$package" == "cython" ] + then + # SPECIFIC FOR CYTHON INTERFACE + cp -R $ROOT_DIR/src/$package $VERSION_DIR else # PACKAGE COPY if [ -d "$ROOT_DIR/src/$package$PACKAGE_INC_DIR" ] diff --git a/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h index 2b8bff94..2b8bff94 100644 --- a/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h +++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h diff --git a/src/Alpha_complex/doc/COPYRIGHT b/src/Alpha_complex/doc/COPYRIGHT new file mode 100644 index 00000000..dbad2380 --- /dev/null +++ b/src/Alpha_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are 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) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index 32bef1cd..d411e90a 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -17,13 +17,13 @@ void usage(int nbArgs, char * const progName) { int main(int argc, char **argv) { if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1)); - std::string off_file_name(argv[1]); - double alpha_square_max_value = atof(argv[2]); + std::string off_file_name {argv[1]}; + double alpha_square_max_value {atof(argv[2])}; // ---------------------------------------------------------------------------- // Init of an alpha complex from an OFF file // ---------------------------------------------------------------------------- - typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; + using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name); std::streambuf* streambufffer; diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index 491b7e6d..c19f7cc8 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -9,9 +9,9 @@ #include <vector> #include <limits> // for numeric limits -typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel; -typedef Kernel::Point_d Point; -typedef std::vector<Point> Vector_of_points; +using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<2> >; +using Point = Kernel::Point_d; +using Vector_of_points = std::vector<Point>; void usage(int nbArgs, char * const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; @@ -24,7 +24,7 @@ int main(int argc, char **argv) { if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1)); // Delaunay complex if alpha_square_max_value is not given by the user. - double alpha_square_max_value = std::numeric_limits<double>::infinity(); + double alpha_square_max_value {std::numeric_limits<double>::infinity()}; if (argc == 2) alpha_square_max_value = atof(argv[1]); diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 71a95d61..b9bcdb55 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -2,32 +2,28 @@ cmake_minimum_required(VERSION 2.6) project(Alpha_complex_examples) # need CGAL 4.7 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../.. -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - if (EIGEN3_FOUND) - add_executable ( alphapoints Alpha_complex_from_points.cpp ) - target_link_libraries(alphapoints ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) - add_executable ( alphaoffreader Alpha_complex_from_off.cpp ) - target_link_libraries(alphaoffreader ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(alphapoints ${TBB_LIBRARIES}) - target_link_libraries(alphaoffreader ${TBB_LIBRARIES}) - endif() +# cmake -DCGAL_DIR=~/workspace/CGAL-4.7 .. +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable ( alphapoints Alpha_complex_from_points.cpp ) + target_link_libraries(alphapoints ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) + add_executable ( alphaoffreader Alpha_complex_from_off.cpp ) + target_link_libraries(alphaoffreader ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(alphapoints ${TBB_LIBRARIES}) + target_link_libraries(alphaoffreader ${TBB_LIBRARIES}) + endif() - add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints) - # Do not forget to copy test files in current binary dir - file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt) - add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt) - if (DIFF_PATH) - # Do not forget to copy test results files in current binary dir - file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints) + # Do not forget to copy test files in current binary dir + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt) + add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt) + if (DIFF_PATH) + # Do not forget to copy test results files in current binary dir + file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) - add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) - endif() - endif(EIGEN3_FOUND) - endif(NOT CGAL_VERSION VERSION_LESS 4.7.0) -endif(CGAL_FOUND) + add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) + endif() +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index efc0565f..32091196 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -10,23 +10,19 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - if (EIGEN3_FOUND) - add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp ) - target_link_libraries(AlphaComplexUT ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES}) - endif() +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp ) + target_link_libraries(AlphaComplexUT ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES}) + endif() - # Do not forget to copy test files in current binary dir - file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + # Do not forget to copy test files in current binary dir + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no) + add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no) - endif(EIGEN3_FOUND) - endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) -endif(CGAL_FOUND) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Bitmap_cubical_complex/doc/COPYRIGHT b/src/Bitmap_cubical_complex/doc/COPYRIGHT new file mode 100644 index 00000000..bcd46b23 --- /dev/null +++ b/src/Bitmap_cubical_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Pawel Dlotko + +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt index 355e8d31..170081ce 100644 --- a/src/Bottleneck_distance/benchmark/CMakeLists.txt +++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt @@ -1,11 +1,9 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_benchmark) - -# requires CGAL 4.8 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../.. -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) - endif () -endif() +if (NOT CGAL_WITH_EIGEN3_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) diff --git a/src/Bottleneck_distance/doc/COPYRIGHT b/src/Bottleneck_distance/doc/COPYRIGHT new file mode 100644 index 00000000..179740a6 --- /dev/null +++ b/src/Bottleneck_distance/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): François Godi + +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 5223678d..3998fe8d 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -35,9 +35,9 @@ namespace persistence_diagram { * * \section bottleneckdefinition Definition * - * The bottleneck distance measures the similarity between two persistence diagrams. It is the shortest distance b for which there exists a perfect matching between - * the points of the two diagrams (completed with all the points on the diagonal in order to ignore cardinality mismatchs) such that - * any couple of matched points are at distance at most b. + * The bottleneck distance measures the similarity between two persistence diagrams. It is the shortest distance b for + * which there exists a perfect matching between the points of the two diagrams (completed with all the points on the + * diagonal in order to ignore cardinality mismatchs) such that any couple of matched points are at distance at most b. * * \image html perturb_pd.png On this picture, the red edges represent the matching. The bottleneck distance is the length of the longest edge. * diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index b36d0f34..b0a19f8b 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -1,22 +1,20 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) -# requires CGAL 4.8 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../.. -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) - add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) +if (NOT CGAL_WITH_EIGEN3_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_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example) + add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example) - add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance - ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3) + add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${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(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3) - endif () -endif() +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp index 6e9be97b..fd9f0858 100644 --- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp +++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp @@ -56,7 +56,7 @@ void program_options(int argc, char * argv[] , int & p , Filtration_value & min_persistence); -static inline std::pair<double, double> compute_root_square (std::pair<double, double> input) { +static inline std::pair<double, double> compute_root_square(std::pair<double, double> input) { return std::make_pair(std::sqrt(input.first), std::sqrt(input.second)); } diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index c7695112..44f4b827 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -25,6 +25,10 @@ #include <gudhi/Internal_point.h> +#ifdef GUDHI_USE_TBB +#include <tbb/parallel_sort.h> +#endif + #include <vector> #include <algorithm> #include <limits> // for numeric_limits @@ -144,7 +148,11 @@ inline std::vector<double> Persistence_graph::sorted_distances() const { for (int v_point_index = 0; v_point_index < size(); ++v_point_index) distances.push_back(distance(u_point_index, v_point_index)); } +#ifdef GUDHI_USE_TBB + tbb::parallel_sort(distances.begin(), distances.end()); +#else std::sort(distances.begin(), distances.end()); +#endif return distances; } diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index 6c8f112d..3d8e1f95 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -11,16 +11,15 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -# requires CGAL 4.8 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../.. -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - add_executable ( bottleneckUT bottleneck_unit_test.cpp ) - target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable ( bottleneckUT bottleneck_unit_test.cpp ) + target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(bottleneckUT ${TBB_LIBRARIES}) + endif(TBB_FOUND) - # Unitary tests - add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no) - endif () -endif() + # Unitary tests + add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index eb349052..4fa73662 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -9,148 +9,85 @@ enable_testing() list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/") -find_package(Boost REQUIRED COMPONENTS system filesystem program_options chrono timer date_time REQUIRED) +# For "make doxygen" +set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR}) +include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt) -if(NOT Boost_FOUND) - message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") +# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH +include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt") + +if(MSVC) + # Turn off some VC++ warnings + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic") +endif() - # For "make doxygen" - set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR}) - include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt) - - find_package(GMP) - if(GMP_FOUND) - message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}") - INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR}) - find_package(GMPXX) - if(GMPXX_FOUND) - message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") - INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR}) - endif() - endif() - - # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten. - # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 - # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11". - # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html - # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html - # but it implies to use cmake version 3.1 at least. - - # find CGAL in QUIET mode for cmake to be less verbose when CGAL is not found. - find_package(CGAL QUIET) - # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL - if (CGAL_VERSION VERSION_LESS 4.4.0 AND CGAL_FOUND) - message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.") - unset(CGAL_FOUND) - endif(CGAL_VERSION VERSION_LESS 4.4.0 AND CGAL_FOUND) - if(CGAL_FOUND) - message(STATUS "CGAL version: ${CGAL_VERSION}.") - include( ${CGAL_USE_FILE} ) - - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - include_directories(BEFORE "include/gudhi_patches") - endif() - endif() - - if(MSVC) - # Turn off some VC++ warnings - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") - else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic") - endif() - - if(CMAKE_BUILD_TYPE MATCHES Debug) - message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") - else() - message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") - endif() - - set(Boost_USE_STATIC_LIBS ON) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) - - # Find TBB package for parallel sort - not mandatory, just optional. - set(TBB_FIND_QUIETLY ON) - find_package(TBB) - if (TBB_FOUND) - include(${TBB_USE_FILE}) - message("TBB found in ${TBB_LIBRARY_DIRS}") - add_definitions(-DGUDHI_USE_TBB) - endif() - - find_package(Eigen3 3.1.0) - if (EIGEN3_FOUND) - message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") - include( ${EIGEN3_USE_FILE} ) - #include_directories (BEFORE "../../include") - endif (EIGEN3_FOUND) - - # BOOST ISSUE result_of vs C++11 - add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) - # BOOST ISSUE with Libraries name resolution under Windows - add_definitions(-DBOOST_ALL_NO_LIB) - - INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) - LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) - - if (DEBUG_TRACES) - message(STATUS "DEBUG_TRACES are activated") - # For programs to be more verbose - add_definitions(-DDEBUG_TRACES) - endif() - - #--------------------------------------------------------------------------------------- - # Gudhi compilation part - include_directories(include) - - add_subdirectory(example/common) - add_subdirectory(example/Simplex_tree) - add_subdirectory(example/Persistent_cohomology) - add_subdirectory(example/Skeleton_blocker) - add_subdirectory(example/Contraction) - add_subdirectory(example/Bitmap_cubical_complex) - add_subdirectory(example/Witness_complex) - add_subdirectory(example/Alpha_complex) - add_subdirectory(example/Rips_complex) - add_subdirectory(example/Spatial_searching) - add_subdirectory(example/Subsampling) - add_subdirectory(example/Tangential_complex) - add_subdirectory(example/Bottleneck_distance) - - # data points generator - add_subdirectory(data/points/generator) - - # Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS - # GudhUI - add_subdirectory(GudhUI) - #--------------------------------------------------------------------------------------- - - #--------------------------------------------------------------------------------------- - # GUDHIConfig.cmake - # Export the package for use from the build-tree - # (this registers the build-tree with a global CMake-registry) - export(PACKAGE GUDHI) - - message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}") - # Create the GUDHIConfig.cmake and GUDHIConfigVersion files - set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include") - configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY) - configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY) - - #--------------------------------------------------------------------------------------- - - #--------------------------------------------------------------------------------------- - # Gudhi installation part - - # Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake - install(FILES - "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" - "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" - DESTINATION share/gudhi) - - # install the include file on "make install" - install(DIRECTORY include/gudhi DESTINATION include) - #--------------------------------------------------------------------------------------- - -endif() +if(CMAKE_BUILD_TYPE MATCHES Debug) + message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") +else() + message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") +endif() + +if (DEBUG_TRACES) + message(STATUS "DEBUG_TRACES are activated") + # For programs to be more verbose + add_definitions(-DDEBUG_TRACES) +endif() + +#--------------------------------------------------------------------------------------- +# Gudhi compilation part +include_directories(include) + +add_subdirectory(example/common) +add_subdirectory(example/Simplex_tree) +add_subdirectory(example/Persistent_cohomology) +add_subdirectory(example/Skeleton_blocker) +add_subdirectory(example/Contraction) +add_subdirectory(example/Bitmap_cubical_complex) +add_subdirectory(example/Witness_complex) +add_subdirectory(example/Alpha_complex) +add_subdirectory(example/Rips_complex) +add_subdirectory(example/Spatial_searching) +add_subdirectory(example/Subsampling) +add_subdirectory(example/Tangential_complex) +add_subdirectory(example/Bottleneck_distance) + +# data points generator +add_subdirectory(data/points/generator) + +# Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS +# GudhUI +add_subdirectory(GudhUI) + +# This variable is used by Cython CMakeLists.txt to know its path +set(GUDHI_CYTHON_PATH "cython") +add_subdirectory(${GUDHI_CYTHON_PATH}) +#--------------------------------------------------------------------------------------- + +#--------------------------------------------------------------------------------------- +# GUDHIConfig.cmake +# Export the package for use from the build-tree +# (this registers the build-tree with a global CMake-registry) +export(PACKAGE GUDHI) + +message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}") +# Create the GUDHIConfig.cmake and GUDHIConfigVersion files +set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include") +configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY) +configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY) + +#--------------------------------------------------------------------------------------- + +#--------------------------------------------------------------------------------------- +# Gudhi installation part + +# Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake +install(FILES + "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" + "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" + DESTINATION share/gudhi) + +# install the include file on "make install" +install(DIRECTORY include/gudhi DESTINATION include) +#--------------------------------------------------------------------------------------- diff --git a/src/Contraction/doc/COPYRIGHT b/src/Contraction/doc/COPYRIGHT new file mode 100644 index 00000000..1de850d7 --- /dev/null +++ b/src/Contraction/doc/COPYRIGHT @@ -0,0 +1,18 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): David Salinas +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp index 4689519f..8b5a6a6c 100644 --- a/src/Contraction/example/Garland_heckbert.cpp +++ b/src/Contraction/example/Garland_heckbert.cpp @@ -35,10 +35,6 @@ #include "Garland_heckbert/Error_quadric.h" -using namespace Gudhi; -using namespace skeleton_blocker; -using namespace contraction; - struct Geometry_trait { typedef Point_d Point; }; @@ -46,7 +42,8 @@ struct Geometry_trait { /** * The vertex stored in the complex contains a quadric. */ -struct Garland_heckbert_traits : public Skeleton_blocker_simple_geometric_traits<Geometry_trait> { +struct Garland_heckbert_traits + : public Gudhi::skeleton_blocker::Skeleton_blocker_simple_geometric_traits<Geometry_trait> { public: struct Garland_heckbert_vertex : public Simple_geometric_vertex { Error_quadric<Geometry_trait::Point> quadric; @@ -54,19 +51,21 @@ struct Garland_heckbert_traits : public Skeleton_blocker_simple_geometric_traits typedef Garland_heckbert_vertex Graph_vertex; }; -typedef Skeleton_blocker_geometric_complex< Garland_heckbert_traits > Complex; -typedef Edge_profile<Complex> EdgeProfile; -typedef Skeleton_blocker_contractor<Complex> Complex_contractor; +using Complex = Gudhi::skeleton_blocker::Skeleton_blocker_geometric_complex< Garland_heckbert_traits >; +using EdgeProfile = Gudhi::contraction::Edge_profile<Complex>; +using Complex_contractor = Gudhi::contraction::Skeleton_blocker_contractor<Complex>; /** * How the new vertex is placed after an edge collapse : here it is placed at * the point minimizing the cost of the quadric. */ class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> { + Complex& complex_; + public: typedef Gudhi::contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type; - GH_placement(Complex& complex) { } + GH_placement(Complex& complex) : complex_(complex) { (void)complex_; } Placement_type operator()(const EdgeProfile& profile) const override { auto sum_quad(profile.v0().quadric); @@ -85,10 +84,12 @@ class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> { * which expresses a squared distances with triangles planes. */ class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> { + Complex& complex_; + public: typedef Gudhi::contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type; - GH_cost(Complex& complex) { } + GH_cost(Complex& complex) : complex_(complex) { (void)complex_; } Cost_type operator()(EdgeProfile const& profile, boost::optional<Point> const& new_point) const override { Cost_type res; @@ -107,8 +108,10 @@ class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> { * and we update them when contracting an edge (the quadric become the sum of both quadrics). */ class GH_visitor : public Gudhi::contraction::Contraction_visitor<EdgeProfile> { + Complex& complex_; + public: - GH_visitor(Complex& complex) { } + GH_visitor(Complex& complex) : complex_(complex) { (void)complex_; } // Compute quadrics for every vertex v // The quadric of v consists in the sum of quadric @@ -147,7 +150,7 @@ int main(int argc, char *argv[]) { typedef Complex::Vertex_handle Vertex_handle; // load the points - Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex); + Gudhi::skeleton_blocker::Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex); if (!off_reader.is_valid()) { std::cerr << "Unable to read file:" << argv[1] << std::endl; return EXIT_FAILURE; @@ -168,7 +171,7 @@ int main(int argc, char *argv[]) { Complex_contractor contractor(complex, new GH_cost(complex), new GH_placement(complex), - contraction::make_link_valid_contraction<EdgeProfile>(), + Gudhi::contraction::make_link_valid_contraction<EdgeProfile>(), new GH_visitor(complex)); std::cout << "Contract " << num_contractions << " edges" << std::endl; @@ -180,7 +183,7 @@ int main(int argc, char *argv[]) { complex.num_triangles() << " triangles." << std::endl; // write simplified complex - Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex); + Gudhi::skeleton_blocker::Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex); return EXIT_SUCCESS; } diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h index 076f1be0..e7dafaa0 100644 --- a/src/Contraction/example/Garland_heckbert/Error_quadric.h +++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h @@ -21,8 +21,8 @@ * */ -#ifndef ERROR_QUADRIC_H_ -#define ERROR_QUADRIC_H_ +#ifndef GARLAND_HECKBERT_ERROR_QUADRIC_H_ +#define GARLAND_HECKBERT_ERROR_QUADRIC_H_ #include <boost/optional/optional.hpp> @@ -179,4 +179,4 @@ template <typename Point> class Error_quadric { } }; -#endif // ERROR_QUADRIC_H_ +#endif // GARLAND_HECKBERT_ERROR_QUADRIC_H_ diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp index 7f19e239..8289b1d3 100644 --- a/src/Contraction/example/Rips_contraction.cpp +++ b/src/Contraction/example/Rips_contraction.cpp @@ -27,19 +27,15 @@ #include <boost/timer/timer.hpp> #include <iostream> -using namespace Gudhi; -using namespace skeleton_blocker; -using namespace contraction; - struct Geometry_trait { typedef Point_d Point; }; -typedef Geometry_trait::Point Point; -typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits; -typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex; -typedef Edge_profile<Complex> Profile; -typedef Skeleton_blocker_contractor<Complex> Complex_contractor; +using Complex_geometric_traits = Gudhi::skeleton_blocker::Skeleton_blocker_simple_geometric_traits<Geometry_trait>; +using Complex = Gudhi::skeleton_blocker::Skeleton_blocker_geometric_complex< Complex_geometric_traits >; +using Profile = Gudhi::contraction::Edge_profile<Complex>; +using Complex_contractor = Gudhi::contraction::Skeleton_blocker_contractor<Complex>; + template<typename ComplexType> void build_rips(ComplexType& complex, double offset) { @@ -62,7 +58,7 @@ int main(int argc, char *argv[]) { Complex complex; // load only the points - Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex, true); + Gudhi::skeleton_blocker::Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex, true); if (!off_reader.is_valid()) { std::cerr << "Unable to read file:" << argv[1] << std::endl; return EXIT_FAILURE; @@ -79,10 +75,10 @@ int main(int argc, char *argv[]) { complex.num_edges() << " edges" << std::endl; Complex_contractor contractor(complex, - new Edge_length_cost<Profile>, - contraction::make_first_vertex_placement<Profile>(), - contraction::make_link_valid_contraction<Profile>(), - contraction::make_remove_popable_blockers_visitor<Profile>()); + new Gudhi::contraction::Edge_length_cost<Profile>, + Gudhi::contraction::make_first_vertex_placement<Profile>(), + Gudhi::contraction::make_link_valid_contraction<Profile>(), + Gudhi::contraction::make_remove_popable_blockers_visitor<Profile>()); contractor.contract_edges(); std::cout << "Counting final number of simplices \n"; diff --git a/src/Doxyfile b/src/Doxyfile index a41c6d6f..d2d0a447 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 = "1.3.1" +PROJECT_NUMBER = "2.0.0" # 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 @@ -781,10 +781,10 @@ RECURSIVE = YES # run. EXCLUDE = data/ \ - example/ \ - GudhUI/ \ - cmake/ \ - debian/ \ + example/ \ + GudhUI/ \ + cmake/ \ + src/cython/ \ include/gudhi_patches/ # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index d3a52b60..ca2e47c1 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -1,11 +1,13 @@ cmake_minimum_required(VERSION 2.8) project(GudhUI) -find_package(CGAL COMPONENTS Qt5) 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.") @@ -25,7 +27,7 @@ endif() -if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND ) +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) set(CMAKE_AUTOUIC ON) diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h index b88293e9..2a18e079 100644 --- a/src/GudhUI/utils/Critical_points.h +++ b/src/GudhUI/utils/Critical_points.h @@ -105,6 +105,9 @@ template<typename SkBlComplex> class Critical_points { if (link.empty()) return 0; + Edge_contractor<Complex> contractor(link, link.num_vertices() - 1); + (void)contractor; + if (link.num_connected_components() > 1) // one than more CC -> not contractible return 0; diff --git a/src/GudhUI/utils/Is_manifold.h b/src/GudhUI/utils/Is_manifold.h index 6dd7898e..d0974463 100644 --- a/src/GudhUI/utils/Is_manifold.h +++ b/src/GudhUI/utils/Is_manifold.h @@ -76,6 +76,8 @@ template<typename SkBlComplex> class Is_manifold { bool is_k_sphere(Vertex_handle v, int k) { auto link = input_complex_.link(v); + Edge_contractor<Complex> contractor(link, link.num_vertices() - 1); + (void)contractor; return (is_sphere_simplex(link) == k); } diff --git a/src/GudhUI/utils/Vertex_collapsor.h b/src/GudhUI/utils/Vertex_collapsor.h index 3f0e7ffd..568dab2f 100644 --- a/src/GudhUI/utils/Vertex_collapsor.h +++ b/src/GudhUI/utils/Vertex_collapsor.h @@ -80,6 +80,8 @@ template<typename SkBlComplex> class Vertex_collapsor { if (link.empty()) return false; if (link.is_cone()) return true; if (link.num_connected_components() > 1) return false; + Edge_contractor<Complex> contractor(link, link.num_vertices() - 1); + (void)contractor; return (link.num_vertices() == 1); } }; diff --git a/src/Persistent_cohomology/doc/COPYRIGHT b/src/Persistent_cohomology/doc/COPYRIGHT new file mode 100644 index 00000000..34345bef --- /dev/null +++ b/src/Persistent_cohomology/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Clément Maria + +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 40dd3f93..e17e5926 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -172,6 +172,28 @@ Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> computes the persiste 2 1 0.0934117 1.00003 2 2 0.56444 1.03938 \endcode +\li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> +Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. +Here, as CGAL computes the exact values, it is slower, but it is necessary when points are on a grid +for instance. +\code $> ./exact_alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off 2 0.1 \endcode +\code Simplex_tree dim: 3 +2 0 0 inf +2 2 0.0002 0.2028 \endcode + +\li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> +Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the weighted alpha complex on points sampling from an OFF file +and a weights file. +\code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off +../../data/points/tore3D_300.weights 2 0.45 \endcode +\code Simplex_tree dim: 3 +2 -0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 \endcode + \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 38d7e9a9..a6b698c3 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -1,10 +1,6 @@ cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_examples) -# problem with Visual Studio link on Boost program_options -add_definitions( -DBOOST_ALL_NO_LIB ) -add_definitions( -DBOOST_ALL_DYN_LINK ) - add_executable(plain_homology plain_homology.cpp) target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY}) @@ -38,53 +34,73 @@ endif() add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology) add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0) -add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence ${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv -r 1.0 -d 3 -p 3 -m 0) -add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3) -add_test(rips_persistence_step_by_step_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_step_by_step ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3) -add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.off -r 0.16 -d 3 -p 3 -m 100) -add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0) -add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100) +add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence + ${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv -r 1.0 -d 3 -p 3 -m 0) +add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3) +add_test(rips_persistence_step_by_step_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_step_by_step + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3) +add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix + ${CMAKE_SOURCE_DIR}/data/points/Kl.off -r 0.16 -d 3 -p 3 -m 100) +add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file + ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0) +add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file + ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100) if(GMP_FOUND) if(GMPXX_FOUND) add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) - target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + target_link_libraries(rips_multifield_persistence + ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if (TBB_FOUND) target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) - add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71) + add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71) endif(GMPXX_FOUND) endif(GMP_FOUND) if(CGAL_FOUND) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp) + target_link_libraries(exact_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) + target_link_libraries(weighted_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) + target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) - add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45) - - - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - if (EIGEN3_FOUND) - add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - - add_executable(custom_persistence_sort custom_persistence_sort.cpp) - target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) - target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) - target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2) - add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0) - add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort) - endif(EIGEN3_FOUND) - endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) + add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence + ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45) + add_test(exact_alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/exact_alpha_complex_3d_persistence + ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45) + add_test(weighted_alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/weighted_alpha_complex_3d_persistence + ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights 2 0.45) + + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) + target_link_libraries(alpha_complex_persistence + ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) + target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + + add_executable(custom_persistence_sort custom_persistence_sort.cpp) + target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence + ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2) + add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence + ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0) + add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) endif(CGAL_FOUND) diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h new file mode 100644 index 00000000..7865e4ec --- /dev/null +++ b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h @@ -0,0 +1,76 @@ +/* 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) 2014 INRIA Saclay (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef ALPHA_COMPLEX_3D_HELPER_H_ +#define ALPHA_COMPLEX_3D_HELPER_H_ + +template<class Vertex_list, class Cell_handle> +Vertex_list from_cell(const Cell_handle& ch) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { +#ifdef DEBUG_TRACES + std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(ch->vertex(i)); + } + return the_list; +} + +template<class Vertex_list, class Facet> +Vertex_list from_facet(const Facet& fct) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if (fct.second != i) { +#ifdef DEBUG_TRACES + std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(fct.first->vertex(i)); + } + } + return the_list; +} + +template<class Vertex_list, class Edge_3> +Vertex_list from_edge(const Edge_3& edg) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if ((edg.second == i) || (edg.third == i)) { +#ifdef DEBUG_TRACES + std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(edg.first->vertex(i)); + } + } + return the_list; +} + +template<class Vertex_list, class Vertex_handle> +Vertex_list from_vertex(const Vertex_handle& vh) { + Vertex_list the_list; +#ifdef DEBUG_TRACES + std::cout << "from vertex=" << vh->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(vh); + return the_list; +} + +#endif // ALPHA_COMPLEX_3D_HELPER_H_ diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index 978dc942..fd227b82 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -20,10 +20,11 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include <boost/variant.hpp> + #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_3D_off_io.h> -#include <boost/variant.hpp> #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> @@ -39,85 +40,42 @@ #include <list> #include <vector> +#include "alpha_complex_3d_helper.h" + // Alpha_shape_3 templates type definitions -typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; -typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb; -typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb; -typedef CGAL::Triangulation_data_structure_3<Vb, Fb> Tds; -typedef CGAL::Delaunay_triangulation_3<Kernel, Tds> Triangulation_3; -typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3; +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel>; +using Fb = CGAL::Alpha_shape_cell_base_3<Kernel>; +using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>; +using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>; +using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>; // From file type definition -typedef Kernel::Point_3 Point_3; +using Point_3 = Kernel::Point_3; // filtration with alpha values needed type definition -typedef Alpha_shape_3::FT Alpha_value_type; -typedef CGAL::Object Object; -typedef CGAL::Dispatch_output_iterator< -CGAL::cpp11::tuple<Object, Alpha_value_type>, -CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, - std::back_insert_iterator< std::vector<Alpha_value_type> > > > Dispatch; -typedef Alpha_shape_3::Cell_handle Cell_handle; -typedef Alpha_shape_3::Facet Facet; -typedef Alpha_shape_3::Edge Edge_3; -typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list; +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple<Object, Alpha_value_type>, + CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, + std::back_insert_iterator< std::vector<Alpha_value_type> > > >; +using Cell_handle = Alpha_shape_3::Cell_handle; +using Facet = Alpha_shape_3::Facet; +using Edge_3 = Alpha_shape_3::Edge; +using Vertex_handle = Alpha_shape_3::Vertex_handle; +using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>; // gudhi type definition -typedef Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence> ST; -typedef ST::Filtration_value Filtration_value; -typedef ST::Vertex_handle Simplex_tree_vertex; -typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map; -typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair; -typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; -typedef Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp > PCOH; - -Vertex_list from(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -Vertex_list from(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -Vertex_list from(const Edge_3& edg) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if ((edg.second == i) || (edg.third == i)) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - } - return the_list; -} - -Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - -void usage(char * const progName) { +using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >; +using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(const std::string& progName) { std::cerr << "Usage: " << progName << " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; exit(-1); @@ -185,30 +143,29 @@ int main(int argc, char * const argv[]) { for (auto object_iterator : the_objects) { // Retrieve Alpha shape vertex list from object if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { - vertex_list = from(*cell); + vertex_list = from_cell<Vertex_list, Cell_handle>(*cell); count_cells++; if (dim_max < 3) { // Cell is of dim 3 dim_max = 3; } } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { - vertex_list = from(*facet); + vertex_list = from_facet<Vertex_list, Facet>(*facet); count_facets++; if (dim_max < 2) { // Facet is of dim 2 dim_max = 2; } } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { - vertex_list = from(*edge); + vertex_list = from_edge<Vertex_list, Edge_3>(*edge); count_edges++; if (dim_max < 1) { // Edge_3 is of dim 1 dim_max = 1; } - } else if (const Alpha_shape_3::Vertex_handle * vertex = - CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) { + } else if (const Vertex_handle * vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) { count_vertices++; - vertex_list = from(*vertex); + vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex); } // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex Simplex_tree_vector_vertex the_simplex_tree; diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..8a335075 --- /dev/null +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -0,0 +1,245 @@ +/* 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) 2014 INRIA Saclay (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <boost/variant.hpp> + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_3D_off_io.h> + +#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> +#include <CGAL/Delaunay_triangulation_3.h> +#include <CGAL/Alpha_shape_3.h> +#include <CGAL/iterator.h> + +#include <fstream> +#include <cmath> +#include <string> +#include <tuple> +#include <map> +#include <utility> +#include <list> +#include <vector> + +#include "alpha_complex_3d_helper.h" + +// Alpha_shape_3 templates type definitions +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Exact_tag = CGAL::Tag_true; +using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel, CGAL::Default, Exact_tag>; +using Fb = CGAL::Alpha_shape_cell_base_3<Kernel, CGAL::Default, Exact_tag>; +using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>; +using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>; +using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3, Exact_tag>; + +// From file type definition +using Point_3 = Kernel::Point_3; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple<Object, Alpha_value_type>, + CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, + std::back_insert_iterator< std::vector<Alpha_value_type> > > >; +using Cell_handle = Alpha_shape_3::Cell_handle; +using Facet = Alpha_shape_3::Facet; +using Edge_3 = Alpha_shape_3::Edge; +using Vertex_handle = Alpha_shape_3::Vertex_handle; +using Vertex_list = std::list<Vertex_handle>; + +// gudhi type definition +using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >; +using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << + " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[2]); + + Filtration_value min_persistence = 0.0; + int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); + if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { + std::cerr << "Error: " << argv[3] << " is not correct\n"; + usage(argv[0]); + } + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector<Point_3> lp = off_reader.get_point_cloud(); + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. + Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES + + // filtration with alpha values from alpha shape + std::vector<Object> the_objects; + std::vector<Alpha_value_type> the_alpha_values; + + Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { + vertex_list = from_cell<Vertex_list, Cell_handle>(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { + vertex_list = from_facet<Vertex_list, Facet>(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { + vertex_list = from_edge<Vertex_list, Edge_3>(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Vertex_handle * vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + // you can also use the_alpha_value_iterator->exact() + Filtration_value filtr = /*std::sqrt*/CGAL::to_double(the_alpha_value_iterator->exact()); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + 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; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + 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 + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + PCOH pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} 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 dbc42706..8928cfc2 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -20,10 +20,11 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include <boost/variant.hpp> + #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_3D_off_io.h> -#include <boost/variant.hpp> #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h> @@ -41,6 +42,8 @@ #include <vector> #include <cstdlib> +#include "alpha_complex_3d_helper.h" + // Traits using K = CGAL::Exact_predicates_inexact_constructions_kernel; using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>; @@ -67,6 +70,7 @@ using Dispatch = CGAL::Dispatch_output_iterator< using Cell_handle = Alpha_shape_3::Cell_handle; using Facet = Alpha_shape_3::Facet; using Edge_3 = Alpha_shape_3::Edge; +using Vertex_handle = Alpha_shape_3::Vertex_handle; using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>; // gudhi type definition @@ -79,52 +83,6 @@ using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; -Vertex_list from(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -Vertex_list from(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -Vertex_list from(const Edge_3& edg) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if ((edg.second == i) || (edg.third == i)) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - } - return the_list; -} - -Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - void usage(char * const progName) { std::cerr << "Usage: " << progName << " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; @@ -203,21 +161,21 @@ int main(int argc, char * const argv[]) { for (auto object_iterator : the_objects) { // Retrieve Alpha shape vertex list from object if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { - vertex_list = from(*cell); + vertex_list = from_cell<Vertex_list, Cell_handle>(*cell); count_cells++; if (dim_max < 3) { // Cell is of dim 3 dim_max = 3; } } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { - vertex_list = from(*facet); + vertex_list = from_facet<Vertex_list, Facet>(*facet); count_facets++; if (dim_max < 2) { // Facet is of dim 2 dim_max = 2; } } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { - vertex_list = from(*edge); + vertex_list = from_edge<Vertex_list, Edge_3>(*edge); count_edges++; if (dim_max < 1) { // Edge_3 is of dim 1 @@ -226,7 +184,7 @@ int main(int argc, char * const argv[]) { } else if (const Alpha_shape_3::Vertex_handle * vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) { count_vertices++; - vertex_list = from(*vertex); + vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex); } // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex Simplex_tree_vector_vertex the_simplex_tree; diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp index ae82c817..50f692f2 100644 --- a/src/Persistent_cohomology/example/plain_homology.cpp +++ b/src/Persistent_cohomology/example/plain_homology.cpp @@ -27,13 +27,11 @@ #include <vector> #include <cstdint> // for std::uint8_t -using namespace Gudhi; - /* We could perfectly well use the default Simplex_tree<> (which uses * Simplex_tree_options_full_featured), the following simply demonstrates * how to save on storage by not storing a filtration value. */ -struct MyOptions : Simplex_tree_options_full_featured { +struct MyOptions : Gudhi::Simplex_tree_options_full_featured { // Implicitly use 0 as filtration value for all simplices static const bool store_filtration = false; // The persistence algorithm needs this @@ -43,7 +41,10 @@ struct MyOptions : Simplex_tree_options_full_featured { // Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key typedef std::uint8_t Simplex_key; }; -typedef Simplex_tree<MyOptions> ST; + +using ST = Gudhi::Simplex_tree<MyOptions>; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Field_Zp>; int main() { ST st; @@ -70,7 +71,7 @@ int main() { st.initialize_filtration(); // Class for homology computation - persistent_cohomology::Persistent_cohomology<ST, persistent_cohomology::Field_Zp> pcoh(st); + Persistent_cohomology pcoh(st); // Initialize the coefficient field Z/2Z for homology pcoh.init_coefficients(2); diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..34b90933 --- /dev/null +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -0,0 +1,263 @@ +/* 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) 2014 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 <http://www.gnu.org/licenses/>. + */ + +#include <boost/variant.hpp> + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_3D_off_io.h> + +#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> +#include <CGAL/Regular_triangulation_euclidean_traits_3.h> +#include <CGAL/Regular_triangulation_3.h> +#include <CGAL/Alpha_shape_3.h> +#include <CGAL/iterator.h> + +#include <fstream> +#include <cmath> +#include <string> +#include <tuple> +#include <map> +#include <utility> +#include <list> +#include <vector> +#include <cstdlib> + +#include "alpha_complex_3d_helper.h" + +// Traits +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>; +using Vb = CGAL::Alpha_shape_vertex_base_3<Gt>; +using Fb = CGAL::Alpha_shape_cell_base_3<Gt>; +using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>; +using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>; +using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>; + +// From file type definition +using Point_3 = Gt::Bare_point; +using Weighted_point_3 = Gt::Weighted_point; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = CGAL::Dispatch_output_iterator< + CGAL::cpp11::tuple<Object, Alpha_value_type>, + CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, + std::back_insert_iterator< std::vector<Alpha_value_type> > > >; +using Cell_handle = Alpha_shape_3::Cell_handle; +using Facet = Alpha_shape_3::Facet; +using Edge_3 = Alpha_shape_3::Edge; +using Vertex_handle = Alpha_shape_3::Vertex_handle; +using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>; + +// gudhi type definition +using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >; +using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; +using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< + ST, Gudhi::persistent_cohomology::Field_Zp >; + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << + " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 5) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[3]); + Filtration_value min_persistence = strtof(argv[4], nullptr); + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << offInputFile << std::endl; + usage(argv[0]); + } + + // Retrieve the triangulation + std::vector<Point_3> lp = off_reader.get_point_cloud(); + + // Read weights information from file + std::ifstream weights_ifstr(argv[2]); + std::vector<Weighted_point_3> wp; + if (weights_ifstr.good()) { + double weight = 0.0; + std::size_t index = 0; + // Attempt read the weight in a double format, return false if it fails + while ((weights_ifstr >> weight) && (index < lp.size())) { + wp.push_back(Weighted_point_3(lp[index], weight)); + index++; + } + if (index != lp.size()) { + std::cerr << "Bad number of weights in file " << argv[2] << std::endl; + usage(argv[0]); + } + } else { + std::cerr << "Unable to read file " << argv[2] << std::endl; + usage(argv[0]); + } + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. + Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES + + // filtration with alpha values from alpha shape + std::vector<Object> the_objects; + std::vector<Alpha_value_type> the_alpha_values; + + Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { + vertex_list = from_cell<Vertex_list, Cell_handle>(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { + vertex_list = from_facet<Vertex_list, Facet>(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { + vertex_list = from_edge<Vertex_list, Edge_3>(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + 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; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + 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 + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree, true); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index b3339b7d..672fda48 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -603,7 +603,7 @@ class Persistent_cohomology { */ std::vector<int> betti_numbers() const { // Init Betti numbers vector with zeros until Simplicial complex dimension - std::vector<int> betti_numbers(cpx_->dimension(), 0); + std::vector<int> betti_numbers(dim_max_, 0); for (auto pair : persistent_pairs_) { // Count never ended persistence intervals @@ -642,8 +642,7 @@ class Persistent_cohomology { */ std::vector<int> persistent_betti_numbers(Filtration_value from, Filtration_value to) const { // Init Betti numbers vector with zeros until Simplicial complex dimension - std::vector<int> betti_numbers(cpx_->dimension(), 0); - + std::vector<int> betti_numbers(dim_max_, 0); for (auto pair : persistent_pairs_) { // Count persistence intervals that covers the given interval // null_simplex test : if the function is called with to=+infinity, we still get something useful. And it will diff --git a/src/Rips_complex/concept/Simplicial_complex_for_rips.h b/src/Rips_complex/concept/SimplicialComplexForRips.h index 7dab0615..7dab0615 100644 --- a/src/Rips_complex/concept/Simplicial_complex_for_rips.h +++ b/src/Rips_complex/concept/SimplicialComplexForRips.h diff --git a/src/Rips_complex/doc/COPYRIGHT b/src/Rips_complex/doc/COPYRIGHT new file mode 100644 index 00000000..594b7d03 --- /dev/null +++ b/src/Rips_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau + +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. 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 ef3a9d13..7ae8126f 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 @@ -1,5 +1,5 @@ #include <gudhi/Rips_complex.h> -// to construct Rips_complex from a OFF file of points +// to construct Rips_complex from a csv file representing a distance matrix #include <gudhi/reader_utils.h> #include <gudhi/Simplex_tree.h> #include <gudhi/distance_functions.h> diff --git a/src/Simplex_tree/doc/COPYRIGHT b/src/Simplex_tree/doc/COPYRIGHT new file mode 100644 index 00000000..34345bef --- /dev/null +++ b/src/Simplex_tree/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Clément Maria + +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp index 7e48aaaf..ad99df23 100644 --- a/src/Simplex_tree/example/mini_simplex_tree.cpp +++ b/src/Simplex_tree/example/mini_simplex_tree.cpp @@ -24,19 +24,18 @@ #include <iostream> #include <initializer_list> -using namespace Gudhi; - -struct MyOptions : Simplex_tree_options_full_featured { +struct MyOptions : Gudhi::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; }; -typedef Simplex_tree<MyOptions> ST; + +using ST = Gudhi::Simplex_tree<MyOptions>; // Dictionary should be private, but for now this is the easiest way. -static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Simplex_tree<>::Dictionary::value_type), +static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Gudhi::Simplex_tree<>::Dictionary::value_type), "Not storing the filtration and key should save some space"); int main() { diff --git a/src/Skeleton_blocker/doc/COPYRIGHT b/src/Skeleton_blocker/doc/COPYRIGHT new file mode 100644 index 00000000..1de850d7 --- /dev/null +++ b/src/Skeleton_blocker/doc/COPYRIGHT @@ -0,0 +1,18 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): David Salinas +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Spatial_searching/test/CMakeLists.txt b/src/Spatial_searching/test/CMakeLists.txt index 2c685c72..bdc95e4a 100644 --- a/src/Spatial_searching/test/CMakeLists.txt +++ b/src/Spatial_searching/test/CMakeLists.txt @@ -10,16 +10,12 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - if (EIGEN3_FOUND) - add_executable( Spatial_searching_test_Kd_tree_search test_Kd_tree_search.cpp ) - target_link_libraries(Spatial_searching_test_Kd_tree_search - ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable( Spatial_searching_test_Kd_tree_search test_Kd_tree_search.cpp ) + target_link_libraries(Spatial_searching_test_Kd_tree_search + ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - add_test(Spatial_searching_test_Kd_tree_search ${CMAKE_CURRENT_BINARY_DIR}/Spatial_searching_test_Kd_tree_search - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Spatial_searching_UT.xml --log_level=test_suite --report_level=no) - endif() - endif () -endif() + add_test(Spatial_searching_test_Kd_tree_search ${CMAKE_CURRENT_BINARY_DIR}/Spatial_searching_test_Kd_tree_search + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Spatial_searching_UT.xml --log_level=test_suite --report_level=no) +endif () diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index 0fd3335c..bb043297 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -1,21 +1,17 @@ cmake_minimum_required(VERSION 2.6) project(Subsampling_examples) -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - if (EIGEN3_FOUND) - add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp) - add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp) - add_executable(Subsampling_example_custom_kernel example_custom_kernel.cpp) - add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp) - target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY}) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp) + add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp) + add_executable(Subsampling_example_custom_kernel example_custom_kernel.cpp) + add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp) + target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY}) - add_test(Subsampling_example_pick_n_random_points - ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_pick_n_random_points) - add_test(Subsampling_example_choose_n_farthest_points - ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_choose_n_farthest_points) - add_test(Subsampling_example_sparsify_point_set - ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_sparsify_point_set) - endif() - endif () -endif() + add_test(Subsampling_example_pick_n_random_points + ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_pick_n_random_points) + add_test(Subsampling_example_choose_n_farthest_points + ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_choose_n_farthest_points) + add_test(Subsampling_example_sparsify_point_set + ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_sparsify_point_set) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Subsampling/test/CMakeLists.txt b/src/Subsampling/test/CMakeLists.txt index 3a2fb649..5517fe9d 100644 --- a/src/Subsampling/test/CMakeLists.txt +++ b/src/Subsampling/test/CMakeLists.txt @@ -10,29 +10,25 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - if (EIGEN3_FOUND) - add_executable( Subsampling_test_pick_n_random_points test_pick_n_random_points.cpp ) - target_link_libraries(Subsampling_test_pick_n_random_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable( Subsampling_test_pick_n_random_points test_pick_n_random_points.cpp ) + target_link_libraries(Subsampling_test_pick_n_random_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - add_executable( Subsampling_test_choose_n_farthest_points test_choose_n_farthest_points.cpp ) - target_link_libraries(Subsampling_test_choose_n_farthest_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + add_executable( Subsampling_test_choose_n_farthest_points test_choose_n_farthest_points.cpp ) + target_link_libraries(Subsampling_test_choose_n_farthest_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp) - target_link_libraries(Subsampling_test_sparsify_point_set ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp) + target_link_libraries(Subsampling_test_sparsify_point_set ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - add_test(Subsampling_test_pick_n_random_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_pick_n_random_points - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_pick_n_random_points_UT.xml --log_level=test_suite --report_level=no) + add_test(Subsampling_test_pick_n_random_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_pick_n_random_points + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_pick_n_random_points_UT.xml --log_level=test_suite --report_level=no) - add_test(Subsampling_test_choose_n_farthest_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_choose_n_farthest_points - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_choose_n_farthest_points_UT.xml --log_level=test_suite --report_level=no) + add_test(Subsampling_test_choose_n_farthest_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_choose_n_farthest_points + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_choose_n_farthest_points_UT.xml --log_level=test_suite --report_level=no) - add_test(Subsampling_test_sparsify_point_set ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_sparsify_point_set - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_sparsify_point_set_UT.xml --log_level=test_suite --report_level=no) - endif() - endif () -endif() + add_test(Subsampling_test_sparsify_point_set ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_sparsify_point_set + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_sparsify_point_set_UT.xml --log_level=test_suite --report_level=no) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt index 788c2b4d..ef772be8 100644 --- a/src/Tangential_complex/benchmark/CMakeLists.txt +++ b/src/Tangential_complex/benchmark/CMakeLists.txt @@ -1,17 +1,11 @@ cmake_minimum_required(VERSION 2.6) project(Tangential_complex_benchmark) -# need CGAL 4.8 -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - if (EIGEN3_FOUND) - add_executable(Tangential_complex_benchmark benchmark_tc.cpp) - target_link_libraries(Tangential_complex_benchmark - ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES}) - endif(TBB_FOUND) - endif(EIGEN3_FOUND) - endif (NOT CGAL_VERSION VERSION_LESS 4.8.0) -endif(CGAL_FOUND) - +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable(Tangential_complex_benchmark benchmark_tc.cpp) + target_link_libraries(Tangential_complex_benchmark + ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES}) + endif(TBB_FOUND) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/doc/COPYRIGHT b/src/Tangential_complex/doc/COPYRIGHT new file mode 100644 index 00000000..c4df0f64 --- /dev/null +++ b/src/Tangential_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Clement Jamin + +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index a75ccd5b..47a56e3b 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -1,23 +1,19 @@ cmake_minimum_required(VERSION 2.6) project(Tangential_complex_examples) -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - if (EIGEN3_FOUND) - add_executable( Tangential_complex_example_basic example_basic.cpp ) - target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) - add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) - target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) - target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) - endif(TBB_FOUND) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable( Tangential_complex_example_basic example_basic.cpp ) + target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) + add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) + target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) + target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) + endif(TBB_FOUND) - add_test(Tangential_complex_example_basic - ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_basic) + add_test(Tangential_complex_example_basic + ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_basic) - add_test(Tangential_complex_example_with_perturb - ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb) - endif(EIGEN3_FOUND) - endif(NOT CGAL_VERSION VERSION_LESS 4.8.0) -endif(CGAL_FOUND) + add_test(Tangential_complex_example_with_perturb + ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb) +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt index 075028c8..b2bf5dd7 100644 --- a/src/Tangential_complex/test/CMakeLists.txt +++ b/src/Tangential_complex/test/CMakeLists.txt @@ -10,22 +10,14 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - if (EIGEN3_FOUND) - message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") - include( ${EIGEN3_USE_FILE} ) - include_directories (BEFORE "../../include") +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable( Tangential_complex_test_TC test_tangential_complex.cpp ) + target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES}) + endif() + add_test(Tangential_complex_test_TC ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_test_TC + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Tangential_complex_UT.xml --log_level=test_suite --report_level=no) - add_executable( Tangential_complex_test_TC test_tangential_complex.cpp ) - target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES}) - endif() - add_test(Tangential_complex_test_TC ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_test_TC - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Tangential_complex_UT.xml --log_level=test_suite --report_level=no) - - endif() - endif () -endif()
\ No newline at end of file +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Witness_complex/concept/Simplicial_complex_for_witness.h b/src/Witness_complex/concept/SimplicialComplexForWitness.h index caaf0db6..d78cc83f 100644 --- a/src/Witness_complex/concept/Simplicial_complex_for_witness.h +++ b/src/Witness_complex/concept/SimplicialComplexForWitness.h @@ -27,57 +27,70 @@ namespace Gudhi { namespace witness_complex { -/** \brief The concept Simplicial_Complex describes the requirements +/** \brief The concept SimplicialComplexForWitness describes the requirements * for a type to implement a simplicial complex, - * used for example to build a 'Witness_complex'. + * used for example to build a Witness_complex or Strong_witness_complex. */ struct SimplicialComplexForWitness { /** Handle to specify a simplex. */ typedef unspecified Simplex_handle; - /** Handle to specify a vertex. Must be a non-negative integer. */ - typedef unspecified Vertex_handle; + // /** Handle to specify a vertex. Must be a non-negative integer. */ + // typedef unspecified Vertex_handle; - /** Returns a Simplex_hanlde that is different from all simplex handles + /** \brief Returns a Simplex_hanlde that is different from all simplex handles * of the simplices. */ Simplex_handle null_simplex(); - /** \brief Iterator over the simplices of the complex, - * in an arbitrary order. - * - * 'value_type' must be 'Simplex_handle'.*/ - typedef unspecified Complex_simplex_range; - - /** - * \brief Returns a range over all the simplices of a - * complex. + /** Returns the number of vertices in the simplicial complex */ - Complex_simplex_range complex_simplex_range(); - - /** \brief Iterator over vertices of a simplex. - * - * 'value type' must be 'Vertex_handle'.*/ - typedef unspecified Simplex_vertex_range; - - /** \brief Returns a range over vertices of a given - * simplex. */ - Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex); - + std::size_t num_vertices(); + /** \brief Return type of an insertion of a simplex */ typedef unspecified Insertion_result_type; /** \brief Inserts a simplex with vertices from a given range * 'vertex_range' in the simplicial complex. + * The function is only used in Witness_complex class + * and by construction, it is not necessary to check if + * the faces are in the simplicial complex before insertion. + * The simplex is given the filtration value 'filtration'. + * Filtration_value should be convertible from double. + * The return type is not used. * */ template< typedef Input_vertex_range > - Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range); + Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range, Filtration_value filtration); + /** \brief Inserts a simplex and all its faces + * with vertices from a given range + * 'vertex_range' in the simplicial complex. + * The function is only used in Strong_witness_complex class. + * All inserted simplices are given the filtration + * value 'filtration'. + * Filtration_value should be convertible from double. + * The return type is not used. + */ + + template< typedef Input_vertex_range, + typedef Filtration_value> + Insertion_result_type insert_simplex_and_subfaces(Input_vertex_range const & vertex_range, Filtration_value filtration); + /** \brief Finds a simplex with vertices given by a range * * If a simplex exists, its Simplex_handle is returned. * Otherwise null_simplex() is returned. */ template< typedef Input_vertex_range > Simplex_handle find(Input_vertex_range const & vertex_range); + + /** \brief Sets the dimension of the simplicial complex to + * 'dimension'. + */ + void set_dimension(int dimension); + + /** \brief Returns the filtration of the simplex given by + * the simplex handle 'sh'. + */ + double filtration(Simplex_handle sh); }; } // namespace witness_complex diff --git a/src/Witness_complex/doc/COPYRIGHT b/src/Witness_complex/doc/COPYRIGHT new file mode 100644 index 00000000..7d032c87 --- /dev/null +++ b/src/Witness_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Siargey Kachanovich + +Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index 60dfd27b..171a185f 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -8,31 +8,106 @@ \image html "Witness_complex_representation.png" "Witness complex representation" - \section Definitions + \section witnessdefinitions Definitions - Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$: + Witness complex is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$: \li \f$W\f$ set of **witnesses** and - \li \f$L \subseteq W\f$ set of **landmarks**. + \li \f$L\f$ set of **landmarks**. - The simplices are based on landmarks - and a simplex belongs to the witness complex if and only if it is witnessed, that is: + Even though often the set of landmarks \f$L\f$ is a subset of the set of witnesses \f$ W\f$, it is not a requirement for the current implementation. - \f$ \sigma \subset L \f$ is witnessed if there exists a point \f$w \in W\f$ such that - w is closer to the vertices of \f$ \sigma \f$ than other points in \f$ L \f$ and all of its faces are witnessed as well. - - The data structure is described in \cite boissonnatmariasimplextreealgorithmica . + Landmarks are the vertices of the simplicial complex + and witnesses help to decide on which simplices are inserted via a predicate "is witnessed". - \section Implementation + De Silva and Carlsson in their paper \cite de2004topological differentiate **weak witnessing** and **strong witnessing**: - The principal class of this module is Gudhi::Witness_complex. + - *weak*: \f$ \sigma \subset L \f$ is witnessed by \f$ w \in W\f$ if \f$ \forall l \in \sigma,\ \forall l' \in \mathbf{L \setminus \sigma},\ d(w,l) \leq d(w,l') \f$ + - *strong*: \f$ \sigma \subset L \f$ is witnessed by \f$ w \in W\f$ if \f$ \forall l \in \sigma,\ \forall l' \in \mathbf{L},\ d(w,l) \leq d(w,l') \f$ - In both cases, the constructor for this class takes a {witness}x{closest_landmarks} table, where each row represents a witness and consists of landmarks sorted by distance to this witness. - This table can be constructed by two additional classes Landmark_choice_by_furthest_point and Landmark_choice_by_random_point also included in the module. + where \f$ d(.,.) \f$ is a distance function. - *\image html "bench_Cy8.png" "Running time as function on number of landmarks" width=10cm - *\image html "bench_sphere.png" "Running time as function on number of witnesses for |L|=300" width=10cm + Both definitions can be relaxed by a real value \f$\alpha\f$: + + - *weak*: \f$ \sigma \subset L \f$ is \f$\alpha\f$-witnessed by \f$ w \in W\f$ if \f$ \forall l \in \sigma,\ \forall l' \in \mathbf{L \setminus \sigma},\ d(w,l)^2 \leq d(w,l')^2 + \alpha^2 \f$ + - *strong*: \f$ \sigma \subset L \f$ is \f$\alpha\f$-witnessed by \f$ w \in W\f$ if \f$ \forall l \in \sigma,\ \forall l' \in \mathbf{L},\ d(w,l)^2 \leq d(w,l')^2 + \alpha^2 \f$ + + which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and **strong relaxed witness complex** respectively. + + \image html "swit.svg" "Strongly witnessed simplex" + + In particular case of 0-relaxation, weak complex corresponds to **witness complex** introduced in \cite de2004topological, whereas 0-relaxed strong witness complex consists of just vertices and is not very interesting. + Hence for small relaxation weak version is preferable. + However, to capture the homotopy type (for example using Gudhi::persistent_cohomology::Persistent_cohomology) it is often necessary to work with higher filtration values. In this case strong relaxed witness complex is faster to compute and offers similar results. + + \section witnessimplementation Implementation + The two complexes described above are implemented in the corresponding classes + - Gudhi::witness_complex::Witness_complex + - Gudhi::witness_complex::Euclidean_witness_complex + - Gudhi::witness_complex::Strong_witness_complex + - Gudhi::witness_complex::Euclidean_strong_witness_complex + + The construction of the Euclidean versions of complexes follow the same scheme: + 1. Construct a search tree on landmarks (for that Gudhi::spatial_searching::Kd_tree_search is used internally). + 2. Construct lists of nearest landmarks for each witness (special structure Gudhi::witness_complex::Active_witness is used internally). + 3. Construct the witness complex for nearest landmark lists. + + In the non-Euclidean classes, the lists of nearest landmarks are supposed to be given as input. + + The constructors take on the steps 1 and 2, while the function 'create_complex' executes the step 3. + + \section witnessexample1 Example 1: Constructing weak relaxed witness complex from an off file + + Let's start with a simple example, which reads an off point file and computes a weak witness complex. + + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{.cpp} + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Euclidean_witness_complex.h> +#include <gudhi/pick_n_random_points.h> +#include <gudhi/Points_off_io.h> + +#include <CGAL/Epick_d.h> + +#include <string> +#include <vector> + +typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K; +typedef typename K::Point_d Point_d; +typedef typename Gudhi::witness_complex::Euclidean_witness_complex<K> Witness_complex; +typedef std::vector< Vertex_handle > typeVectorVertex; +typedef std::vector< Point_d > Point_vector; + +int main(int argc, char * const argv[]) { + std::string file_name = argv[1]; + int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); + double alpha2 = atof(argv[3]); + Gudhi::Simplex_tree<> simplex_tree; + + // Read the point file + Point_vector point_vector, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + point_vector = Point_vector(off_reader.get_point_cloud()); + + // Choose landmarks + Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + Witness_complex witness_complex(landmarks, + point_vector); + + witness_complex.create_complex(simplex_tree, alpha2, lim_dim); +} + + + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + \section witnessexample2 Example2: Computing persistence using strong relaxed witness complex + + Here is an example of constructing a strong witness complex filtration and computing persistence on it: + + \include Witness_complex/example_strong_witness_persistence.cpp \copyright GNU General Public License v3. diff --git a/src/Witness_complex/doc/Witness_complex_representation.ipe b/src/Witness_complex/doc/Witness_complex_representation.ipe new file mode 100644 index 00000000..f9c45d5d --- /dev/null +++ b/src/Witness_complex/doc/Witness_complex_representation.ipe @@ -0,0 +1,280 @@ +<?xml version="1.0"?> +<!DOCTYPE ipe SYSTEM "ipe.dtd"> +<ipe version="70107" creator="Ipe 7.1.10"> +<info created="D:20161010162425" modified="D:20161010162828"/> +<ipestyle name="basic"> +<symbol name="arrow/arc(spx)"> +<path stroke="sym-stroke" fill="sym-stroke" pen="sym-pen"> +0 0 m +-1 0.333 l +-1 -0.333 l +h +</path> +</symbol> +<symbol name="arrow/farc(spx)"> +<path stroke="sym-stroke" fill="white" pen="sym-pen"> +0 0 m +-1 0.333 l +-1 -0.333 l +h +</path> +</symbol> +<symbol name="arrow/ptarc(spx)"> +<path stroke="sym-stroke" fill="sym-stroke" pen="sym-pen"> +0 0 m +-1 0.333 l +-0.8 0 l +-1 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witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10) - endif(EIGEN3_FOUND) - endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) +add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp ) +target_link_libraries(Witness_complex_example_nearest_landmark_table ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Witness_complex_example_nearest_landmark_table ${TBB_LIBRARIES}) endif() +add_test(Witness_complex_test_nearest_landmark_table Witness_complex_example_nearest_landmark_table) + +# CGAL and Eigen3 are required for Euclidean version of Witness +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) + target_link_libraries(Witness_complex_example_off ${Boost_SYSTEM_LIBRARY}) + add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) + target_link_libraries(Witness_complex_example_strong_off ${Boost_SYSTEM_LIBRARY}) + add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) + target_link_libraries(Witness_complex_example_sphere ${Boost_SYSTEM_LIBRARY}) + + add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp ) + target_link_libraries(Witness_complex_example_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES}) + endif() + + add_test(Witness_complex_off_test_torus + ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_off + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3) + add_test(Witness_complex_strong_off_test_torus + ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_off + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3) + add_test(Witness_complex_test_sphere_10 Witness_complex_example_sphere 10) + add_test(Witness_complex_test_torus_persistence + ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_witness_persistence + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5) + add_test(Witness_complex_strong_test_torus_persistence + ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_witness_persistence + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/example/example_nearest_landmark_table.cpp b/src/Witness_complex/example/example_nearest_landmark_table.cpp new file mode 100644 index 00000000..b8594212 --- /dev/null +++ b/src/Witness_complex/example/example_nearest_landmark_table.cpp @@ -0,0 +1,69 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#define BOOST_PARAMETER_MAX_ARITY 12 + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Witness_complex.h> +#include <gudhi/Persistent_cohomology.h> + +#include <iostream> +#include <fstream> +#include <utility> +#include <string> +#include <vector> + +int main(int argc, char * const argv[]) { + using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>; + using Nearest_landmark_table = std::vector<Nearest_landmark_range>; + using Witness_complex = Gudhi::witness_complex::Witness_complex<Nearest_landmark_table>; + using Simplex_tree = Gudhi::Simplex_tree<>; + using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; + using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; + + Simplex_tree simplex_tree; + Nearest_landmark_table nlt; + + // Example contains 5 witnesses and 5 landmarks + Nearest_landmark_range w0 = {std::make_pair(0, 0), std::make_pair(1, 1), std::make_pair(2, 2), + std::make_pair(3, 3), std::make_pair(4, 4)}; nlt.push_back(w0); + Nearest_landmark_range w1 = {std::make_pair(1, 0), std::make_pair(2, 1), std::make_pair(3, 2), + std::make_pair(4, 3), std::make_pair(0, 4)}; nlt.push_back(w1); + Nearest_landmark_range w2 = {std::make_pair(2, 0), std::make_pair(3, 1), std::make_pair(4, 2), + std::make_pair(0, 3), std::make_pair(1, 4)}; nlt.push_back(w2); + Nearest_landmark_range w3 = {std::make_pair(3, 0), std::make_pair(4, 1), std::make_pair(0, 2), + std::make_pair(1, 3), std::make_pair(2, 4)}; nlt.push_back(w3); + Nearest_landmark_range w4 = {std::make_pair(4, 0), std::make_pair(0, 1), std::make_pair(1, 2), + std::make_pair(2, 3), std::make_pair(3, 4)}; nlt.push_back(w4); + + Witness_complex witness_complex(nlt); + witness_complex.create_complex(simplex_tree, 4.1); + + std::cout << "Number of simplices: " << simplex_tree.num_simplices() << std::endl; + + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(11); + + pcoh.compute_persistent_cohomology(-0.1); + pcoh.output_diagram(); +} diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp index 5dd18d0a..0ee9ee90 100644 --- a/src/Witness_complex/example/witness_complex_from_file.cpp +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA + * Copyright (C) 2016 INRIA (France) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -20,15 +20,12 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <sys/types.h> -#include <sys/stat.h> - -#include <gudhi/Points_off_io.h> #include <gudhi/Simplex_tree.h> -#include <gudhi/Witness_complex.h> -#include <gudhi/Construct_closest_landmark_table.h> +#include <gudhi/Euclidean_strong_witness_complex.h> #include <gudhi/pick_n_random_points.h> -#include <gudhi/reader_utils.h> +#include <gudhi/Points_off_io.h> + +#include <CGAL/Epick_d.h> #include <iostream> #include <fstream> @@ -36,49 +33,47 @@ #include <string> #include <vector> -typedef Gudhi::Simplex_tree<> Simplex_tree; -typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; -typedef std::vector< std::vector <double> > Point_Vector; +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = typename K::Point_d; +using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>; +using Point_vector = std::vector<Point_d>; int main(int argc, char * const argv[]) { - if (argc != 3) { + if (argc != 5) { std::cerr << "Usage: " << argv[0] - << " path_to_point_file.off nbL \n"; + << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; return 0; } - std::string off_file_name = argv[1]; - int nbL = atoi(argv[2]); + std::string file_name = argv[1]; + int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); + double alpha2 = atof(argv[3]); clock_t start, end; + Gudhi::Simplex_tree<> simplex_tree; - // Construct the Simplex Tree - Simplex_tree simplex_tree; - - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_off_reader<std::vector <double>> off_reader(off_file_name); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << off_file_name << std::endl; - } // Read the point file - Point_Vector point_vector = off_reader.get_point_cloud(); + Point_vector point_vector, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + point_vector = Point_vector(off_reader.get_point_cloud()); + std::cout << "Successfully read " << point_vector.size() << " points.\n"; - std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n"; + std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; // Choose landmarks - start = clock(); - std::vector<std::vector< int > > knn; - Point_Vector landmarks; - Gudhi::subsampling::pick_n_random_points(point_vector, 100, std::back_inserter(landmarks)); - Gudhi::witness_complex::construct_closest_landmark_table<Simplex_tree::Filtration_value>(point_vector, landmarks, knn); - end = clock(); - std::cout << "Landmark choice for " << nbL << " landmarks took " - << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; + Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); // Compute witness complex start = clock(); - Gudhi::witness_complex::witness_complex(knn, nbL, point_vector[0].size(), simplex_tree); + Witness_complex witness_complex(landmarks, + point_vector); + + witness_complex.create_complex(simplex_tree, alpha2, lim_dim); end = clock(); - std::cout << "Witness complex took " + std::cout << "Strong witness complex took " << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; + std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; } diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp new file mode 100644 index 00000000..f786fe7b --- /dev/null +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -0,0 +1,171 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Euclidean_strong_witness_complex.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/pick_n_random_points.h> + +#include <boost/program_options.hpp> + +#include <CGAL/Epick_d.h> + +#include <string> +#include <vector> +#include <limits> // infinity + +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = K::Point_d; + +using Point_vector = std::vector<Point_d>; +using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>; +using SimplexTree = Gudhi::Simplex_tree<>; + +using Filtration_value = SimplexTree::Filtration_value; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string file_name; + std::string filediag; + Filtration_value max_squared_alpha; + int p, nbL, lim_d; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + witnesses = Point_vector(off_reader.get_point_cloud()); + std::cout << "Successfully read " << witnesses.size() << " points.\n"; + std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; + + // Choose landmarks from witnesses + Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + Strong_witness_complex strong_witness_complex(landmarks, + witnesses); + + strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value<std::string>(&file_name), + "Name of file containing a point set in off format."); + + po::options_description visible("Allowed options", 100); + Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity(); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value<int>(&nbL), + "Number of landmarks to choose from the point cloud.") + ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha), + "Maximal squared relaxation parameter.") + ("field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()), + "Maximal dimension of the strong witness complex we want to compute."); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + po::variables_map vm; + + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Strong witness complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} + diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp new file mode 100644 index 00000000..b36dac0d --- /dev/null +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -0,0 +1,60 @@ +#include <sys/types.h> +#include <sys/stat.h> + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Euclidean_witness_complex.h> +#include <gudhi/pick_n_random_points.h> +#include <gudhi/Points_off_io.h> + +#include <CGAL/Epick_d.h> + +#include <iostream> +#include <fstream> +#include <ctime> +#include <string> +#include <vector> + +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = K::Point_d; +using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>; +using Point_vector = std::vector< Point_d >; + +int main(int argc, char * const argv[]) { + if (argc != 5) { + std::cerr << "Usage: " << argv[0] + << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; + return 0; + } + + std::string file_name = argv[1]; + int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); + double alpha2 = atof(argv[3]); + clock_t start, end; + Gudhi::Simplex_tree<> simplex_tree; + + // Read the point file + Point_vector point_vector, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + point_vector = Point_vector(off_reader.get_point_cloud()); + + std::cout << "Successfully read " << point_vector.size() << " points.\n"; + std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; + + // Choose landmarks + Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + start = clock(); + Witness_complex witness_complex(landmarks, + point_vector); + + witness_complex.create_complex(simplex_tree, alpha2, lim_dim); + end = clock(); + std::cout << "Witness complex took " + << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; + std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; +} diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp new file mode 100644 index 00000000..a1146922 --- /dev/null +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -0,0 +1,171 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Euclidean_witness_complex.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/pick_n_random_points.h> + +#include <boost/program_options.hpp> + +#include <CGAL/Epick_d.h> + +#include <string> +#include <vector> +#include <limits> // infinity + +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = K::Point_d; + +using Point_vector = std::vector<Point_d>; +using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>; +using SimplexTree = Gudhi::Simplex_tree<>; + +using Filtration_value = SimplexTree::Filtration_value; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string file_name; + std::string filediag; + Filtration_value max_squared_alpha; + int p, nbL, lim_d; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + witnesses = Point_vector(off_reader.get_point_cloud()); + std::cout << "Successfully read " << witnesses.size() << " points.\n"; + std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; + + // Choose landmarks from witnesses + Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + Witness_complex witness_complex(landmarks, + witnesses); + + witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value<std::string>(&file_name), + "Name of file containing a point set in off format."); + + Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity(); + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value<int>(&nbL), + "Number of landmarks to choose from the point cloud.") + ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha), + "Maximal squared relaxation parameter.") + ("field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()), + "Maximal dimension of the weak witness complex we want to compute."); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + po::variables_map vm; + + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Weak witness complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index 60e02225..124fd99b 100644 --- a/src/Witness_complex/example/witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA + * Copyright (C) 2016 INRIA (France) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -19,18 +19,16 @@ * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#define BOOST_PARAMETER_MAX_ARITY 12 - -#include <sys/types.h> -#include <sys/stat.h> +#define BOOST_PARAMETER_MAX_ARITY 12 #include <gudhi/Simplex_tree.h> -#include <gudhi/Witness_complex.h> -#include <gudhi/Construct_closest_landmark_table.h> +#include <gudhi/Euclidean_witness_complex.h> #include <gudhi/pick_n_random_points.h> #include <gudhi/reader_utils.h> +#include <CGAL/Epick_d.h> + #include <iostream> #include <fstream> #include <ctime> @@ -40,8 +38,6 @@ #include "generators.h" -typedef Gudhi::Simplex_tree<> Simplex_tree; - /** Write a gnuplot readable file. * Data range is a random access range of pairs (arg, value) */ @@ -54,6 +50,9 @@ void write_data(Data_range & data, std::string filename) { } int main(int argc, char * const argv[]) { + using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; + using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<Kernel>; + if (argc != 2) { std::cerr << "Usage: " << argv[0] << " number_of_landmarks \n"; @@ -61,15 +60,14 @@ int main(int argc, char * const argv[]) { } int number_of_landmarks = atoi(argv[1]); - clock_t start, end; - - // Construct the Simplex Tree - Simplex_tree simplex_tree; std::vector< std::pair<int, double> > l_time; - // Read the point file + // Generate points for (int nbP = 500; nbP < 10000; nbP += 500) { + clock_t start, end; + // Construct the Simplex Tree + Gudhi::Simplex_tree<> simplex_tree; Point_Vector point_vector, landmarks; generate_points_sphere(point_vector, nbP, 4); std::cout << "Successfully generated " << point_vector.size() << " points.\n"; @@ -77,12 +75,12 @@ int main(int argc, char * const argv[]) { // Choose landmarks start = clock(); - std::vector<std::vector< int > > knn; - Gudhi::subsampling::pick_n_random_points(point_vector, 100, std::back_inserter(landmarks)); - Gudhi::witness_complex::construct_closest_landmark_table<Simplex_tree::Filtration_value>(point_vector, landmarks, knn); + Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks)); // Compute witness complex - Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree); + Witness_complex witness_complex(landmarks, + point_vector); + witness_complex.create_complex(simplex_tree, 0); end = clock(); double time = static_cast<double>(end - start) / CLOCKS_PER_SEC; std::cout << "Witness complex for " << number_of_landmarks << " landmarks took " diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h index ac445261..7df43db5 100644 --- a/src/Witness_complex/example/generators.h +++ b/src/Witness_complex/example/generators.h @@ -25,17 +25,19 @@ #include <CGAL/Epick_d.h> #include <CGAL/point_generators_d.h> +#include <CGAL/Random.h> #include <fstream> #include <string> #include <vector> +#include <cmath> -typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K; -typedef K::FT FT; -typedef K::Point_d Point_d; -typedef std::vector<Point_d> Point_Vector; -typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator; -typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator; +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using FT = K::FT; +using Point_d = K::Point_d; +using Point_Vector = std::vector<Point_d>; +using Random_cube_iterator = CGAL::Random_points_in_cube_d<Point_d>; +using Random_point_iterator = CGAL::Random_points_in_ball_d<Point_d>; /** * \brief Rock age method of reading off file @@ -144,4 +146,21 @@ void generate_points_sphere(Point_Vector& W, int nbP, int dim) { W.push_back(*rp++); } +/** \brief Generate nbP points on a (flat) d-torus embedded in R^{2d} + * + */ +void generate_points_torus(Point_Vector& W, int nbP, int dim) { + CGAL::Random rand; + const double pi = std::acos(-1); + for (int i = 0; i < nbP; i++) { + std::vector<FT> point; + for (int j = 0; j < dim; j++) { + double alpha = rand.uniform_real(static_cast<double>(0), 2*pi); + point.push_back(sin(alpha)); + point.push_back(cos(alpha)); + } + W.push_back(Point_d(point)); + } +} + #endif // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_ diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h new file mode 100644 index 00000000..d41a6811 --- /dev/null +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -0,0 +1,67 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef ACTIVE_WITNESS_ACTIVE_WITNESS_H_ +#define ACTIVE_WITNESS_ACTIVE_WITNESS_H_ + +#include <gudhi/Active_witness/Active_witness_iterator.h> +#include <list> + +namespace Gudhi { + +namespace witness_complex { + + /* \class Active_witness + * \brief Class representing a list of nearest neighbors to a given witness. + * \details Every element is a pair of a landmark identifier and the squared distance to it. + */ +template< typename Id_distance_pair, + typename INS_range > +class Active_witness { + public: + typedef Active_witness<Id_distance_pair, INS_range> ActiveWitness; + typedef typename INS_range::iterator INS_iterator; + typedef Active_witness_iterator< ActiveWitness, Id_distance_pair, INS_iterator > iterator; + typedef typename std::list<Id_distance_pair> Table; + + Table nearest_landmark_table_; + INS_range search_range_; + INS_iterator iterator_next_; + INS_iterator iterator_end_; + + Active_witness(const INS_range& search_range) + : search_range_(search_range), iterator_next_(search_range_.begin()), iterator_end_(search_range_.end()) { + } + + iterator begin() { + return iterator(this, nearest_landmark_table_.begin()); + } + + iterator end() { + return iterator(this); + } +}; + +} // namespace witness_complex +} // namespace Gudhi + +#endif // ACTIVE_WITNESS_ACTIVE_WITNESS_H_ diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h new file mode 100644 index 00000000..0a05173a --- /dev/null +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h @@ -0,0 +1,108 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_ +#define ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_ + +#include <boost/iterator/iterator_facade.hpp> +#include <list> + +namespace Gudhi { + +namespace witness_complex { + +/* \brief Iterator in the nearest landmark list. + * \details After the iterator reaches the end of the list, + * the list is augmented by a (nearest landmark, distance) pair if possible. + * If all the landmarks are present in the list, iterator returns the specific end value + * of the corresponding 'Active_witness' object. + */ +template< typename Active_witness, + typename Id_distance_pair, + typename INS_iterator > +class Active_witness_iterator + : public boost::iterator_facade< Active_witness_iterator <Active_witness, Id_distance_pair, INS_iterator>, + Id_distance_pair const, + boost::forward_traversal_tag, + Id_distance_pair const> { + friend class boost::iterator_core_access; + + typedef typename std::list<Id_distance_pair>::iterator Pair_iterator; + typedef typename Gudhi::witness_complex::Active_witness_iterator<Active_witness, + Id_distance_pair, + INS_iterator> Iterator; + + Active_witness *aw_; + Pair_iterator lh_; // landmark handle + bool is_end_; // true only if the pointer is end and there are no more neighbors to add + + public: + Active_witness_iterator(Active_witness* aw) + : aw_(aw), lh_(aw_->nearest_landmark_table_.end()), is_end_(true) { + } + + Active_witness_iterator(Active_witness* aw, const Pair_iterator& lh) + : aw_(aw), lh_(lh) { + is_end_ = false; + if (lh_ == aw_->nearest_landmark_table_.end()) { + if (aw_->iterator_next_ == aw_->iterator_end_) { + is_end_ = true; + } else { + aw_->nearest_landmark_table_.push_back(*aw_->iterator_next_); + lh_ = --aw_->nearest_landmark_table_.end(); + ++(aw_->iterator_next_); + } + } + } + + private : + Id_distance_pair& dereference() const { + return *lh_; + } + + bool equal(const Iterator& other) const { + return (is_end_ == other.is_end_) || (lh_ == other.lh_); + } + + void increment() { + // the neighbor search can't be at the end iterator of a list + GUDHI_CHECK(!is_end_ && lh_ != aw_->nearest_landmark_table_.end(), + std::logic_error("Wrong active witness increment.")); + // if the id of the current landmark is the same as the last one + + lh_++; + if (lh_ == aw_->nearest_landmark_table_.end()) { + if (aw_->iterator_next_ == aw_->iterator_end_) { + is_end_ = true; + } else { + aw_->nearest_landmark_table_.push_back(*aw_->iterator_next_); + lh_ = std::prev(aw_->nearest_landmark_table_.end()); + ++(aw_->iterator_next_); + } + } + } +}; + +} // namespace witness_complex +} // namespace Gudhi + +#endif // ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_ diff --git a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h b/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h deleted file mode 100644 index a8cdd096..00000000 --- a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h +++ /dev/null @@ -1,92 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Siargey Kachanovich - * - * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>. - */ - -#ifndef CONSTRUCT_CLOSEST_LANDMARK_TABLE_H_ -#define CONSTRUCT_CLOSEST_LANDMARK_TABLE_H_ - -#include <boost/range/size.hpp> - -#include <queue> // for priority_queue<> -#include <utility> // for pair<> -#include <iterator> -#include <vector> -#include <set> - -namespace Gudhi { - -namespace witness_complex { - - /** - * \ingroup witness_complex - * \brief Construct the closest landmark tables for all witnesses. - * \details Output a table 'knn', each line of which represents a witness and - * consists of landmarks sorted by - * euclidean distance from the corresponding witness. - * - * The type WitnessContainer is a random access range and - * the type LandmarkContainer is a range. - * The type KNearestNeighbors can be seen as - * Witness_range<Closest_landmark_range<Vertex_handle>>, where - * Witness_range and Closest_landmark_range are random access ranges and - * Vertex_handle is the label type of a vertex in a simplicial complex. - * Closest_landmark_range needs to have push_back operation. - */ - - template <typename FiltrationValue, - typename WitnessContainer, - typename LandmarkContainer, - typename KNearestNeighbours> - void construct_closest_landmark_table(WitnessContainer const &points, - LandmarkContainer const &landmarks, - KNearestNeighbours &knn) { - int nbP = boost::size(points); - assert(nbP >= boost::size(landmarks)); - - int dim = boost::size(*std::begin(points)); - typedef std::pair<double, int> dist_i; - typedef bool (*comp)(dist_i, dist_i); - knn = KNearestNeighbours(nbP); - for (int points_i = 0; points_i < nbP; points_i++) { - std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([](dist_i j1, dist_i j2) { - return j1.first > j2.first; - }); - typename LandmarkContainer::const_iterator landmarks_it; - int landmarks_i = 0; - for (landmarks_it = landmarks.begin(), landmarks_i = 0; landmarks_it != landmarks.end(); - ++landmarks_it, landmarks_i++) { - dist_i dist = std::make_pair(Euclidean_distance()(points[points_i], *landmarks_it), - landmarks_i); - l_heap.push(dist); - } - for (int i = 0; i < dim + 1; i++) { - dist_i dist = l_heap.top(); - knn[points_i].push_back(dist.second); - l_heap.pop(); - } - } - } - -} // namespace witness_complex - -} // namespace Gudhi - -#endif // CONSTRUCT_CLOSEST_LANDMARK_TABLE_H_ diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h new file mode 100644 index 00000000..fb669ef8 --- /dev/null +++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h @@ -0,0 +1,104 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_ +#define EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_ + +#include <gudhi/Strong_witness_complex.h> +#include <gudhi/Active_witness/Active_witness.h> +#include <gudhi/Kd_tree_search.h> + +#include <utility> +#include <vector> + +namespace Gudhi { + +namespace witness_complex { + +/** + * \private + * \class Euclidean_strong_witness_complex + * \brief Constructs strong witness complex for given sets of witnesses and landmarks in Euclidean space. + * \ingroup witness_complex + * + * \tparam Kernel_ requires a <a target="_blank" + * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> class. + */ +template< class Kernel_ > +class Euclidean_strong_witness_complex + : public Strong_witness_complex<std::vector<typename Gudhi::spatial_searching::Kd_tree_search<Kernel_, + std::vector<typename Kernel_::Point_d>>::INS_range>> { + private: + typedef Kernel_ K; + typedef typename K::Point_d Point_d; + typedef std::vector<Point_d> Point_range; + typedef Gudhi::spatial_searching::Kd_tree_search<Kernel_, Point_range> Kd_tree; + typedef typename Kd_tree::INS_range Nearest_landmark_range; + typedef typename std::vector<Nearest_landmark_range> Nearest_landmark_table; + + typedef typename Nearest_landmark_range::Point_with_transformed_distance Id_distance_pair; + typedef typename Id_distance_pair::first_type Landmark_id; + typedef Landmark_id Vertex_handle; + + private: + Point_range landmarks_; + Kd_tree landmark_tree_; + using Strong_witness_complex<Nearest_landmark_table>::nearest_landmark_table_; + + public: + ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /* @name Constructor + */ + + //@{ + + /** + * \brief Initializes member variables before constructing simplicial complex. + * \details Records landmarks from the range 'landmarks' into a + * table internally, as well as witnesses from the range 'witnesses'. + * Both ranges should have value_type Kernel_::Point_d. + */ + template< typename LandmarkRange, + typename WitnessRange > + Euclidean_strong_witness_complex(const LandmarkRange & landmarks, + const WitnessRange & witnesses) + : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) { + nearest_landmark_table_.reserve(boost::size(witnesses)); + for (auto w : witnesses) + nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w)); + } + + /** \brief Returns the point corresponding to the given vertex. + */ + template <typename Vertex_handle> + Point_d get_point(Vertex_handle vertex) const { + return landmarks_[vertex]; + } + + //@} +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif // EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_ diff --git a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h new file mode 100644 index 00000000..6afe9a5d --- /dev/null +++ b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h @@ -0,0 +1,106 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef EUCLIDEAN_WITNESS_COMPLEX_H_ +#define EUCLIDEAN_WITNESS_COMPLEX_H_ + +#include <gudhi/Witness_complex.h> +#include <gudhi/Active_witness/Active_witness.h> +#include <gudhi/Kd_tree_search.h> + +#include <utility> +#include <vector> +#include <list> +#include <limits> + +namespace Gudhi { + +namespace witness_complex { + +/** + * \private + * \class Euclidean_witness_complex + * \brief Constructs (weak) witness complex for given sets of witnesses and landmarks in Euclidean space. + * \ingroup witness_complex + * + * \tparam Kernel_ requires a <a target="_blank" + * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> class. + */ +template< class Kernel_ > +class Euclidean_witness_complex + : public Witness_complex<std::vector<typename Gudhi::spatial_searching::Kd_tree_search<Kernel_, + std::vector<typename Kernel_::Point_d>>::INS_range>> { + private: + typedef Kernel_ K; + typedef typename K::Point_d Point_d; + typedef std::vector<Point_d> Point_range; + typedef Gudhi::spatial_searching::Kd_tree_search<Kernel_, Point_range> Kd_tree; + typedef typename Kd_tree::INS_range Nearest_landmark_range; + typedef typename std::vector<Nearest_landmark_range> Nearest_landmark_table; + + typedef typename Nearest_landmark_range::Point_with_transformed_distance Id_distance_pair; + typedef typename Id_distance_pair::first_type Landmark_id; + typedef Landmark_id Vertex_handle; + + private: + Point_range landmarks_; + Kd_tree landmark_tree_; + using Witness_complex<Nearest_landmark_table>::nearest_landmark_table_; + + public: + ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /* @name Constructor + */ + + //@{ + + /** + * \brief Initializes member variables before constructing simplicial complex. + * \details Records landmarks from the range 'landmarks' into a + * table internally, as well as witnesses from the range 'witnesses'. + * Both ranges should have value_type Kernel_::Point_d. + */ + template< typename LandmarkRange, + typename WitnessRange > + Euclidean_witness_complex(const LandmarkRange & landmarks, + const WitnessRange & witnesses) + : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks) { + nearest_landmark_table_.reserve(boost::size(witnesses)); + for (auto w : witnesses) + nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w)); + } + + /** \brief Returns the point corresponding to the given vertex. + * @param[in] vertex Vertex handle of the point to retrieve. + */ + Point_d get_point(Vertex_handle vertex) const { + return landmarks_[vertex]; + } + + //@} +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif // EUCLIDEAN_WITNESS_COMPLEX_H_ diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h new file mode 100644 index 00000000..a973ddb7 --- /dev/null +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -0,0 +1,185 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef STRONG_WITNESS_COMPLEX_H_ +#define STRONG_WITNESS_COMPLEX_H_ + +#include <gudhi/Active_witness/Active_witness.h> + +#include <utility> +#include <vector> +#include <list> +#include <limits> + +namespace Gudhi { + +namespace witness_complex { + +/* \private + * \class Strong_witness_complex + * \brief Constructs strong witness complex for a given table of nearest landmarks with respect to witnesses. + * \ingroup witness_complex + * + * \tparam Nearest_landmark_table_ needs to be a range of a range of pairs of nearest landmarks and distances. + * The class Nearest_landmark_table_::value_type must be a copiable range. + * The range of pairs must admit a member type 'iterator'. The dereference type + * of the pair range iterator needs to be 'std::pair<std::size_t, double>'. + */ +template< class Nearest_landmark_table_ > +class Strong_witness_complex { + private: + typedef typename Nearest_landmark_table_::value_type Nearest_landmark_range; + typedef std::size_t Witness_id; + typedef std::size_t Landmark_id; + typedef std::pair<Landmark_id, double> Id_distance_pair; + typedef Active_witness<Id_distance_pair, Nearest_landmark_range> ActiveWitness; + typedef std::list< ActiveWitness > ActiveWitnessList; + typedef std::vector< Landmark_id > typeVectorVertex; + typedef std::vector<Nearest_landmark_range> Nearest_landmark_table_internal; + typedef Landmark_id Vertex_handle; + + protected: + Nearest_landmark_table_internal nearest_landmark_table_; + + public: + ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /* @name Constructor + */ + + //@{ + + Strong_witness_complex() { + } + + /** + * \brief Initializes member variables before constructing simplicial complex. + * \details Records nearest landmark table. + * @param[in] nearest_landmark_table needs to be a range of a range of pairs of nearest landmarks and distances. + * The class Nearest_landmark_table_::value_type must be a copiable range. + * The range of pairs must admit a member type 'iterator'. The dereference type + * of the pair range iterator needs to be 'std::pair<std::size_t, double>'. + */ + Strong_witness_complex(Nearest_landmark_table_ const & nearest_landmark_table) + : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) { + } + + /** \brief Outputs the strong witness complex of relaxation 'max_alpha_square' + * in a simplicial complex data structure. + * \details The function returns true if the construction is successful and false otherwise. + * @param[out] complex Simplicial complex data structure, which is a model of + * SimplicialComplexForWitness concept. + * @param[in] max_alpha_square Maximal squared relaxation parameter. + * @param[in] limit_dimension Represents the maximal dimension of the simplicial complex + * (default value = no limit). + */ + template < typename SimplicialComplexForWitness > + bool create_complex(SimplicialComplexForWitness& complex, + double max_alpha_square, + Landmark_id limit_dimension = std::numeric_limits<Landmark_id>::max()) const { + Landmark_id complex_dim = 0; + if (complex.num_vertices() > 0) { + std::cerr << "Strong witness complex cannot create complex - complex is not empty.\n"; + return false; + } + if (max_alpha_square < 0) { + std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be " + << "non-negative.\n"; + return false; + } + if (limit_dimension < 0) { + std::cerr << "Strong witness complex cannot create complex - limit dimension must be non-negative.\n"; + return false; + } + for (auto w : nearest_landmark_table_) { + ActiveWitness aw(w); + typeVectorVertex simplex; + typename ActiveWitness::iterator aw_it = aw.begin(); + float lim_dist2 = aw.begin()->second + max_alpha_square; + while ((Landmark_id)simplex.size() <= limit_dimension && aw_it != aw.end() && aw_it->second < lim_dist2) { + simplex.push_back(aw_it->first); + complex.insert_simplex_and_subfaces(simplex, aw_it->second - aw.begin()->second); + aw_it++; + } + // continue inserting limD-faces of the following simplices + typeVectorVertex& vertices = simplex; // 'simplex' now will be called vertices + while (aw_it != aw.end() && aw_it->second < lim_dist2) { + typeVectorVertex facet = {}; + add_all_faces_of_dimension(limit_dimension, vertices, vertices.begin(), aw_it, + aw_it->second - aw.begin()->second, facet, complex); + vertices.push_back(aw_it->first); + aw_it++; + } + if ((Landmark_id)simplex.size() - 1 > complex_dim) + complex_dim = simplex.size() - 1; + } + complex.set_dimension(complex_dim); + return true; + } + + private: + /* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness. + * Iterator is needed to know until how far we can take landmarks to form simplexes. + * simplex is the prefix of the simplexes to insert. + * The landmark pointed by aw_it is added to all formed simplices. + */ + template < typename SimplicialComplexForWitness > + void add_all_faces_of_dimension(Landmark_id dim, + typeVectorVertex& vertices, + typename typeVectorVertex::iterator curr_it, + typename ActiveWitness::iterator aw_it, + double filtration_value, + typeVectorVertex& simplex, + SimplicialComplexForWitness& sc) const { + if (dim > 0) { + while (curr_it != vertices.end()) { + simplex.push_back(*curr_it); + ++curr_it; + add_all_faces_of_dimension(dim-1, + vertices, + curr_it, + aw_it, + filtration_value, + simplex, + sc); + simplex.pop_back(); + add_all_faces_of_dimension(dim, + vertices, + curr_it, + aw_it, + filtration_value, + simplex, + sc); + } + } else if (dim == 0) { + simplex.push_back(aw_it->first); + sc.insert_simplex_and_subfaces(simplex, filtration_value); + simplex.pop_back(); + } + } + //@} +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif // STRONG_WITNESS_COMPLEX_H_ diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 1eb126f1..63f03687 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 INRIA (France) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -23,64 +23,44 @@ #ifndef WITNESS_COMPLEX_H_ #define WITNESS_COMPLEX_H_ -// Needed for the adjacency graph in bad link search -#include <boost/graph/graph_traits.hpp> -#include <boost/graph/adjacency_list.hpp> -#include <boost/graph/connected_components.hpp> +#include <gudhi/Active_witness/Active_witness.h> +#include <gudhi/Witness_complex/all_faces_in.h> -#include <boost/range/size.hpp> - -#include <gudhi/distance_functions.h> - -#include <algorithm> #include <utility> #include <vector> #include <list> -#include <set> -#include <queue> #include <limits> -#include <ctime> -#include <iostream> namespace Gudhi { namespace witness_complex { -// /* -// * \private -// \class Witness_complex -// \brief Constructs the witness complex for the given set of witnesses and landmarks. -// \ingroup witness_complex -// */ -template< class SimplicialComplex> +/** + * \private + * \class Witness_complex + * \brief Constructs (weak) witness complex for a given table of nearest landmarks with respect to witnesses. + * \ingroup witness_complex + * + * \tparam Nearest_landmark_table_ needs to be a range of a range of pairs of nearest landmarks and distances. + * The class Nearest_landmark_table_::value_type must be a copiable range. + * The range of pairs must admit a member type 'iterator'. The dereference type + * of the pair range iterator needs to be 'std::pair<std::size_t, double>'. +*/ +template< class Nearest_landmark_table_ > class Witness_complex { private: - struct Active_witness { - int witness_id; - int landmark_id; - - Active_witness(int witness_id_, int landmark_id_) - : witness_id(witness_id_), - landmark_id(landmark_id_) { } - }; - - private: - typedef typename SimplicialComplex::Simplex_handle Simplex_handle; - typedef typename SimplicialComplex::Vertex_handle Vertex_handle; - - typedef std::vector< double > Point_t; - typedef std::vector< Point_t > Point_Vector; - - typedef std::vector< Vertex_handle > typeVectorVertex; - typedef std::pair< Simplex_handle, bool > typePairSimplexBool; - - typedef int Witness_id; - typedef int Landmark_id; - typedef std::list< Vertex_handle > ActiveWitnessList; - - private: - int nbL_; // Number of landmarks - SimplicialComplex& sc_; // Simplicial complex + typedef typename Nearest_landmark_table_::value_type Nearest_landmark_range; + typedef std::size_t Witness_id; + typedef std::size_t Landmark_id; + typedef std::pair<Landmark_id, double> Id_distance_pair; + typedef Active_witness<Id_distance_pair, Nearest_landmark_range> ActiveWitness; + typedef std::list< ActiveWitness > ActiveWitnessList; + typedef std::vector< Landmark_id > typeVectorVertex; + typedef std::vector<Nearest_landmark_range> Nearest_landmark_table_internal; + typedef Landmark_id Vertex_handle; + + protected: + Nearest_landmark_table_internal nearest_landmark_table_; public: ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// @@ -89,174 +69,136 @@ class Witness_complex { //@{ - // Witness_range<Closest_landmark_range<Vertex_handle>> + Witness_complex() { + } - /* - * \brief Iterative construction of the witness complex. - * \details The witness complex is written in sc_ basing on a matrix knn of - * nearest neighbours of the form {witnesses}x{landmarks}. - * - * The type KNearestNeighbors can be seen as - * Witness_range<Closest_landmark_range<Vertex_handle>>, where - * Witness_range and Closest_landmark_range are random access ranges. - * - * Constructor takes into account at most (dim+1) - * first landmarks from each landmark range to construct simplices. - * - * Landmarks are supposed to be in [0,nbL_-1] + /** + * \brief Initializes member variables before constructing simplicial complex. + * \details Records nearest landmark table. + * @param[in] nearest_landmark_table needs to be a range of a range of pairs of nearest landmarks and distances. + * The class Nearest_landmark_table_::value_type must be a copiable range. + * The range of pairs must admit a member type 'iterator'. The dereference type + * of the pair range iterator needs to be 'std::pair<std::size_t, double>'. */ - template< typename KNearestNeighbors > - Witness_complex(KNearestNeighbors const & knn, - int nbL, - int dim, - SimplicialComplex & sc) : nbL_(nbL), sc_(sc) { - // Construction of the active witness list - int nbW = boost::size(knn); - typeVectorVertex vv; - int counter = 0; - /* The list of still useful witnesses - * it will diminuish in the course of iterations - */ - ActiveWitnessList active_w; // = new ActiveWitnessList(); - for (Vertex_handle i = 0; i != nbL_; ++i) { - // initial fill of 0-dimensional simplices - // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore - counter++; - vv = {i}; - sc_.insert_simplex(vv); - // TODO(SK) Error if not inserted : normally no need here though + + Witness_complex(Nearest_landmark_table_ const & nearest_landmark_table) + : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) { + } + + /** \brief Outputs the (weak) witness complex of relaxation 'max_alpha_square' + * in a simplicial complex data structure. + * \details The function returns true if the construction is successful and false otherwise. + * @param[out] complex Simplicial complex data structure compatible which is a model of + * SimplicialComplexForWitness concept. + * @param[in] max_alpha_square Maximal squared relaxation parameter. + * @param[in] limit_dimension Represents the maximal dimension of the simplicial complex + * (default value = no limit). + */ + template < typename SimplicialComplexForWitness > + bool create_complex(SimplicialComplexForWitness& complex, + double max_alpha_square, + std::size_t limit_dimension = std::numeric_limits<std::size_t>::max()) const { + if (complex.num_vertices() > 0) { + std::cerr << "Witness complex cannot create complex - complex is not empty.\n"; + return false; } - int k = 1; /* current dimension in iterative construction */ - for (int i = 0; i != nbW; ++i) - active_w.push_back(i); - while (!active_w.empty() && k < dim) { - typename ActiveWitnessList::iterator it = active_w.begin(); - while (it != active_w.end()) { - typeVectorVertex simplex_vector; - /* THE INSERTION: Checking if all the subfaces are in the simplex tree*/ - bool ok = all_faces_in(knn, *it, k); - if (ok) { - for (int i = 0; i != k + 1; ++i) - simplex_vector.push_back(knn[*it][i]); - sc_.insert_simplex(simplex_vector); - // TODO(SK) Error if not inserted : normally no need here though - ++it; - } else { - active_w.erase(it++); // First increase the iterator and then erase the previous element - } + if (max_alpha_square < 0) { + std::cerr << "Witness complex cannot create complex - squared relaxation parameter must be non-negative.\n"; + return false; + } + if (limit_dimension < 0) { + std::cerr << "Witness complex cannot create complex - limit dimension must be non-negative.\n"; + return false; + } + ActiveWitnessList active_witnesses; + Landmark_id k = 0; /* current dimension in iterative construction */ + for (auto w : nearest_landmark_table_) + active_witnesses.push_back(ActiveWitness(w)); + while (!active_witnesses.empty() && k <= limit_dimension) { + typename ActiveWitnessList::iterator aw_it = active_witnesses.begin(); + std::vector<Landmark_id> simplex; + simplex.reserve(k+1); + while (aw_it != active_witnesses.end()) { + bool ok = add_all_faces_of_dimension(k, + max_alpha_square, + std::numeric_limits<double>::infinity(), + aw_it->begin(), + simplex, + complex, + aw_it->end()); + assert(simplex.empty()); + if (!ok) + active_witnesses.erase(aw_it++); // First increase the iterator and then erase the previous element + else + aw_it++; } k++; } + complex.set_dimension(k-1); + return true; } //@} private: - /* \brief Check if the facets of the k-dimensional simplex witnessed - * by witness witness_id are already in the complex. - * inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id + /* \brief Adds recursively all the faces of a certain dimension dim witnessed by the same witness. + * Iterator is needed to know until how far we can take landmarks to form simplexes. + * simplex is the prefix of the simplexes to insert. + * The output value indicates if the witness rests active or not. */ - template <typename KNearestNeighbors> - bool all_faces_in(KNearestNeighbors const &knn, int witness_id, int k) { - std::vector< Vertex_handle > facet; - // CHECK ALL THE FACETS - for (int i = 0; i != k + 1; ++i) { - facet = {}; - for (int j = 0; j != k + 1; ++j) { - if (j != i) { - facet.push_back(knn[witness_id][j]); + template < typename SimplicialComplexForWitness > + bool add_all_faces_of_dimension(int dim, + double alpha2, + double norelax_dist2, + typename ActiveWitness::iterator curr_l, + std::vector<Landmark_id>& simplex, + SimplicialComplexForWitness& sc, + typename ActiveWitness::iterator end) const { + if (curr_l == end) + return false; + bool will_be_active = false; + typename ActiveWitness::iterator l_it = curr_l; + if (dim > 0) { + for (; l_it != end && l_it->second - alpha2 <= norelax_dist2; ++l_it) { + simplex.push_back(l_it->first); + if (sc.find(simplex) != sc.null_simplex()) { + typename ActiveWitness::iterator next_it = l_it; + will_be_active = add_all_faces_of_dimension(dim-1, + alpha2, + norelax_dist2, + ++next_it, + simplex, + sc, + end) || will_be_active; } - } // endfor - if (sc_.find(facet) == sc_.null_simplex()) - return false; - } // endfor - return true; - } - - template <typename T> - static void print_vector(const std::vector<T>& v) { - std::cout << "["; - if (!v.empty()) { - std::cout << *(v.begin()); - for (auto it = v.begin() + 1; it != v.end(); ++it) { - std::cout << ","; - std::cout << *it; + assert(!simplex.empty()); + simplex.pop_back(); + // If norelax_dist is infinity, change to first omitted distance + if (l_it->second <= norelax_dist2) + norelax_dist2 = l_it->second; } - } - std::cout << "]"; - } - - public: - // /* - // * \brief Verification if every simplex in the complex is witnessed by witnesses in knn. - // * \param print_output =true will print the witnesses for each simplex - // * \remark Added for debugging purposes. - // */ - template< class KNearestNeighbors > - bool is_witness_complex(KNearestNeighbors const & knn, bool print_output) { - for (Simplex_handle sh : sc_.complex_simplex_range()) { - bool is_witnessed = false; - typeVectorVertex simplex; - int nbV = 0; // number of verticed in the simplex - for (Vertex_handle v : sc_.simplex_vertex_range(sh)) - simplex.push_back(v); - nbV = simplex.size(); - for (typeVectorVertex w : knn) { - bool has_vertices = true; - for (Vertex_handle v : simplex) - if (std::find(w.begin(), w.begin() + nbV, v) == w.begin() + nbV) { - has_vertices = false; - } - if (has_vertices) { - is_witnessed = true; - if (print_output) { - std::cout << "The simplex "; - print_vector(simplex); - std::cout << " is witnessed by the witness "; - print_vector(w); - std::cout << std::endl; - } - break; - } - } - if (!is_witnessed) { - if (print_output) { - std::cout << "The following simplex is not witnessed "; - print_vector(simplex); - std::cout << std::endl; + } else if (dim == 0) { + for (; l_it != end && l_it->second - alpha2 <= norelax_dist2; ++l_it) { + simplex.push_back(l_it->first); + double filtration_value = 0; + // if norelax_dist is infinite, relaxation is 0. + if (l_it->second > norelax_dist2) + filtration_value = l_it->second - norelax_dist2; + if (all_faces_in(simplex, &filtration_value, sc)) { + will_be_active = true; + sc.insert_simplex(simplex, filtration_value); } - assert(is_witnessed); - return false; + assert(!simplex.empty()); + simplex.pop_back(); + // If norelax_dist is infinity, change to first omitted distance + if (l_it->second < norelax_dist2) + norelax_dist2 = l_it->second; } } - return true; + return will_be_active; } }; - /** - * \ingroup witness_complex - * \brief Iterative construction of the witness complex. - * \details The witness complex is written in simplicial complex sc_ - * basing on a matrix knn of - * nearest neighbours of the form {witnesses}x{landmarks}. - * - * The type KNearestNeighbors can be seen as - * Witness_range<Closest_landmark_range<Vertex_handle>>, where - * Witness_range and Closest_landmark_range are random access ranges. - * - * Procedure takes into account at most (dim+1) - * first landmarks from each landmark range to construct simplices. - * - * Landmarks are supposed to be in [0,nbL_-1] - */ - template <class KNearestNeighbors, class SimplicialComplexForWitness> - void witness_complex(KNearestNeighbors const & knn, - int nbL, - int dim, - SimplicialComplexForWitness & sc) { - Witness_complex<SimplicialComplexForWitness>(knn, nbL, dim, sc); - } - } // namespace witness_complex } // namespace Gudhi diff --git a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h new file mode 100644 index 00000000..b68d75a1 --- /dev/null +++ b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h @@ -0,0 +1,55 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef WITNESS_COMPLEX_ALL_FACES_IN_H_ +#define WITNESS_COMPLEX_ALL_FACES_IN_H_ + +/* \brief Check if the facets of the k-dimensional simplex witnessed + * by witness witness_id are already in the complex. + * inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id + */ +template < typename SimplicialComplexForWitness, + typename Simplex > + bool all_faces_in(Simplex& simplex, + double* filtration_value, + SimplicialComplexForWitness& sc) { + typedef typename SimplicialComplexForWitness::Simplex_handle Simplex_handle; + + if (simplex.size() == 1) + return true; /* Add vertices unconditionally */ + + Simplex facet; + for (typename Simplex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) { + facet.clear(); + for (typename Simplex::iterator it = simplex.begin(); it != simplex.end(); ++it) + if (it != not_it) + facet.push_back(*it); + Simplex_handle facet_sh = sc.find(facet); + if (facet_sh == sc.null_simplex()) + return false; + else if (sc.filtration(facet_sh) > *filtration_value) + *filtration_value = sc.filtration(facet_sh); + } + return true; + } + +#endif // WITNESS_COMPLEX_ALL_FACES_IN_H_ diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt index bb55b0f1..e73f9c3a 100644 --- a/src/Witness_complex/test/CMakeLists.txt +++ b/src/Witness_complex/test/CMakeLists.txt @@ -10,21 +10,29 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -add_executable ( simple_witness_complexUT simple_witness_complex.cpp ) -target_link_libraries(simple_witness_complexUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +add_executable ( Witness_complex_test_simple_witness_complex test_simple_witness_complex.cpp ) +target_link_libraries(Witness_complex_test_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Witness_complex_test_simple_witness_complex ${TBB_LIBRARIES}) +endif(TBB_FOUND) # Unitary tests definition and xml result file generation -add_test(NAME simple_witness_complexUT - COMMAND ${CMAKE_CURRENT_BINARY_DIR}/simple_witness_complexUT +add_test(NAME simple_witness_complex + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_simple_witness_complex # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/simple_witness_complexUT.xml --log_level=test_suite --report_level=no) + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_simple_witness_complexUT.xml --log_level=test_suite --report_level=no) -add_executable ( witness_complex_pointsUT witness_complex_points.cpp ) -target_link_libraries(witness_complex_pointsUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - -# Unitary tests definition and xml result file generation -add_test(NAME witness_complex_pointsUT - COMMAND ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_pointsUT - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/witness_complex_pointsUT.xml --log_level=test_suite --report_level=no) +# CGAL and Eigen3 are required for Euclidean version of Witness +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + add_executable ( Witness_complex_test_euclidean_simple_witness_complex test_euclidean_simple_witness_complex.cpp ) + target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${TBB_LIBRARIES}) + endif(TBB_FOUND) + # Unitary tests definition and xml result file generation + add_test(NAME euclidean_simple_witness_complex + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_euclidean_simple_witness_complex + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_euclidean_simple_witness_complexUT.xml --log_level=test_suite --report_level=no) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp deleted file mode 100644 index 6be39f58..00000000 --- a/src/Witness_complex/test/simple_witness_complex.cpp +++ /dev/null @@ -1,59 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Siargey Kachanovich - * - * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "simple_witness_complex" -#include <boost/test/unit_test.hpp> -#include <boost/mpl/list.hpp> - -#include <gudhi/Simplex_tree.h> -#include <gudhi/Witness_complex.h> - -#include <iostream> -#include <ctime> -#include <vector> - -typedef Gudhi::Simplex_tree<> Simplex_tree; -typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; -typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex; - -BOOST_AUTO_TEST_CASE(simple_witness_complex) { - Simplex_tree complex; - std::vector< typeVectorVertex > knn; - - knn.push_back({1, 0, 5, 2, 6, 3, 4}); - knn.push_back({2, 6, 4, 5, 0, 1, 3}); - knn.push_back({3, 4, 2, 1, 5, 6, 0}); - knn.push_back({4, 2, 1, 3, 5, 6, 0}); - knn.push_back({5, 1, 6, 0, 2, 3, 4}); - knn.push_back({6, 0, 5, 2, 1, 3, 4}); - knn.push_back({0, 5, 6, 1, 2, 3, 4}); - knn.push_back({2, 6, 4, 5, 3, 1, 0}); - knn.push_back({1, 2, 5, 4, 3, 6, 0}); - knn.push_back({3, 4, 0, 6, 5, 1, 2}); - knn.push_back({5, 0, 1, 3, 6, 2, 4}); - knn.push_back({5, 6, 1, 0, 2, 3, 4}); - knn.push_back({1, 6, 0, 5, 2, 3, 4}); - WitnessComplex witnessComplex(knn, 7, 7, complex); - - BOOST_CHECK(witnessComplex.is_witness_complex(knn, false)); -} diff --git a/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp new file mode 100644 index 00000000..62fd1157 --- /dev/null +++ b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp @@ -0,0 +1,135 @@ +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "euclidean_simple_witness_complex" +#include <boost/test/unit_test.hpp> +#include <boost/mpl/list.hpp> + +#include <CGAL/Epick_d.h> + +#include <gudhi/Simplex_tree.h> + +#include <gudhi/Witness_complex.h> +#include <gudhi/Euclidean_witness_complex.h> +#include <gudhi/Strong_witness_complex.h> +#include <gudhi/Euclidean_strong_witness_complex.h> + +#include <gudhi/Kd_tree_search.h> + +#include <iostream> +#include <ctime> +#include <vector> + +typedef Gudhi::Simplex_tree<> Simplex_tree; +typedef typename Simplex_tree::Vertex_handle Vertex_handle; +typedef std::vector< Vertex_handle > typeVectorVertex; +typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> Kernel; +typedef typename Kernel::FT FT; +typedef typename Kernel::Point_d Point_d; +typedef Gudhi::witness_complex::Euclidean_witness_complex<Kernel> EuclideanWitnessComplex; +typedef Gudhi::witness_complex::Euclidean_strong_witness_complex<Kernel> EuclideanStrongWitnessComplex; + +typedef std::vector<Point_d> Point_range; +typedef Gudhi::spatial_searching::Kd_tree_search<Kernel, Point_range> Kd_tree; +typedef Kd_tree::INS_range Nearest_landmark_range; +typedef std::vector<Nearest_landmark_range> Nearest_landmark_table; +typedef Gudhi::witness_complex::Witness_complex<Nearest_landmark_table> WitnessComplex; +typedef Gudhi::witness_complex::Strong_witness_complex<Nearest_landmark_table> StrongWitnessComplex; + + +/* All landmarks and witnesses are taken on the grid in the following manner. + LWLWL + WW.WW + L...L + WW.WW + LWLWL + + Witness complex consists of 8 vertices, 12 edges and 4 triangles + */ + +BOOST_AUTO_TEST_CASE(simple_witness_complex) { + Simplex_tree complex, relaxed_complex, strong_relaxed_complex, strong_relaxed_complex2; + Simplex_tree complex_ne, relaxed_complex_ne, strong_relaxed_complex_ne, strong_relaxed_complex2_ne; + + Point_range witnesses, landmarks; + + landmarks.push_back(Point_d(std::vector<FT>{-2,-2})); + landmarks.push_back(Point_d(std::vector<FT>{-2, 0})); + landmarks.push_back(Point_d(std::vector<FT>{-2, 2})); + landmarks.push_back(Point_d(std::vector<FT>{ 0,-2})); + landmarks.push_back(Point_d(std::vector<FT>{ 0, 2})); + landmarks.push_back(Point_d(std::vector<FT>{ 2,-2})); + landmarks.push_back(Point_d(std::vector<FT>{ 2, 0})); + landmarks.push_back(Point_d(std::vector<FT>{ 2, 2})); + witnesses.push_back(Point_d(std::vector<FT>{-2,-1})); + witnesses.push_back(Point_d(std::vector<FT>{-2, 1})); + witnesses.push_back(Point_d(std::vector<FT>{-1,-2})); + witnesses.push_back(Point_d(std::vector<FT>{-1,-1})); + witnesses.push_back(Point_d(std::vector<FT>{-1, 1})); + witnesses.push_back(Point_d(std::vector<FT>{-1, 2})); + witnesses.push_back(Point_d(std::vector<FT>{ 1,-2})); + witnesses.push_back(Point_d(std::vector<FT>{ 1,-1})); + witnesses.push_back(Point_d(std::vector<FT>{ 1, 1})); + witnesses.push_back(Point_d(std::vector<FT>{ 1, 2})); + witnesses.push_back(Point_d(std::vector<FT>{ 2,-1})); + witnesses.push_back(Point_d(std::vector<FT>{ 2, 1})); + + Kd_tree landmark_tree(landmarks); + Nearest_landmark_table nearest_landmark_table; + for (auto w: witnesses) + nearest_landmark_table.push_back(landmark_tree.query_incremental_nearest_neighbors(w)); + + // Weak witness complex: Euclidean version + EuclideanWitnessComplex eucl_witness_complex(landmarks, + witnesses); + eucl_witness_complex.create_complex(complex, 0); + + std::cout << "complex.num_simplices() = " << complex.num_simplices() << std::endl; + BOOST_CHECK(complex.num_simplices() == 24); + + eucl_witness_complex.create_complex(relaxed_complex, 8.01); + + std::cout << "relaxed_complex.num_simplices() = " << relaxed_complex.num_simplices() << std::endl; + BOOST_CHECK(relaxed_complex.num_simplices() == 239); + // The corner simplex {0,2,5,7} and its cofaces are missing. + + // Weak witness complex: non-Euclidean version + WitnessComplex witness_complex(nearest_landmark_table); + witness_complex.create_complex(complex_ne, 0); + + std::cout << "complex.num_simplices() = " << complex_ne.num_simplices() << std::endl; + BOOST_CHECK(complex_ne.num_simplices() == 24); + + witness_complex.create_complex(relaxed_complex_ne, 8.01); + + std::cout << "relaxed_complex.num_simplices() = " << relaxed_complex_ne.num_simplices() << std::endl; + BOOST_CHECK(relaxed_complex_ne.num_simplices() == 239); + + + // Strong complex : Euclidean version + EuclideanStrongWitnessComplex eucl_strong_witness_complex(landmarks, + witnesses); + + eucl_strong_witness_complex.create_complex(strong_relaxed_complex, 9.1); + eucl_strong_witness_complex.create_complex(strong_relaxed_complex2, 9.1, 2); + + std::cout << "strong_relaxed_complex.num_simplices() = " << strong_relaxed_complex.num_simplices() << std::endl; + BOOST_CHECK(strong_relaxed_complex.num_simplices() == 239); + + std::cout << "strong_relaxed_complex2.num_simplices() = " << strong_relaxed_complex2.num_simplices() << std::endl; + BOOST_CHECK(strong_relaxed_complex2.num_simplices() == 92); + + + // Strong complex : non-Euclidean version + StrongWitnessComplex strong_witness_complex(nearest_landmark_table); + + strong_witness_complex.create_complex(strong_relaxed_complex_ne, 9.1); + strong_witness_complex.create_complex(strong_relaxed_complex2_ne, 9.1, 2); + + std::cout << "strong_relaxed_complex.num_simplices() = " << strong_relaxed_complex_ne.num_simplices() << std::endl; + BOOST_CHECK(strong_relaxed_complex_ne.num_simplices() == 239); + + std::cout << "strong_relaxed_complex2.num_simplices() = " << strong_relaxed_complex2_ne.num_simplices() << std::endl; + BOOST_CHECK(strong_relaxed_complex2_ne.num_simplices() == 92); + + + // 8 vertices, 28 edges, 56 triangles +} diff --git a/src/Witness_complex/test/test_simple_witness_complex.cpp b/src/Witness_complex/test/test_simple_witness_complex.cpp new file mode 100644 index 00000000..9e3509d3 --- /dev/null +++ b/src/Witness_complex/test/test_simple_witness_complex.cpp @@ -0,0 +1,53 @@ +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "simple_witness_complex" +#include <boost/test/unit_test.hpp> +#include <boost/mpl/list.hpp> + +#include <gudhi/Simplex_tree.h> + +#include <gudhi/Witness_complex.h> + +#include <iostream> +#include <vector> +#include <utility> + + +BOOST_AUTO_TEST_CASE(simple_witness_complex) { + using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>; + using Nearest_landmark_table = std::vector<Nearest_landmark_range>; + using Witness_complex = Gudhi::witness_complex::Witness_complex<Nearest_landmark_table>; + using Simplex_tree = Gudhi::Simplex_tree<>; + + Simplex_tree stree; + Nearest_landmark_table nlt; + + // Example contains 5 witnesses and 5 landmarks + Nearest_landmark_range w0 = {std::make_pair(0, 0), std::make_pair(1, 1), std::make_pair(2, 2), + std::make_pair(3, 3), std::make_pair(4, 4)}; nlt.push_back(w0); + Nearest_landmark_range w1 = {std::make_pair(1, 0), std::make_pair(2, 1), std::make_pair(3, 2), + std::make_pair(4, 3), std::make_pair(0, 4)}; nlt.push_back(w1); + Nearest_landmark_range w2 = {std::make_pair(2, 0), std::make_pair(3, 1), std::make_pair(4, 2), + std::make_pair(0, 3), std::make_pair(1, 4)}; nlt.push_back(w2); + Nearest_landmark_range w3 = {std::make_pair(3, 0), std::make_pair(4, 1), std::make_pair(0, 2), + std::make_pair(1, 3), std::make_pair(2, 4)}; nlt.push_back(w3); + Nearest_landmark_range w4 = {std::make_pair(4, 0), std::make_pair(0, 1), std::make_pair(1, 2), + std::make_pair(2, 3), std::make_pair(3, 4)}; nlt.push_back(w4); + + Witness_complex witness_complex(nlt); + BOOST_CHECK(witness_complex.create_complex(stree, 4.1)); + + std::cout << "Number of simplices: " << stree.num_simplices() << std::endl; + BOOST_CHECK(stree.num_simplices() == 31); + + // Check when complex not empty + BOOST_CHECK(!witness_complex.create_complex(stree, 4.1)); + + // Check when max_alpha_square negative + Simplex_tree stree2; + BOOST_CHECK(!witness_complex.create_complex(stree2, -0.02)); + + witness_complex.create_complex(stree2, 4.1, 2); + std::cout << "Number of simplices: " << stree2.num_simplices() << std::endl; + BOOST_CHECK(stree2.num_simplices() == 25); + +} diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp deleted file mode 100644 index 92f53417..00000000 --- a/src/Witness_complex/test/witness_complex_points.cpp +++ /dev/null @@ -1,58 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Siargey Kachanovich - * - * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "witness_complex_points" -#include <boost/test/unit_test.hpp> -#include <boost/mpl/list.hpp> - -#include <gudhi/Simplex_tree.h> -#include <gudhi/Witness_complex.h> -#include <gudhi/Construct_closest_landmark_table.h> -#include <gudhi/pick_n_random_points.h> - -#include <iostream> -#include <vector> - -typedef std::vector<double> Point; -typedef Gudhi::Simplex_tree<> Simplex_tree; -typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; -typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex; - -BOOST_AUTO_TEST_CASE(witness_complex_points) { - std::vector< typeVectorVertex > knn; - std::vector< Point > points, landmarks; - // Add grid points as witnesses - for (double i = 0; i < 10; i += 1.0) - for (double j = 0; j < 10; j += 1.0) - for (double k = 0; k < 10; k += 1.0) - points.push_back(Point({i, j, k})); - - bool b_print_output = false; - // First test: random choice - Simplex_tree complex1; - Gudhi::subsampling::pick_n_random_points(points, 100, std::back_inserter(landmarks)); - Gudhi::witness_complex::construct_closest_landmark_table<Simplex_tree::Filtration_value>(points, landmarks, knn); - assert(!knn.empty()); - WitnessComplex witnessComplex1(knn, 100, 3, complex1); - BOOST_CHECK(witnessComplex1.is_witness_complex(knn, b_print_output)); -} diff --git a/src/cmake/modules/FindGMPXX.cmake b/src/cmake/modules/FindGMPXX.cmake index 277e4b19..dda302c0 100644 --- a/src/cmake/modules/FindGMPXX.cmake +++ b/src/cmake/modules/FindGMPXX.cmake @@ -33,6 +33,10 @@ if(GMP_FOUND) DOC "Path to the GMPXX library" ) + if ( GMPXX_LIBRARIES ) + get_filename_component(GMPXX_LIBRARIES_DIR ${GMPXX_LIBRARIES} PATH CACHE ) + endif() + include(FindPackageHandleStandardArgs) find_package_handle_standard_args(GMPXX "DEFAULT_MSG" GMPXX_LIBRARIES GMPXX_INCLUDE_DIR ) diff --git a/src/cmake/modules/GUDHI_third_party_libraries.txt b/src/cmake/modules/GUDHI_third_party_libraries.txt new file mode 100644 index 00000000..75f73537 --- /dev/null +++ b/src/cmake/modules/GUDHI_third_party_libraries.txt @@ -0,0 +1,107 @@ +# This files manage third party libraries required by GUDHI + +find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread REQUIRED) + +if(NOT Boost_FOUND) + message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") +endif(NOT Boost_FOUND) + +find_package(GMP) +if(GMP_FOUND) + message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}") + INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR}) + find_package(GMPXX) + if(GMPXX_FOUND) + message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") + INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR}) + endif() +endif() + +# In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten. +# cf. http://doc.cgal.org/latest/Manual/installation.html#title40 +# A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11". +# A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html +# or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html +# but it implies to use cmake version 3.1 at least. +find_package(CGAL) + +# Only CGAL versions > 4.4 supports what Gudhi uses from CGAL +if (CGAL_VERSION VERSION_LESS 4.4.0) + message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.") + unset(CGAL_FOUND) +endif() +if(CGAL_FOUND) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + include( ${CGAL_USE_FILE} ) + + if (NOT CGAL_VERSION VERSION_LESS 4.8.0) + # HACK to detect CGAL version 4.8.0 + # CGAL version 4.8, 4.8.1 and 4.8.2 are identified as version 4.8.1000) + # cf. https://github.com/CGAL/cgal/issues/1559 + # Limit the HACK between CGAL versions 4.8 and 4.9 because of file read + if (NOT CGAL_VERSION VERSION_GREATER 4.9.0) + foreach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS}) + if (EXISTS "${CGAL_INCLUDE_DIR}/CGAL/version.h") + FILE(READ "${CGAL_INCLUDE_DIR}/CGAL/version.h" contents) + STRING(REGEX REPLACE "\n" ";" contents "${contents}") + foreach(Line ${contents}) + if("${Line}" STREQUAL "#define CGAL_VERSION 4.8") + set(CGAL_VERSION 4.8.0) + message (">>>>> HACK CGAL version to ${CGAL_VERSION}") + endif("${Line}" STREQUAL "#define CGAL_VERSION 4.8") + endforeach(Line ${contents}) + endif (EXISTS "${CGAL_INCLUDE_DIR}/CGAL/version.h") + endforeach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS}) + endif(NOT CGAL_VERSION VERSION_GREATER 4.9.0) + + # For dev version + include_directories(BEFORE "src/common/include/gudhi_patches") + # For user version + include_directories(BEFORE "include/gudhi_patches") + endif() +endif() + +# Find TBB package for parallel sort - not mandatory, just optional. +set(TBB_FIND_QUIETLY ON) +find_package(TBB) +if (TBB_FOUND) + include(${TBB_USE_FILE}) + message("TBB found in ${TBB_LIBRARY_DIRS}") + add_definitions(-DGUDHI_USE_TBB) +endif() + +set(CGAL_WITH_EIGEN3_VERSION 0.0.0) +find_package(Eigen3 3.1.0) +if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + set(CGAL_WITH_EIGEN3_VERSION ${CGAL_VERSION}) +endif (EIGEN3_FOUND) + +# Required programs for unitary tests purpose +FIND_PROGRAM( GCOVR_PATH gcovr ) +if (GCOVR_PATH) + message("gcovr found in ${GCOVR_PATH}") +endif() +# Required programs for unitary tests purpose +FIND_PROGRAM( GPROF_PATH gprof ) +if (GPROF_PATH) + message("gprof found in ${GPROF_PATH}") +endif() +FIND_PROGRAM( DIFF_PATH diff ) +if (DIFF_PATH) + message("diff found in ${DIFF_PATH}") +endif() + +# BOOST ISSUE result_of vs C++11 +add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE) +# BOOST ISSUE with Libraries name resolution under Windows +add_definitions(-DBOOST_ALL_NO_LIB) +# problem with Visual Studio link on Boost program_options +add_definitions( -DBOOST_ALL_DYN_LINK ) + +INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) +LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) + +message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS}) +message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index 6332b065..13fccd32 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -1,8 +1,6 @@ # Some functionnalities requires CMake 2.8.11 minimum if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) - string(TIMESTAMP DATE_AND_TIME "%Y-%m-%d-%H-%M-%S") - # Definition of the custom target user_version add_custom_target(user_version) @@ -11,6 +9,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${USER_VERSION_DIR}) else() # set the GUDHI_USER_VERSION_DIR with timestamp and Gudhi version number + string(TIMESTAMP DATE_AND_TIME "%Y-%m-%d-%H-%M-%S") set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${DATE_AND_TIME}_GUDHI_${GUDHI_VERSION}) endif() @@ -21,6 +20,8 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) COMMENT "user_version creation in ${GUDHI_USER_VERSION_DIR}") add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy ${CMAKE_SOURCE_DIR}/Conventions.txt ${GUDHI_USER_VERSION_DIR}/Conventions.txt) + add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/README ${GUDHI_USER_VERSION_DIR}/README) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/COPYING ${GUDHI_USER_VERSION_DIR}/COPYING) @@ -40,76 +41,53 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy_directory ${CMAKE_SOURCE_DIR}/src/cython ${GUDHI_USER_VERSION_DIR}/cython) + add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/data ${GUDHI_USER_VERSION_DIR}/data) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/src/cmake ${GUDHI_USER_VERSION_DIR}/cmake) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${CMAKE_SOURCE_DIR}/src/debian ${GUDHI_USER_VERSION_DIR}/debian) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex") - + set(GUDHI_DIRECTORIES "doc;example;concept") + set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches") + foreach(GUDHI_MODULE ${GUDHI_MODULES}) - # doc files - file(GLOB GUDHI_DOC_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/doc/*) - - foreach(GUDHI_DOC_FILE ${GUDHI_DOC_FILES}) - get_filename_component(GUDHI_DOC_FILE_NAME ${GUDHI_DOC_FILE} NAME) - # GUDHI_DOC_FILE can be a file or a directory - if(IS_DIRECTORY ${GUDHI_DOC_FILE}) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${GUDHI_DOC_FILE} ${GUDHI_USER_VERSION_DIR}/doc/${GUDHI_MODULE}/${GUDHI_DOC_FILE_NAME}) - else() - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${GUDHI_DOC_FILE} ${GUDHI_USER_VERSION_DIR}/doc/${GUDHI_MODULE}/${GUDHI_DOC_FILE_NAME}) - endif() - endforeach() - - # example files - file(GLOB GUDHI_EXAMPLE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/example/*) - - foreach(GUDHI_EXAMPLE_FILE ${GUDHI_EXAMPLE_FILES}) - get_filename_component(GUDHI_EXAMPLE_FILE_NAME ${GUDHI_EXAMPLE_FILE} NAME) - # GUDHI_EXAMPLE_FILE can be a file or a directory - if(IS_DIRECTORY ${GUDHI_EXAMPLE_FILE}) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${GUDHI_EXAMPLE_FILE} ${GUDHI_USER_VERSION_DIR}/example/${GUDHI_MODULE}/${GUDHI_EXAMPLE_FILE_NAME}) - else() - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${GUDHI_EXAMPLE_FILE} ${GUDHI_USER_VERSION_DIR}/example/${GUDHI_MODULE}/${GUDHI_EXAMPLE_FILE_NAME}) - endif() - endforeach() - - # include files - file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/gudhi/*) - - foreach(GUDHI_INCLUDE_FILE ${GUDHI_INCLUDE_FILES}) - get_filename_component(GUDHI_INCLUDE_FILE_NAME ${GUDHI_INCLUDE_FILE} NAME) - # GUDHI_INCLUDE_FILE can be a file or a directory - if(IS_DIRECTORY ${GUDHI_INCLUDE_FILE}) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME}) - else() - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME}) - endif() - endforeach() - - # concept files - file(GLOB GUDHI_CONCEPT_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/concept/*.h) - - foreach(GUDHI_CONCEPT_FILE ${GUDHI_CONCEPT_FILES}) - get_filename_component(GUDHI_CONCEPT_FILE_NAME ${GUDHI_CONCEPT_FILE} NAME) - # GUDHI_CONCEPT_FILE can be a file or a directory - if(IS_DIRECTORY ${GUDHI_CONCEPT_FILE}) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${GUDHI_CONCEPT_FILE} ${GUDHI_USER_VERSION_DIR}/concept/${GUDHI_MODULE}/${GUDHI_CONCEPT_FILE_NAME}) - else() - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${GUDHI_CONCEPT_FILE} ${GUDHI_USER_VERSION_DIR}/concept/${GUDHI_MODULE}/${GUDHI_CONCEPT_FILE_NAME}) - endif() - endforeach() - endforeach() + foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES}) + # Find files + file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*) + + foreach(GUDHI_FILE ${GUDHI_FILES}) + get_filename_component(GUDHI_FILE_NAME ${GUDHI_FILE} NAME) + # GUDHI_FILE can be a file or a directory + if(IS_DIRECTORY ${GUDHI_FILE}) + add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy_directory ${GUDHI_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_DIRECTORY}/${GUDHI_MODULE}/${GUDHI_FILE_NAME}) + else() + add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy ${GUDHI_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_DIRECTORY}/${GUDHI_MODULE}/${GUDHI_FILE_NAME}) + endif() + endforeach() + endforeach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES}) + + foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) + # include files + file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_INCLUDE_DIRECTORY}/*) + + foreach(GUDHI_INCLUDE_FILE ${GUDHI_INCLUDE_FILES}) + get_filename_component(GUDHI_INCLUDE_FILE_NAME ${GUDHI_INCLUDE_FILE} NAME) + # GUDHI_INCLUDE_FILE can be a file or a directory + if(IS_DIRECTORY ${GUDHI_INCLUDE_FILE}) + add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_INCLUDE_DIRECTORY}/${GUDHI_INCLUDE_FILE_NAME}) + else() + add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_INCLUDE_DIRECTORY}/${GUDHI_INCLUDE_FILE_NAME}) + endif() + endforeach() + endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) + + endforeach(GUDHI_MODULE ${GUDHI_MODULES}) endif() diff --git a/src/common/doc/header.html b/src/common/doc/header.html index a6f3ed9c..94e641b2 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -9,7 +9,7 @@ <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME--> <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME--> <!-- GUDHI website css for header BEGIN --> -<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" /> +<link rel="stylesheet" type="text/css" href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/gudhi-doc-2.0.0/assets/css/styles_feeling_responsive.css" /> <!-- GUDHI website css for header END --> <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/> <script type="text/javascript" src="$relpath^jquery.js"></script> @@ -25,6 +25,13 @@ $extrastylesheet <!-- GUDHI website header BEGIN --> <div id="navigation" class="sticky"> <nav class="top-bar" role="navigation" data-topbar> + <ul class="title-area"> + <li class="name"> + <h1 class="show-for-small-only"><a href="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ library</a></h1> + </li> + <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone --> + <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li> + </ul> <section class="top-bar-section"> <ul class="right"> <li class="divider"></li> @@ -37,7 +44,7 @@ $extrastylesheet <a href="#">Project</a> <ul class="dropdown"> <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li> - <li><a href="http://gudhi.gforge.inria.fr/getinvolved/">Get involved</a></li> + <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li> <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li> <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li> <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li> @@ -49,11 +56,18 @@ $extrastylesheet <ul class="dropdown"> <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li> <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">Installation manual</a></li> </ul> </li> <li class="divider"></li> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">Documentation</a></li> + <li class="has-dropdown"> + <a href="#">Documentation</a> + <ul class="dropdown"> + <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li> + <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> + <li><a href="http://gudhi.gforge.inria.fr/cython/latest/">Cython documentation</a></li> + <li><a href="http://gudhi.gforge.inria.fr/cython/latest/installation.html">Cython installation manual</a></li> + </ul> + </li> <li class="divider"></li> <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li> <li class="divider"></li> @@ -62,7 +76,7 @@ $extrastylesheet </nav> </div><!-- /#navigation --> <!-- GUDHI website header BEGIN --> - + <div id="top"><!-- do not remove this div, it is closed by doxygen! --> <!--BEGIN TITLEAREA--> diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 60c9cd07..e6f29fa8 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -3,7 +3,9 @@ * \image html "Gudhi_banner.png" "" width=20cm * * \section Introduction Introduction - * The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic open source C++ library for + * The GUDHI library (Geometry Understanding in Higher Dimensions) is a generic open source + * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/doc/latest/">C++ library</a>, with a + * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/cython/latest/">Cython interface</a>, for * Computational Topology and Topological Data Analysis * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>). * The GUDHI library intends to help the development of new algorithmic solutions in TDA and their transfer to @@ -62,7 +64,7 @@ <tr> <td width="25%"> <b>Author:</b> Clément Maria, Pawel Dlotko, Vincent Rouvreau<br> - <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Introduced in:</b> GUDHI 2.0.0<br> <b>Copyright:</b> GPL v3<br> </td> <td width="75%"> @@ -118,8 +120,9 @@ <tr> <td width="25%"> <b>Author:</b> Clément Jamin<br> - <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Introduced in:</b> GUDHI 2.0.0<br> <b>Copyright:</b> GPL v3<br> + <b>Requires:</b> \ref cgal ≥ 4.8.1 and \ref eigen3 </td> <td width="75%"> A Tangential Delaunay complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> @@ -139,6 +142,7 @@ <b>Author:</b> Siargey Kachanovich<br> <b>Introduced in:</b> GUDHI 1.3.0<br> <b>Copyright:</b> GPL v3<br> + <b>Euclidean version requires:</b> \ref cgal ≥ 4.6.0 and \ref eigen3 </td> <td width="75%"> Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$. @@ -155,9 +159,9 @@ <tr> <td width="25%"> <b>Author:</b> François Godi<br> - <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Introduced in:</b> GUDHI 2.0.0<br> <b>Copyright:</b> GPL v3<br> - <b>Requires:</b> \ref cgal ≥ 4.8.0 and \ref eigen3 + <b>Requires:</b> \ref cgal ≥ 4.8.1 and \ref eigen3 </td> <td width="75%"> Bottleneck distance measures the similarity between two persistence diagrams. @@ -211,11 +215,11 @@ </table> */ -/*! \page installation Gudhi installation +/*! \page installation GUDHI installation * \tableofcontents - * As Gudhi is a header only library, there is no need to install the library. + * As GUDHI is a header only library, there is no need to install the library. * - * Examples of Gudhi headers inclusion can be found in \ref demos. + * Examples of GUDHI headers inclusion can be found in \ref demos. * * \section compiling Compiling * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or @@ -234,6 +238,15 @@ make \endverbatim * To test your build, run the following command in a terminal: * \verbatim make test \endverbatim * + * \subsection documentationgeneration Documentation + * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required. + * Run the following command in a terminal: +\verbatim +make doxygen +# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/ +# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder` +\endverbatim + * * \section optionallibrary Optional third-party library * \subsection gmp GMP * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision @@ -249,6 +262,10 @@ make \endverbatim * \subsection cgal CGAL * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ * library which provides easy access to efficient and reliable geometric algorithms. + * + * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even + * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version ≥ 4.8.0), thereafter you will be able to compile + * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> * * Having CGAL version 4.4.0 or higher installed is recommended. The procedure to install this library according to * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html @@ -257,6 +274,10 @@ make \endverbatim * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> * @@ -276,11 +297,27 @@ make \endverbatim * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * - * The following example requires CGAL version ≥ 4.8.0: - * \li <a href="_bottleneck_distance_2_bottleneck_basic_example_8cpp-example.html"> + * The following example requires CGAL version ≥ 4.8.1: + * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> + * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> + * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html"> * Bottleneck_distance/bottleneck_basic_example.cpp</a> - * \li <a href="_bottleneck_distance_2_bottleneck_read_file_example_8cpp-example.html"> + * \li <a href="_bottleneck_distance_2bottleneck_read_file_example_8cpp-example.html"> * Bottleneck_distance/bottleneck_read_file_example.cpp</a> + * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> + * Spatial_searching/example_spatial_searching.cpp</a> + * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> + * Subsampling/example_choose_n_farthest_points.cpp</a> + * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> + * Subsampling/example_custom_kernel.cpp</a> + * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> + * Subsampling/example_pick_n_random_points.cpp</a> + * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> + * Subsampling/example_sparsify_point_set.cpp</a> + * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> + * Tangential_complex/example_basic.cpp</a> + * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> + * Tangential_complex/example_with_perturb.cpp</a> * * \subsection eigen3 Eigen3 * The \ref alpha_complex data structure and few examples requires @@ -348,6 +385,10 @@ make \endverbatim * Persistent_cohomology/rips_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> + * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> @@ -361,7 +402,7 @@ make \endverbatim * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim * - * Gudhi is open to external contributions. If you want to join our development team, please contact us. + * GUDHI is open to external contributions. If you want to join our development team, please contact us. * */ @@ -376,10 +417,11 @@ make \endverbatim * \verbinclude biblio/how_to_cite_gudhi.bib */ -// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments +// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments /*! @file Examples * @example Alpha_complex/Alpha_complex_from_off.cpp * @example Alpha_complex/Alpha_complex_from_points.cpp + * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp * @example Bottleneck_distance/bottleneck_basic_example.cpp * @example Bottleneck_distance/bottleneck_read_file_example.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp @@ -392,6 +434,8 @@ make \endverbatim * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/alpha_complex_persistence.cpp * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp + * @example Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp + * @example Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/persistence_from_file.cpp * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp @@ -410,9 +454,18 @@ make \endverbatim * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp * @example Skeleton_blocker/Skeleton_blocker_link.cpp + * @example Spatial_searching/example_spatial_searching.cpp + * @example Subsampling/example_choose_n_farthest_points.cpp + * @example Subsampling/example_custom_kernel.cpp + * @example Subsampling/example_pick_n_random_points.cpp + * @example Subsampling/example_sparsify_point_set.cpp * @example Tangential_complex/example_basic.cpp * @example Tangential_complex/example_with_perturb.cpp - * @example Witness_complex/witness_complex_from_file.cpp - * @example Witness_complex/witness_complex_sphere.cpp + * @example Witness_complex/example_nearest_landmark_table.cpp + * @example Witness_complex/example_strong_witness_complex_off.cpp + * @example Witness_complex/example_strong_witness_persistence.cpp + * @example Witness_complex/example_witness_complex_off.cpp + * @example Witness_complex/example_witness_complex_persistence.cpp + * @example Witness_complex/example_witness_complex_sphere.cpp */ diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index b0c6d69a..61c94391 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -10,12 +10,10 @@ if(CGAL_FOUND) target_link_libraries(cgal_3D_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) add_test(cgal_3D_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_3D_off_reader ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - # need CGAL 4.7 - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - if (EIGEN3_FOUND) - add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp ) - target_link_libraries(cgal_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off) - endif(EIGEN3_FOUND) - endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) + # need CGAL 4.7and Eigen3 + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp ) + target_link_libraries(cgal_off_reader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) endif() diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index 5891ef0e..22747637 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -24,6 +24,8 @@ #define DISTANCE_FUNCTIONS_H_ #include <cmath> // for std::sqrt +#include <type_traits> // for std::decay +#include <iterator> // for std::begin, std::end /** @file * @brief Global distance functions @@ -34,7 +36,7 @@ class Euclidean_distance { public: template< typename Point > - auto operator()(const Point& p1, const Point& p2) -> typename std::decay<decltype(*std::begin(p1))>::type { + auto operator()(const Point& p1, const Point& p2) const -> typename std::decay<decltype(*std::begin(p1))>::type { auto it1 = p1.begin(); auto it2 = p2.begin(); typename Point::value_type dist = 0.; diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt new file mode 100644 index 00000000..2131505d --- /dev/null +++ b/src/cython/CMakeLists.txt @@ -0,0 +1,225 @@ +cmake_minimum_required(VERSION 2.8) +project(Cython) + +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 ${THE_LIBS}) +endmacro( find_the_lib ) + +FIND_PROGRAM( PYTHON_PATH python ) +FIND_PROGRAM( CYTHON_PATH cython ) + +if(PYTHON_PATH AND CYTHON_PATH) + find_package(Boost REQUIRED COMPONENTS system REQUIRED) + + if(NOT Boost_FOUND) + message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.") + else(NOT Boost_FOUND) + + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${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}'${BOOST_SYSTEM_LIB_NAME}', ") + + # Gudhi and CGAL compilation option + if(MSVC) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") + else(MSVC) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ") + endif(MSVC) + if(CMAKE_COMPILER_IS_GNUCXX) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") + endif(CMAKE_COMPILER_IS_GNUCXX) + if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") + endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + if (DEBUG_TRACES) + # For programs to be more verbose + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") + endif() + + find_package(Eigen3 3.1.0) + + if (EIGEN3_FOUND) + # No problem, even if no CGAL 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 + # 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") + 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 "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${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 'cython/subsampling.pyx'") + set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'") + set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '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 + set(GUDHI_CYTHON_ALPHA_COMPLEX "include '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 + set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX + "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n") + else (NOT CGAL_VERSION VERSION_LESS 4.6.0) + # Remove alpha 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 "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst") + endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) + + if(CGAL_FOUND) + # Add CGAL compilation args + if(CGAL_HEADER_ONLY) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${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) + 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") + if(WIN32) + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ") + else(WIN32) + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ") + endif(WIN32) + set(GUDHI_CYTHON_LIBRARY_DIRS "${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 "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") + endif(GMPXX_FOUND) + endif(GMP_FOUND) + endif(CGAL_FOUND) + + # Specific for Mac + if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.9', ") + set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.9', ") + endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + + # Loop on INCLUDE_DIRECTORIES PROPERTY + get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) + foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") + endforeach() + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") + + 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', ") + 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() + + # Generate cythonize_gudhi.py file to cythonize Gudhi + configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY) + # Generate gudhi.pyx - Gudhi cython file + configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY) + + add_custom_command( + OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND python "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace") + + add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/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) + + # Unitary tests are available through py.test + find_program( PYTEST_PATH py.test ) + if(PYTEST_PATH) + add_test( + NAME gudhi_cython_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTEST_PATH}) + set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + endif(PYTEST_PATH) + + # Documentation generation is available through sphinx + find_program( SPHINX_PATH sphinx-build ) + 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 ${CMAKE_CURRENT_BINARY_DIR}/doc + COMMAND make.bat html) + endif (UNIX) + endif(SPHINX_PATH) + endif(NOT Boost_FOUND) +endif(PYTHON_PATH AND CYTHON_PATH) diff --git a/src/cython/CONVENTIONS b/src/cython/CONVENTIONS new file mode 100644 index 00000000..804e97f3 --- /dev/null +++ b/src/cython/CONVENTIONS @@ -0,0 +1,9 @@ +Gudhi is following PEP8 conventions. + +Please refer to: +https://www.python.org/dev/peps/pep-0008/ + +A summary: + - modules (filenames) should have short, all-lowercase names, and they can contain underscores. + - packages (directories) should have short, all-lowercase names, preferably without underscores. + - classes should use the CapWords convention.
\ No newline at end of file diff --git a/src/cython/README b/src/cython/README new file mode 100644 index 00000000..7d2c4491 --- /dev/null +++ b/src/cython/README @@ -0,0 +1,3 @@ + +If you do not want to install the package, just launch the following command to help Python to find the compiled package : +$> export PYTHONPATH=`pwd`:$PYTHONPATH diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx new file mode 100644 index 00000000..da537c2e --- /dev/null +++ b/src/cython/cython/alpha_complex.pyx @@ -0,0 +1,121 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp.string cimport string +from libcpp cimport bool +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": + cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface": + Alpha_complex_interface(vector[vector[double]] points) + # bool from_file is a workaround for cython to find the correct signature + Alpha_complex_interface(string off_file, bool from_file) + vector[double] get_point(int vertex) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + +# AlphaComplex python interface +cdef class AlphaComplex: + """AlphaComplex is a simplicial complex constructed from the finite cells + of a Delaunay Triangulation. + + The filtration value of each simplex is computed as the square of the + circumradius of the simplex if the circumsphere is empty (the simplex is + then said to be Gabriel), and as the minimum of the filtration values of + the codimension 1 cofaces that make it not Gabriel otherwise. + + All simplices that have a filtration value strictly greater than a given + alpha squared value are not inserted into the complex. + + .. note:: + + When Alpha_complex is constructed with an infinite value of alpha, the + complex is a Delaunay complex. + + """ + + cdef Alpha_complex_interface * thisptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, points=None, off_file=''): + """AlphaComplex constructor. + + :param points: A list of points in d-Dimension. + :type points: list of list of double + + Or + + :param off_file: An OFF file style name. + :type off_file: string + """ + + # The real cython constructor + def __cinit__(self, points=None, off_file=''): + if off_file is not '': + if os.path.isfile(off_file): + self.thisptr = new Alpha_complex_interface(off_file, True) + else: + print("file " + off_file + " not found.") + else: + if points is None: + # Empty Alpha construction + points=[] + self.thisptr = new Alpha_complex_interface(points) + + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + + def __is_defined(self): + """Returns true if AlphaComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def get_point(self, vertex): + """This function returns the point corresponding to a given vertex. + + :param vertex: The vertex. + :type vertex: int + :rtype: list of float + :returns: the point. + """ + cdef vector[double] point = self.thisptr.get_point(vertex) + return point + + def create_simplex_tree(self, max_alpha_square=float('inf')): + """ + :param max_alpha_square: The maximum alpha square threshold the + simplices shall not exceed. Default is set to infinity. + :type max_alpha_square: float + :returns: A simplex tree created from the Delaunay Triangulation. + :rtype: SimplexTree + """ + simplex_tree = SimplexTree() + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square) + return simplex_tree diff --git a/src/cython/cython/bottleneck_distance.pyx b/src/cython/cython/bottleneck_distance.pyx new file mode 100644 index 00000000..ee3e6ef9 --- /dev/null +++ b/src/cython/cython/bottleneck_distance.pyx @@ -0,0 +1,59 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility 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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Bottleneck_distance_interface.h" namespace "Gudhi::persistence_diagram": + double bottleneck(vector[pair[double, double]], vector[pair[double, double]], double) + double bottleneck(vector[pair[double, double]], vector[pair[double, double]]) + +def bottleneck_distance(diagram_1, diagram_2, e=0.0): + """This function returns the point corresponding to a given vertex. + + :param diagram_1: The first diagram. + :type diagram_1: vector[pair[double, double]] + :param diagram_2: The second diagram. + :type diagram_2: vector[pair[double, double]] + :param e: If `e` is 0, this uses an expensive algorithm to compute the + exact distance. + If `e` is not 0, it asks for an additive `e`-approximation, and + currently also allows a small multiplicative error (the last 2 or 3 + bits of the mantissa may be wrong). This version of the algorithm takes + advantage of the limited precision of `double` and is usually a lot + faster to compute, whatever the value of `e`. + + Thus, by default, `e` is the smallest positive double. + :type e: float + :rtype: float + :returns: the bottleneck distance. + """ + if e is 0.0: + return bottleneck(diagram_1, diagram_2) + else: + return bottleneck(diagram_1, diagram_2, e) diff --git a/src/cython/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx new file mode 100644 index 00000000..e1344f49 --- /dev/null +++ b/src/cython/cython/cubical_complex.pyx @@ -0,0 +1,197 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp.string cimport string +from libcpp cimport bool +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": + cdef cppclass Bitmap_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface<>": + Bitmap_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells) + Bitmap_cubical_complex_base_interface(string perseus_file) + int num_simplices() + int dimension() + +cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": + cdef cppclass Cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<>>": + Cubical_complex_persistence_interface(Bitmap_cubical_complex_base_interface * st, bool persistence_dim_max) + vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence) + vector[int] betti_numbers() + vector[int] persistent_betti_numbers(double from_value, double to_value) + vector[pair[double,double]] intervals_in_dimension(int dimension) + +# CubicalComplex python interface +cdef class CubicalComplex: + """The CubicalComplex is an example of a structured complex useful in + computational mathematics (specially rigorous numerics) and image + analysis. + """ + cdef Bitmap_cubical_complex_base_interface * thisptr + + cdef Cubical_complex_persistence_interface * pcohptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, dimensions=None, top_dimensional_cells=None, + perseus_file=''): + """CubicalComplex constructor from dimensions and + top_dimensional_cells or from a perseus file style name. + + :param dimensions: A list of number of top dimensional cells. + :type dimensions: list of int + :param top_dimensional_cells: A list of top dimensional cells. + :type top_dimensional_cells: list of double + + Or + + :param perseus_file: A perseus file style name. + :type perseus_file: string + """ + + # The real cython constructor + def __cinit__(self, dimensions=None, top_dimensional_cells=None, + perseus_file=''): + if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''): + self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells) + elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''): + if os.path.isfile(perseus_file): + self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file) + else: + print("file " + perseus_file + " not found.") + else: + print("CubicalComplex can be constructed from dimensions and " + "top_dimensional_cells or from a perseus file style name.") + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + if self.pcohptr != NULL: + del self.pcohptr + + def __is_defined(self): + """Returns true if CubicalComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def __is_persistence_defined(self): + """Returns true if Persistence pointer is not NULL. + """ + return self.pcohptr != NULL + + def num_simplices(self): + """This function returns the number of simplices of the simplicial + complex. + + :returns: int -- the simplicial complex number of simplices. + """ + return self.thisptr.num_simplices() + + def dimension(self): + """This function returns the dimension of the simplicial complex. + + :returns: int -- the simplicial complex dimension. + """ + return self.thisptr.dimension() + + def persistence(self, homology_coeff_field=11, min_persistence=0): + """This function returns the persistence of the simplicial complex. + + :param homology_coeff_field: The homology coefficient field. Must be a + prime number + :type homology_coeff_field: int. + :param min_persistence: The minimum persistence value to take into + account (strictly greater than min_persistence). Default value is + 0.0. + Sets min_persistence to -1.0 to see all values. + :type min_persistence: float. + :returns: list of pairs(dimension, pair(birth, death)) -- the + persistence of the simplicial complex. + """ + if self.pcohptr != NULL: + del self.pcohptr + if self.thisptr != NULL: + self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr, True) + cdef vector[pair[int, pair[double, double]]] persistence_result + if self.pcohptr != NULL: + persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) + return persistence_result + + def betti_numbers(self): + """This function returns the Betti numbers of the simplicial complex. + + :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]). + + :note: betti_numbers function requires persistence function to be + launched first. + """ + cdef vector[int] bn_result + if self.pcohptr != NULL: + bn_result = self.pcohptr.betti_numbers() + return bn_result + + def persistent_betti_numbers(self, from_value, to_value): + """This function returns the persistent Betti numbers of the + simplicial complex. + + :param from_value: The persistence birth limit to be added in the + numbers (persistent birth <= from_value). + :type from_value: float. + :param to_value: The persistence death limit to be added in the + numbers (persistent death > to_value). + :type to_value: float. + + :returns: list of int -- The persistent Betti numbers ([B0, B1, ..., + Bn]). + + :note: persistent_betti_numbers function requires persistence + function to be launched first. + """ + cdef vector[int] pbn_result + if self.pcohptr != NULL: + pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value) + return pbn_result + + def persistence_intervals_in_dimension(self, dimension): + """This function returns the persistence intervals of the simplicial + complex in a specific dimension. + + :param dimension: The specific dimension. + :type from_value: int. + :returns: The persistence intervals. + :rtype: list of pair of float + + :note: intervals_in_dim function requires persistence function to be + launched first. + """ + cdef vector[pair[double,double]] intervals_result + if self.pcohptr != NULL: + intervals_result = self.pcohptr.intervals_in_dimension(dimension) + else: + print("intervals_in_dim function requires persistence function" + " to be launched first.") + return intervals_result diff --git a/src/cython/cython/euclidean_strong_witness_complex.pyx b/src/cython/cython/euclidean_strong_witness_complex.pyx new file mode 100644 index 00000000..c1523892 --- /dev/null +++ b/src/cython/cython/euclidean_strong_witness_complex.pyx @@ -0,0 +1,97 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi": + cdef cppclass Euclidean_strong_witness_complex_interface "Gudhi::witness_complex::Euclidean_strong_witness_complex_interface": + Euclidean_strong_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, + unsigned limit_dimension) + vector[double] get_point(unsigned vertex) + +# EuclideanStrongWitnessComplex python interface +cdef class EuclideanStrongWitnessComplex: + """Constructs strong witness complex for given sets of witnesses and + landmarks in Euclidean space. + """ + + cdef Euclidean_strong_witness_complex_interface * thisptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, landmarks=None, witnesses=None): + """WitnessComplex constructor. + + :param landmarks: A list of landmarks (in the point cloud). + :type landmarks: list of list of double + + :param witnesses: The point cloud. + :type witnesses: list of list of double + """ + + # The real cython constructor + def __cinit__(self, landmarks=None, witnesses=None): + if landmarks is not None and witnesses is not None: + self.thisptr = new Euclidean_strong_witness_complex_interface(landmarks, witnesses) + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + + def __is_defined(self): + """Returns true if WitnessComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def create_simplex_tree(self, max_alpha_square, limit_dimension = -1): + """ + :param max_alpha_square: The maximum alpha square threshold the + simplices shall not exceed. Default is set to infinity. + :type max_alpha_square: float + :returns: A simplex tree created from the Delaunay Triangulation. + :rtype: SimplexTree + """ + simplex_tree = SimplexTree() + if limit_dimension is not -1: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension) + else: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square) + return simplex_tree + + def get_point(self, vertex): + """This function returns the point corresponding to a given vertex. + + :param vertex: The vertex. + :type vertex: int. + :returns: The point. + :rtype: list of float + """ + cdef vector[double] point = self.thisptr.get_point(vertex) + return point + diff --git a/src/cython/cython/euclidean_witness_complex.pyx b/src/cython/cython/euclidean_witness_complex.pyx new file mode 100644 index 00000000..7c443b6b --- /dev/null +++ b/src/cython/cython/euclidean_witness_complex.pyx @@ -0,0 +1,97 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi": + cdef cppclass Euclidean_witness_complex_interface "Gudhi::witness_complex::Euclidean_witness_complex_interface": + Euclidean_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, + unsigned limit_dimension) + vector[double] get_point(unsigned vertex) + +# EuclideanWitnessComplex python interface +cdef class EuclideanWitnessComplex: + """Constructs (weak) witness complex for given sets of witnesses and + landmarks in Euclidean space. + """ + + cdef Euclidean_witness_complex_interface * thisptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, landmarks=None, witnesses=None): + """WitnessComplex constructor. + + :param landmarks: A list of landmarks (in the point cloud). + :type landmarks: list of list of double + + :param witnesses: The point cloud. + :type witnesses: list of list of double + """ + + # The real cython constructor + def __cinit__(self, landmarks=None, witnesses=None): + if landmarks is not None and witnesses is not None: + self.thisptr = new Euclidean_witness_complex_interface(landmarks, witnesses) + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + + def __is_defined(self): + """Returns true if WitnessComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def create_simplex_tree(self, max_alpha_square, limit_dimension = -1): + """ + :param max_alpha_square: The maximum alpha square threshold the + simplices shall not exceed. Default is set to infinity. + :type max_alpha_square: float + :returns: A simplex tree created from the Delaunay Triangulation. + :rtype: SimplexTree + """ + simplex_tree = SimplexTree() + if limit_dimension is not -1: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension) + else: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square) + return simplex_tree + + def get_point(self, vertex): + """This function returns the point corresponding to a given vertex. + + :param vertex: The vertex. + :type vertex: int. + :returns: The point. + :rtype: list of float + """ + cdef vector[double] point = self.thisptr.get_point(vertex) + return point + diff --git a/src/cython/cython/off_reader.pyx b/src/cython/cython/off_reader.pyx new file mode 100644 index 00000000..78c37969 --- /dev/null +++ b/src/cython/cython/off_reader.pyx @@ -0,0 +1,49 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.string cimport string +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Off_reader_interface.h" namespace "Gudhi": + vector[vector[double]] read_points_from_OFF_file(string off_file) + +def read_off(off_file=''): + """Read points from OFF file. + + :param off_file: An OFF file style name. + :type off_file: string + + :returns: The point set. + :rtype: vector[vector[double]] + """ + if off_file is not '': + if os.path.isfile(off_file): + return read_points_from_OFF_file(off_file) + else: + print("file " + off_file + " not found.") + diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx new file mode 100644 index 00000000..1445d429 --- /dev/null +++ b/src/cython/cython/periodic_cubical_complex.pyx @@ -0,0 +1,197 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp.string cimport string +from libcpp cimport bool +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": + cdef cppclass Periodic_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>": + Periodic_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells) + Periodic_cubical_complex_base_interface(string perseus_file) + int num_simplices() + int dimension() + +cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": + cdef cppclass Periodic_cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>>": + Periodic_cubical_complex_persistence_interface(Periodic_cubical_complex_base_interface * st, bool persistence_dim_max) + vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence) + vector[int] betti_numbers() + vector[int] persistent_betti_numbers(double from_value, double to_value) + vector[pair[double,double]] intervals_in_dimension(int dimension) + +# PeriodicCubicalComplex python interface +cdef class PeriodicCubicalComplex: + """The PeriodicCubicalComplex is an example of a structured complex useful + in computational mathematics (specially rigorous numerics) and image + analysis. + """ + cdef Periodic_cubical_complex_base_interface * thisptr + + cdef Periodic_cubical_complex_persistence_interface * pcohptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, dimensions=None, top_dimensional_cells=None, + perseus_file=''): + """PeriodicCubicalComplex constructor from dimensions and + top_dimensional_cells or from a perseus file style name. + + :param dimensions: A list of number of top dimensional cells. + :type dimensions: list of int + :param top_dimensional_cells: A list of top dimensional cells. + :type top_dimensional_cells: list of double + + Or + + :param perseus_file: A perseus file style name. + :type perseus_file: string + """ + + # The real cython constructor + def __cinit__(self, dimensions=None, top_dimensional_cells=None, + perseus_file=''): + if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''): + self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells) + elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''): + if os.path.isfile(perseus_file): + self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file) + else: + print("file " + perseus_file + " not found.") + else: + print("CubicalComplex can be constructed from dimensions and " + "top_dimensional_cells or from a perseus file style name.") + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + if self.pcohptr != NULL: + del self.pcohptr + + def __is_defined(self): + """Returns true if PeriodicCubicalComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def __is_persistence_defined(self): + """Returns true if Persistence pointer is not NULL. + """ + return self.pcohptr != NULL + + def num_simplices(self): + """This function returns the number of simplices of the simplicial + complex. + + :returns: int -- the simplicial complex number of simplices. + """ + return self.thisptr.num_simplices() + + def dimension(self): + """This function returns the dimension of the simplicial complex. + + :returns: int -- the simplicial complex dimension. + """ + return self.thisptr.dimension() + + def persistence(self, homology_coeff_field=11, min_persistence=0): + """This function returns the persistence of the simplicial complex. + + :param homology_coeff_field: The homology coefficient field. Must be a + prime number + :type homology_coeff_field: int. + :param min_persistence: The minimum persistence value to take into + account (strictly greater than min_persistence). Default value is + 0.0. + Sets min_persistence to -1.0 to see all values. + :type min_persistence: float. + :returns: list of pairs(dimension, pair(birth, death)) -- the + persistence of the simplicial complex. + """ + if self.pcohptr != NULL: + del self.pcohptr + if self.thisptr != NULL: + self.pcohptr = new Periodic_cubical_complex_persistence_interface(self.thisptr, True) + cdef vector[pair[int, pair[double, double]]] persistence_result + if self.pcohptr != NULL: + persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) + return persistence_result + + def betti_numbers(self): + """This function returns the Betti numbers of the simplicial complex. + + :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]). + + :note: betti_numbers function requires persistence function to be + launched first. + """ + cdef vector[int] bn_result + if self.pcohptr != NULL: + bn_result = self.pcohptr.betti_numbers() + return bn_result + + def persistent_betti_numbers(self, from_value, to_value): + """This function returns the persistent Betti numbers of the + simplicial complex. + + :param from_value: The persistence birth limit to be added in the + numbers (persistent birth <= from_value). + :type from_value: float. + :param to_value: The persistence death limit to be added in the + numbers (persistent death > to_value). + :type to_value: float. + + :returns: list of int -- The persistent Betti numbers ([B0, B1, ..., + Bn]). + + :note: persistent_betti_numbers function requires persistence + function to be launched first. + """ + cdef vector[int] pbn_result + if self.pcohptr != NULL: + pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value) + return pbn_result + + def persistence_intervals_in_dimension(self, dimension): + """This function returns the persistence intervals of the simplicial + complex in a specific dimension. + + :param dimension: The specific dimension. + :type from_value: int. + :returns: The persistence intervals. + :rtype: list of pair of float + + :note: intervals_in_dim function requires persistence function to be + launched first. + """ + cdef vector[pair[double,double]] intervals_result + if self.pcohptr != NULL: + intervals_result = self.pcohptr.intervals_in_dimension(dimension) + else: + print("intervals_in_dim function requires persistence function" + " to be launched first.") + return intervals_result diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py new file mode 100755 index 00000000..a984633e --- /dev/null +++ b/src/cython/cython/persistence_graphical_tools.py @@ -0,0 +1,152 @@ +import matplotlib.pyplot as plt +import numpy as np + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +def __min_birth_max_death(persistence): + """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)). + :returns: (float, float) -- (min_birth, max_death). + """ + # Look for minimum birth date and maximum death date for plot optimisation + max_death = 0 + min_birth = persistence[0][1][0] + for interval in reversed(persistence): + if float(interval[1][1]) != float('inf'): + if float(interval[1][1]) > max_death: + max_death = float(interval[1][1]) + if float(interval[1][0]) > max_death: + max_death = float(interval[1][0]) + if float(interval[1][0]) < min_birth: + min_birth = float(interval[1][0]) + return (min_birth, max_death) + +""" +Only 13 colors for the palette +""" +palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00', + '#000000', '#880000', '#008800', '#000088', '#888800', '#880088', + '#008888'] + +def show_palette_values(alpha=0.6): + """This function shows palette color values in function of the dimension. + + :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6). + :type alpha: float. + :returns: plot -- An horizontal bar plot of dimensions color. + """ + colors = [] + for color in palette: + colors.append(color) + + y_pos = np.arange(len(palette)) + + plt.barh(y_pos, y_pos + 1, align='center', alpha=alpha, color=colors) + plt.ylabel('Dimension') + plt.title('Dimension palette values') + + plt.show() + +def plot_persistence_barcode(persistence, alpha=0.6): + """This function plots the persistence bar code. + + :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 horizontal bars (default is 0.6). + :type alpha: float. + :returns: plot -- An horizontal bar plot of persistence. + """ + (min_birth, max_death) = __min_birth_max_death(persistence) + ind = 0 + delta = ((max_death - min_birth) / 10.0) + # Replace infinity values with max_death + delta for bar code to be more + # readable + infinity = max_death + delta + axis_start = min_birth - delta + # Draw horizontal bars in loop + for interval in reversed(persistence): + if float(interval[1][1]) != float('inf'): + # Finite death case + plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8, + left = interval[1][0], alpha=alpha, + color = palette[interval[0]]) + else: + # Infinite death case for diagram to be nicer + plt.barh(ind, (infinity - interval[1][0]), height=0.8, + left = interval[1][0], alpha=alpha, + color = palette[interval[0]]) + ind = ind + 1 + + plt.title('Persistence barcode') + # Ends plot on infinity value and starts a little bit before min_birth + plt.axis([axis_start, infinity, 0, ind]) + plt.show() + +def plot_persistence_diagram(persistence, alpha=0.6): + """This function plots the persistence diagram. + + :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. + """ + (min_birth, max_death) = __min_birth_max_death(persistence) + ind = 0 + delta = ((max_death - min_birth) / 10.0) + # Replace infinity values with max_death + delta for diagram to be more + # readable + infinity = max_death + delta + axis_start = min_birth - delta + + # line display of equation : birth = death + x = np.linspace(axis_start, infinity, 1000) + # infinity line and text + 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) + + # Draw points in loop + for interval in reversed(persistence): + if float(interval[1][1]) != float('inf'): + # Finite death case + plt.scatter(interval[1][0], interval[1][1], alpha=alpha, + color = palette[interval[0]]) + else: + # Infinite death case for diagram to be nicer + plt.scatter(interval[1][0], infinity, alpha=alpha, + color = palette[interval[0]]) + ind = ind + 1 + + plt.title('Persistence diagram') + plt.xlabel('Birth') + 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() diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx new file mode 100644 index 00000000..6bfb4482 --- /dev/null +++ b/src/cython/cython/rips_complex.pyx @@ -0,0 +1,125 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp.string cimport string +from libcpp cimport bool +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Rips_complex_interface.h" namespace "Gudhi": + cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface": + Rips_complex_interface(vector[vector[double]] values, double threshold, bool euclidean) + # bool from_file is a workaround for cython to find the correct signature + Rips_complex_interface(string file_name, double threshold, bool euclidean, bool from_file) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) + +# RipsComplex python interface +cdef class RipsComplex: + """The data structure is a one skeleton graph, or Rips graph, containing + edges when the edge length is less or equal to a given threshold. Edge + length is computed from a user given point cloud with a given distance + function, or a distance matrix. + """ + + cdef Rips_complex_interface * thisptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')): + """RipsComplex constructor. + + :param max_edge_length: Rips value. + :type max_edge_length: int + + :param points: A list of points in d-Dimension. + :type points: list of list of double + + Or + + :param off_file: An OFF file style name. + :type off_file: string + + Or + + :param distance_matrix: A distance matrix (full square or lower + triangular). + :type points: list of list of double + + Or + + :param csv_file: A csv file style name containing a full square or a + lower triangular distance matrix. + :type csv_file: string + """ + + # The real cython constructor + def __cinit__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')): + if off_file is not '': + if os.path.isfile(off_file): + self.thisptr = new Rips_complex_interface(off_file, + max_edge_length, + True, + True) + else: + print("file " + off_file + " not found.") + elif csv_file is not '': + if os.path.isfile(csv_file): + self.thisptr = new Rips_complex_interface(csv_file, + max_edge_length, + False, + True) + else: + print("file " + csv_file + " not found.") + elif distance_matrix is not None: + self.thisptr = new Rips_complex_interface(distance_matrix, max_edge_length, False) + else: + if points is None: + # Empty Rips construction + points=[] + self.thisptr = new Rips_complex_interface(points, max_edge_length, True) + + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + + def __is_defined(self): + """Returns true if RipsComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def create_simplex_tree(self, max_dimension=1): + """ + :param max_dimension: graph expansion for rips until this given maximal + dimension. + :type max_dimension: int + :returns: A simplex tree created from the Delaunay Triangulation. + :rtype: SimplexTree + """ + simplex_tree = SimplexTree() + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_dimension) + return simplex_tree diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx new file mode 100644 index 00000000..148227e1 --- /dev/null +++ b/src/cython/cython/simplex_tree.pyx @@ -0,0 +1,427 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp cimport bool + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": + cdef cppclass Simplex_tree_options_full_featured: + pass + + cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>": + Simplex_tree() + double filtration() + double simplex_filtration(vector[int] simplex) + void set_filtration(double filtration) + void initialize_filtration() + int num_vertices() + int num_simplices() + void set_dimension(int dimension) + int dimension() + bint find_simplex(vector[int] simplex) + bint insert_simplex_and_subfaces(vector[int] simplex, + double filtration) + bint insert_simplex(vector[int] simplex, double filtration) + vector[pair[vector[int], double]] get_filtered_tree() + vector[pair[vector[int], double]] get_skeleton_tree(int dimension) + vector[pair[vector[int], double]] get_star(vector[int] simplex) + vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, + int dimension) + void remove_maximal_simplex(vector[int] simplex) + void expansion(int max_dim) + +cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": + cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>": + Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max) + vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence) + vector[int] betti_numbers() + vector[int] persistent_betti_numbers(double from_value, double to_value) + vector[pair[double,double]] intervals_in_dimension(int dimension) + +# SimplexTree python interface +cdef class SimplexTree: + """The simplex tree is an efficient and flexible data structure for + representing general (filtered) simplicial complexes. The data structure + is described in Jean-Daniel Boissonnat and Clément Maria. The Simplex + Tree: An Efficient Data Structure for General Simplicial Complexes. + Algorithmica, pages 1–22, 2014. + + This class is a filtered, with keys, and non contiguous vertices version + of the simplex tree. + """ + cdef Simplex_tree_interface_full_featured * thisptr + + cdef Simplex_tree_persistence_interface * pcohptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self): + """SimplexTree constructor. + """ + + # The real cython constructor + def __cinit__(self): + self.thisptr = new Simplex_tree_interface_full_featured() + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + if self.pcohptr != NULL: + del self.pcohptr + + def __is_defined(self): + """Returns true if SimplexTree pointer is not NULL. + """ + return self.thisptr != NULL + + def __is_persistence_defined(self): + """Returns true if Persistence pointer is not NULL. + """ + return self.pcohptr != NULL + + def get_filtration(self): + """This function returns the main simplicial complex filtration value. + + :returns: The simplicial complex filtration value. + :rtype: float + """ + return self.thisptr.filtration() + + def filtration(self, simplex): + """This function returns the simplicial complex filtration value for a + given N-simplex. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + :returns: The simplicial complex filtration value. + :rtype: float + """ + 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(<double> filtration) + + def initialize_filtration(self): + """This function initializes and sorts the simplicial complex + filtration vector. + + .. note:: + + This function must be launched before persistence, betti_numbers, + persistent_betti_numbers or get_filtered_tree after inserting or + removing simplices. + """ + self.thisptr.initialize_filtration() + + def num_vertices(self): + """This function returns the number of vertices of the simplicial + complex. + + :returns: The simplicial complex number of vertices. + :rtype: int + """ + return self.thisptr.num_vertices() + + def num_simplices(self): + """This function returns the number of simplices of the simplicial + complex. + + :returns: the simplicial complex number of simplices. + :rtype: int + """ + return self.thisptr.num_simplices() + + def dimension(self): + """This function returns the dimension of the simplicial complex. + + :returns: the simplicial complex dimension. + :rtype: int + """ + return self.thisptr.dimension() + + def set_dimension(self, dimension): + """This function sets the dimension of the simplicial complex. + + insert and remove_maximal_simplex functions do not update dimension + value of the `SimplexTree`. + + `AlphaComplex`, `RipsComplex`, `TangentialComplex` and `WitnessComplex` + automatically sets the correct dimension in their `create_simplex_tree` + functions. + + :param dimension: The new dimension value. + :type dimension: int. + """ + self.thisptr.set_dimension(<int>dimension) + + def find(self, simplex): + """This function returns if the N-simplex was found in the simplicial + complex or not. + + :param simplex: The N-simplex to find, represented by a list of vertex. + :type simplex: list of int. + :returns: true if the simplex was found, false otherwise. + :rtype: bool + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + return self.thisptr.find_simplex(complex) + + def insert_simplex(self, simplex, filtration=0.0): + """This function inserts the given N-simplex with the given filtration + value (default value is '0.0'). + + :param simplex: The N-simplex to insert, represented by a list of + vertex. + :type simplex: list of int. + :param filtration: The filtration value of the simplex. + :type filtration: float. + :returns: true if the simplex was found, false otherwise. + :rtype: bool + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + return self.thisptr.insert_simplex(complex, <double>filtration) + + def insert_simplex_and_subfaces(self, simplex, filtration=0.0): + """This function inserts the given N-simplex and its subfaces with the + given filtration value (default value is '0.0'). + + :param simplex: The N-simplex to insert, represented by a list of + vertex. + :type simplex: list of int. + :param filtration: The filtration value of the simplex. + :type filtration: float. + :returns: true if the simplex was found, false otherwise. + :rtype: bool + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + return self.thisptr.insert_simplex_and_subfaces(complex, + <double>filtration) + + def get_filtered_tree(self): + """This function returns the tree sorted by increasing filtration + values. + + :returns: The tree sorted by increasing filtration values. + :rtype: list of tuples(simplex, filtration) + """ + cdef vector[pair[vector[int], double]] filtered_tree \ + = self.thisptr.get_filtered_tree() + ct = [] + for filtered_complex in filtered_tree: + v = [] + for vertex in filtered_complex.first: + v.append(vertex) + ct.append((v, filtered_complex.second)) + return ct + + def get_skeleton_tree(self, dimension): + """This function returns the tree skeleton of a maximum given + dimension. + + :param dimension: The skeleton dimension value. + :type dimension: int. + :returns: The skeleton tree of a maximum dimension. + :rtype: list of tuples(simplex, filtration) + """ + cdef vector[pair[vector[int], double]] sk_tree \ + = self.thisptr.get_skeleton_tree(<int>dimension) + ct = [] + for filtered_complex in sk_tree: + v = [] + for vertex in filtered_complex.first: + v.append(vertex) + ct.append((v, filtered_complex.second)) + return ct + + def get_star(self, simplex): + """This function returns the stars of a given N-simplex. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + :returns: The star tree of a simplex. + :rtype: list of tuples(simplex, filtration) + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + cdef vector[pair[vector[int], double]] stars \ + = self.thisptr.get_star(complex) + ct = [] + for filtered_complex in stars: + v = [] + for vertex in filtered_complex.first: + v.append(vertex) + ct.append((v, filtered_complex.second)) + return ct + + def get_cofaces(self, simplex, codimension): + """This function returns the cofaces of a given N-simplex with a + given codimension. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + :param codimension: The codimension. If codimension = 0, all cofaces + are returned (equivalent of get_star function) + :type codimension: int. + :returns: The coface tree of a simplex. + :rtype: list of tuples(simplex, filtration) + """ + cdef vector[int] complex + for i in simplex: + complex.push_back(i) + cdef vector[pair[vector[int], double]] cofaces \ + = self.thisptr.get_cofaces(complex, <int>codimension) + ct = [] + for filtered_complex in cofaces: + v = [] + for vertex in filtered_complex.first: + v.append(vertex) + ct.append((v, filtered_complex.second)) + return ct + + def remove_maximal_simplex(self, simplex): + """This function removes a given maximal N-simplex from the simplicial + complex. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + """ + self.thisptr.remove_maximal_simplex(simplex) + + def expansion(self, max_dim): + """Expands the Simplex_tree containing only its one skeleton + until dimension max_dim. + + The expanded simplicial complex until dimension :math:`d` + attached to a graph :math:`G` is the maximal simplicial complex of + dimension at most :math:`d` admitting the graph :math:`G` as + :math:`1`-skeleton. + The filtration value assigned to a simplex is the maximal filtration + value of one of its edges. + + The Simplex_tree must contain no simplex of dimension bigger than + 1 when calling the method. + + :param max_dim: The maximal dimension. + :type max_dim: int. + """ + self.thisptr.expansion(max_dim) + + def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False): + """This function returns the persistence of the simplicial complex. + + :param homology_coeff_field: The homology coefficient field. Must be a + prime number + :type homology_coeff_field: int. + :param min_persistence: The minimum persistence value to take into + account (strictly greater than min_persistence). Default value is + 0.0. + Sets min_persistence to -1.0 to see all values. + :type min_persistence: float. + :returns: The persistence of the simplicial complex. + :rtype: list of pairs(dimension, pair(birth, death)) + """ + if self.pcohptr != NULL: + del self.pcohptr + self.pcohptr = new Simplex_tree_persistence_interface(self.thisptr, persistence_dim_max) + cdef vector[pair[int, pair[double, double]]] persistence_result + if self.pcohptr != NULL: + persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) + return persistence_result + + def betti_numbers(self): + """This function returns the Betti numbers of the simplicial complex. + + :returns: The Betti numbers ([B0, B1, ..., Bn]). + :rtype: list of int + + :note: betti_numbers function requires persistence function to be + launched first. + """ + cdef vector[int] bn_result + if self.pcohptr != NULL: + bn_result = self.pcohptr.betti_numbers() + else: + print("betti_numbers function requires persistence function" + " to be launched first.") + return bn_result + + def persistent_betti_numbers(self, from_value, to_value): + """This function returns the persistent Betti numbers of the + simplicial complex. + + :param from_value: The persistence birth limit to be added in the + numbers (persistent birth <= from_value). + :type from_value: float. + :param to_value: The persistence death limit to be added in the + numbers (persistent death > to_value). + :type to_value: float. + + :returns: The persistent Betti numbers ([B0, B1, ..., Bn]). + :rtype: list of int + + :note: persistent_betti_numbers function requires persistence + function to be launched first. + """ + cdef vector[int] pbn_result + if self.pcohptr != NULL: + pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value) + else: + print("persistent_betti_numbers function requires persistence function" + " to be launched first.") + return pbn_result + + def persistence_intervals_in_dimension(self, dimension): + """This function returns the persistence intervals of the simplicial + complex in a specific dimension. + + :param dimension: The specific dimension. + :type from_value: int. + :returns: The persistence intervals. + :rtype: list of pair of float + + :note: intervals_in_dim function requires persistence function to be + launched first. + """ + cdef vector[pair[double,double]] intervals_result + if self.pcohptr != NULL: + intervals_result = self.pcohptr.intervals_in_dimension(dimension) + else: + print("intervals_in_dim function requires persistence function" + " to be launched first.") + return intervals_result diff --git a/src/cython/cython/strong_witness_complex.pyx b/src/cython/cython/strong_witness_complex.pyx new file mode 100644 index 00000000..770b46f5 --- /dev/null +++ b/src/cython/cython/strong_witness_complex.pyx @@ -0,0 +1,81 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi": + cdef cppclass Strong_witness_complex_interface "Gudhi::witness_complex::Strong_witness_complex_interface": + Strong_witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, + unsigned limit_dimension) + +# StrongWitnessComplex python interface +cdef class StrongWitnessComplex: + """Constructs (strong) witness complex for a given table of nearest + landmarks with respect to witnesses. + """ + + cdef Strong_witness_complex_interface * thisptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, nearest_landmark_table=None): + """StrongWitnessComplex constructor. + + :param nearest_landmark_table: A list of nearest landmark. + :type nearest_landmark_table: list of list of pair of unsigned and double + """ + + # The real cython constructor + def __cinit__(self, nearest_landmark_table=None): + if nearest_landmark_table is not None: + self.thisptr = new Strong_witness_complex_interface(nearest_landmark_table) + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + + def __is_defined(self): + """Returns true if StrongWitnessComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def create_simplex_tree(self, max_alpha_square, limit_dimension = -1): + """ + :param max_alpha_square: The maximum alpha square threshold the + simplices shall not exceed. Default is set to infinity. + :type max_alpha_square: float + :returns: A simplex tree created from the Delaunay Triangulation. + :rtype: SimplexTree + """ + simplex_tree = SimplexTree() + if limit_dimension is not -1: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension) + else: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square) + return simplex_tree diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx new file mode 100644 index 00000000..a25d196d --- /dev/null +++ b/src/cython/cython/subsampling.pyx @@ -0,0 +1,139 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.string cimport string +from libcpp cimport bool +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Subsampling_interface.h" namespace "Gudhi::subsampling": + vector[vector[double]] subsampling_n_farthest_points(vector[vector[double]] points, unsigned nb_points) + vector[vector[double]] subsampling_n_farthest_points(vector[vector[double]] points, unsigned nb_points, unsigned starting_point) + vector[vector[double]] subsampling_n_farthest_points_from_file(string off_file, unsigned nb_points) + vector[vector[double]] subsampling_n_farthest_points_from_file(string off_file, unsigned nb_points, unsigned starting_point) + vector[vector[double]] subsampling_n_random_points(vector[vector[double]] points, unsigned nb_points) + vector[vector[double]] subsampling_n_random_points_from_file(string off_file, unsigned nb_points) + vector[vector[double]] subsampling_sparsify_points(vector[vector[double]] points, double min_squared_dist) + vector[vector[double]] subsampling_sparsify_points_from_file(string off_file, double min_squared_dist) + +def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_point = ''): + """Subsample by a greedy strategy of iteratively adding the farthest point + from the current chosen point set to the subsampling. + The iteration starts with the landmark `starting point`. + + :param points: The input point set. + :type points: vector[vector[double]]. + + Or + + :param off_file: An OFF file style name. + :type off_file: string + + :param nb_points: Number of points of the subsample. + :type nb_points: unsigned. + :param starting_point: The iteration starts with the landmark `starting \ + point`,which is the index of the poit to start with. If not set, this \ + index is choosen randomly. + :type starting_point: unsigned. + :returns: The subsample point set. + :rtype: vector[vector[double]] + """ + if off_file is not '': + if os.path.isfile(off_file): + if starting_point is '': + return subsampling_n_farthest_points_from_file(off_file, + nb_points) + else: + return subsampling_n_farthest_points_from_file(off_file, + nb_points, + starting_point) + else: + print("file " + off_file + " not found.") + else: + if points is None: + # Empty points + points=[] + if starting_point is '': + return subsampling_n_farthest_points(points, nb_points) + else: + return subsampling_n_farthest_points(points, nb_points, + starting_point) + +def pick_n_random_points(points=None, off_file='', nb_points=0): + """Subsample a point set by picking random vertices. + + :param points: The input point set. + :type points: vector[vector[double]]. + + Or + + :param off_file: An OFF file style name. + :type off_file: string + + :param nb_points: Number of points of the subsample. + :type nb_points: unsigned. + :returns: The subsample point set. + :rtype: vector[vector[double]] + """ + if off_file is not '': + if os.path.isfile(off_file): + return subsampling_n_random_points_from_file(off_file, nb_points) + else: + print("file " + off_file + " not found.") + else: + if points is None: + # Empty points + points=[] + return subsampling_n_random_points(points, nb_points) + +def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): + """Subsample a point set by picking random vertices. + + :param points: The input point set. + :type points: vector[vector[double]]. + + Or + + :param off_file: An OFF file style name. + :type off_file: string + + :param min_squared_dist: Number of points of the subsample. + :type min_squared_dist: unsigned. + :returns: The subsample point set. + :rtype: vector[vector[double]] + """ + if off_file is not '': + if os.path.isfile(off_file): + return subsampling_sparsify_points_from_file(off_file, + min_squared_dist) + else: + print("file " + off_file + " not found.") + else: + if points is None: + # Empty points + points=[] + return subsampling_sparsify_points(points, min_squared_dist) diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx new file mode 100644 index 00000000..52bd8111 --- /dev/null +++ b/src/cython/cython/tangential_complex.pyx @@ -0,0 +1,151 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair +from libcpp.string cimport string +from libcpp cimport bool +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Tangential_complex_interface.h" namespace "Gudhi": + cdef cppclass Tangential_complex_interface "Gudhi::tangential_complex::Tangential_complex_interface": + Tangential_complex_interface(vector[vector[double]] points) + # bool from_file is a workaround for cython to find the correct signature + Tangential_complex_interface(string off_file, bool from_file) + vector[double] get_point(unsigned vertex) + unsigned number_of_vertices() + unsigned number_of_simplices() + unsigned number_of_inconsistent_simplices() + unsigned number_of_inconsistent_stars() + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree) + void fix_inconsistencies_using_perturbation(double max_perturb, double time_limit) + +# TangentialComplex python interface +cdef class TangentialComplex: + """The class Tangential_complex represents a tangential complex. After the + computation of the complex, an optional post-processing called perturbation + can be run to attempt to remove inconsistencies. + """ + + cdef Tangential_complex_interface * thisptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, points=None, off_file=''): + """TangentialComplex constructor. + + :param points: A list of points in d-Dimension. + :type points: list of list of double + + Or + + :param off_file: An OFF file style name. + :type off_file: string + """ + + # The real cython constructor + def __cinit__(self, points=None, off_file=''): + if off_file is not '': + if os.path.isfile(off_file): + self.thisptr = new Tangential_complex_interface(off_file, True) + else: + print("file " + off_file + " not found.") + else: + if points is None: + # Empty tangential construction + points=[] + self.thisptr = new Tangential_complex_interface(points) + + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + + def __is_defined(self): + """Returns true if TangentialComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def get_point(self, vertex): + """This function returns the point corresponding to a given vertex. + + :param vertex: The vertex. + :type vertex: int. + :returns: The point. + :rtype: list of float + """ + cdef vector[double] point = self.thisptr.get_point(vertex) + return point + + def num_vertices(self): + """ + :returns: The number of vertices. + :rtype: unsigned + """ + return self.thisptr.number_of_vertices() + + def num_simplices(self): + """ + :returns: Total number of simplices in stars (including duplicates that appear in several stars). + :rtype: unsigned + """ + return self.thisptr.number_of_simplices() + + def num_inconsistent_simplices(self): + """ + :returns: The number of inconsistent simplices. + :rtype: unsigned + """ + return self.thisptr.number_of_inconsistent_simplices() + + def num_inconsistent_stars(self): + """ + :returns: The number of stars containing at least one inconsistent simplex. + :rtype: unsigned + """ + return self.thisptr.number_of_inconsistent_stars() + + def create_simplex_tree(self): + """Exports the complex into a simplex tree. + + :returns: A simplex tree created from the complex. + :rtype: SimplexTree + """ + simplex_tree = SimplexTree() + self.thisptr.create_simplex_tree(simplex_tree.thisptr) + return simplex_tree + + def fix_inconsistencies_using_perturbation(self, max_perturb, time_limit=-1.0): + """Attempts to fix inconsistencies by perturbing the point positions. + + :param max_perturb: Maximum length of the translations used by the + perturbation. + :type max_perturb: double + :param time_limit: Time limit in seconds. If -1, no time limit is set. + :type time_limit: double + """ + self.thisptr.fix_inconsistencies_using_perturbation(max_perturb, + time_limit) diff --git a/src/cython/cython/witness_complex.pyx b/src/cython/cython/witness_complex.pyx new file mode 100644 index 00000000..96d122bb --- /dev/null +++ b/src/cython/cython/witness_complex.pyx @@ -0,0 +1,81 @@ +from cython cimport numeric +from libcpp.vector cimport vector +from libcpp.utility cimport pair + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +cdef extern from "Witness_complex_interface.h" namespace "Gudhi": + cdef cppclass Witness_complex_interface "Gudhi::witness_complex::Witness_complex_interface": + Witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, + unsigned limit_dimension) + +# WitnessComplex python interface +cdef class WitnessComplex: + """Constructs (weak) witness complex for a given table of nearest landmarks + with respect to witnesses. + """ + + cdef Witness_complex_interface * thisptr + + # Fake constructor that does nothing but documenting the constructor + def __init__(self, nearest_landmark_table=None): + """WitnessComplex constructor. + + :param nearest_landmark_table: A list of nearest landmark. + :type nearest_landmark_table: list of list of pair of unsigned and double + """ + + # The real cython constructor + def __cinit__(self, nearest_landmark_table=None): + if nearest_landmark_table is not None: + self.thisptr = new Witness_complex_interface(nearest_landmark_table) + + def __dealloc__(self): + if self.thisptr != NULL: + del self.thisptr + + def __is_defined(self): + """Returns true if WitnessComplex pointer is not NULL. + """ + return self.thisptr != NULL + + def create_simplex_tree(self, max_alpha_square, limit_dimension = -1): + """ + :param max_alpha_square: The maximum alpha square threshold the + simplices shall not exceed. Default is set to infinity. + :type max_alpha_square: float + :returns: A simplex tree created from the Delaunay Triangulation. + :rtype: SimplexTree + """ + simplex_tree = SimplexTree() + if limit_dimension is not -1: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension) + else: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square) + return simplex_tree diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in new file mode 100644 index 00000000..5a97e9f3 --- /dev/null +++ b/src/cython/cythonize_gudhi.py.in @@ -0,0 +1,48 @@ +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 <http://www.gnu.org/licenses/>. +""" + +__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@], +) + +setup( + name = 'gudhi', + author='Vincent Rouvreau', + author_email='gudhi-contact@lists.gforge.inria.fr', + version='0.1.0', + url='http://gudhi.gforge.inria.fr/', + ext_modules = cythonize(gudhi), +) diff --git a/src/cython/doc/Makefile b/src/cython/doc/Makefile new file mode 100644 index 00000000..be3ff7c4 --- /dev/null +++ b/src/cython/doc/Makefile @@ -0,0 +1,181 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +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 <target>' where <target> is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @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." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pouet.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pouet.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/pouet" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pouet" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. 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The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +xml: + $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml + @echo + @echo "Build finished. The XML files are in $(BUILDDIR)/xml." + +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html new file mode 100644 index 00000000..af0eef64 --- /dev/null +++ b/src/cython/doc/_templates/layout.html @@ -0,0 +1,270 @@ +{# + basic/layout.html + ~~~~~~~~~~~~~~~~~ + + Master layout template for Sphinx themes. + + :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS. + :license: BSD, see LICENSE for details. +#} +{%- block doctype -%} +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +{%- endblock %} +{%- set reldelim1 = reldelim1 is not defined and ' »' or reldelim1 %} +{%- set reldelim2 = reldelim2 is not defined and ' |' or reldelim2 %} +{%- set render_sidebar = (not embedded) and (not theme_nosidebar|tobool) and + (sidebars != []) %} +{%- set url_root = pathto('', 1) %} +{# XXX necessary? #} +{%- if url_root == '#' %}{% set url_root = '' %}{% endif %} +{%- if not embedded and docstitle %} + {%- set titlesuffix = " — "|safe + docstitle|e %} +{%- else %} + {%- set titlesuffix = "" %} +{%- endif %} + +{%- macro relbar() %} + <div class="related" role="navigation" aria-label="related navigation"> + <h3>{{ _('Navigation') }}</h3> + <ul> + {%- for rellink in rellinks %} + <li class="right" {% if loop.first %}style="margin-right: 10px"{% endif %}> + <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}" + {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a> + {%- if not loop.first %}{{ reldelim2 }}{% endif %}</li> + {%- endfor %} + {%- block rootrellink %} + <li class="nav-item nav-item-0"><a href="{{ pathto(master_doc) }}">{{ shorttitle|e }}</a>{{ reldelim1 }}</li> + {%- endblock %} + {%- for parent in parents %} + <li class="nav-item nav-item-{{ loop.index }}"><a href="{{ parent.link|e }}" {% if loop.last %}{{ accesskey("U") }}{% endif %}>{{ parent.title }}</a>{{ reldelim1 }}</li> + {%- endfor %} + {%- block relbaritems %} {% endblock %} + </ul> + </div> +{%- endmacro %} + +{%- macro sidebar() %} + {%- if render_sidebar %} + <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> + <div class="sphinxsidebarwrapper"> + {%- block sidebarlogo %} + {%- if logo %} + <p class="logo"><a href="{{ pathto(master_doc) }}"> + <img class="logo" src="{{ pathto('_static/' + logo, 1) }}" alt="Logo"/> + </a></p> + {%- endif %} + {%- endblock %} + {%- if sidebars != None %} + {#- new style sidebar: explicitly include/exclude templates #} + {%- for sidebartemplate in sidebars %} + {%- include sidebartemplate %} + {%- endfor %} + {%- else %} + {#- old style sidebars: using blocks -- should be deprecated #} + {%- block sidebartoc %} +<h2><a href="index.html">GUDHI</a></h2> +<h2><a href="installation.html">GUDHI installation</a></h2> +<h2><a href="citation.html">Acknowledging the GUDHI library</a></h2> +<h2><a href="genindex.html">Index</a></h2> +<h2><a href="examples.html">Examples</a></h2> + + {%- include "localtoc.html" %} + {%- endblock %} + {%- block sidebarrel %} + {%- include "relations.html" %} + {%- endblock %} + {%- block sidebarsourcelink %} + {%- include "sourcelink.html" %} + {%- endblock %} + {%- if customsidebar %} + {%- include customsidebar %} + {%- endif %} + {%- block sidebarsearch %} + {%- include "searchbox.html" %} + {%- endblock %} + {%- endif %} + </div> + </div> + {%- endif %} +{%- endmacro %} + +{%- macro script() %} + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '{{ url_root }}', + VERSION: '{{ release|e }}', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '{{ '' if no_search_suffix else file_suffix }}', + HAS_SOURCE: {{ has_source|lower }} + }; + </script> + {%- for scriptfile in script_files %} + <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script> + {%- endfor %} +{%- endmacro %} + +{%- macro css() %} +<!-- GUDHI website css for header BEGIN --> +<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" /> +<!-- GUDHI website css for header END --> + <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" /> + <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" /> + {%- for cssfile in css_files %} + <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" /> + {%- endfor %} +{%- endmacro %} +<!-- GUDHI website html class for header BEGIN --> +<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en"> +<!-- GUDHI website html class for header END --> + <head> + <meta http-equiv="Content-Type" content="text/html; charset={{ encoding }}" /> + {{ metatags }} + {%- block htmltitle %} + <title>{{ title|striptags|e }}{{ titlesuffix }}</title> + {%- endblock %} + {{ css() }} + {%- if not embedded %} + {{ script() }} + {%- if use_opensearch %} + <link rel="search" type="application/opensearchdescription+xml" + title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}" + href="{{ pathto('_static/opensearch.xml', 1) }}"/> + {%- endif %} + {%- if favicon %} + <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/> + {%- endif %} + {%- endif %} +{%- block linktags %} + {%- if hasdoc('about') %} + <link rel="author" title="{{ _('About these documents') }}" href="{{ pathto('about') }}" /> + {%- endif %} + {%- if hasdoc('genindex') %} + <link rel="index" title="{{ _('Index') }}" href="{{ pathto('genindex') }}" /> + {%- endif %} + {%- if hasdoc('search') %} + <link rel="search" title="{{ _('Search') }}" href="{{ pathto('search') }}" /> + {%- endif %} + {%- if hasdoc('copyright') %} + <link rel="copyright" title="{{ _('Copyright') }}" href="{{ pathto('copyright') }}" /> + {%- endif %} + <link rel="top" title="{{ docstitle|e }}" href="{{ pathto(master_doc) }}" /> + {%- if parents %} + <link rel="up" title="{{ parents[-1].title|striptags|e }}" href="{{ parents[-1].link|e }}" /> + {%- endif %} + {%- if next %} + <link rel="next" title="{{ next.title|striptags|e }}" href="{{ next.link|e }}" /> + {%- endif %} + {%- if prev %} + <link rel="prev" title="{{ prev.title|striptags|e }}" href="{{ prev.link|e }}" /> + {%- endif %} +{%- endblock %} +{%- block extrahead %} {% endblock %} + </head> + <body role="document"> + <!-- GUDHI website header BEGIN --> + <div id="navigation" class="sticky"> + <nav class="top-bar" role="navigation" data-topbar> + <ul class="title-area"> + <li class="name"> + <h1 class="show-for-small-only"><a href="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ library</a></h1> + </li> + <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone --> + <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li> + </ul> + <section class="top-bar-section"> + <ul class="right"> + <li class="divider"></li> + <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li> + </ul> + <ul class="left"> + <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt=" GUDHI"> GUDHI </a></li> + <li class="divider"></li> + <li class="has-dropdown"> + <a href="#">Project</a> + <ul class="dropdown"> + <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li> + <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li> + <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li> + <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li> + <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li> + </ul> + </li> + <li class="divider"></li> + <li class="has-dropdown"> + <a href="#">Download</a> + <ul class="dropdown"> + <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li> + <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li> + </ul> + </li> + <li class="divider"></li> + <li class="has-dropdown"> + <a href="#">Documentation</a> + <ul class="dropdown"> + <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li> + <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> + <li><a href="http://gudhi.gforge.inria.fr/cython/latest/">Cython documentation</a></li> + <li><a href="http://gudhi.gforge.inria.fr/cython/latest/installation.html">Cython installation manual</a></li> + </ul> + </li> + <li class="divider"></li> + <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li> + <li class="divider"></li> + </ul> + </section> + </nav> + </div><!-- /#navigation --> + <!-- GUDHI website header BEGIN --> + + +{%- block header %}{% endblock %} + +{%- block relbar1 %}{% endblock %} + +{%- block content %} + {%- block sidebar1 %} {# possible location for sidebar #} {% endblock %} + + <div class="document"> + {%- block document %} + <div class="documentwrapper"> + {%- if render_sidebar %} + <div class="bodywrapper"> + {%- endif %} + <div class="body" role="main"> + {% block body %} {% endblock %} + </div> + {%- if render_sidebar %} + </div> + {%- endif %} + </div> + {%- endblock %} + + {%- block sidebar2 %}{{ sidebar() }}{% endblock %} + <div class="clearer"></div> + </div> +{%- endblock %} + +{%- block relbar2 %}{% endblock %} + +{%- block footer %} + <div class="footer" role="contentinfo"> + {%- if show_copyright %} + {%- if hasdoc('copyright') %} + {% trans path=pathto('copyright'), copyright=copyright|e %}© <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %} + {%- else %} + {% trans copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %} + {%- endif %} + {%- endif %} + {%- if last_updated %} + {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %} + {%- endif %} + {%- if show_sphinx %} + {% trans sphinx_version=sphinx_version|e %}Created using <a href="http://sphinx-doc.org/">Sphinx</a> {{ sphinx_version }}.{% endtrans %} + {%- endif %} + </div> +{%- endblock %} + </body> +</html> + diff --git a/src/cython/doc/alpha_complex_ref.rst b/src/cython/doc/alpha_complex_ref.rst new file mode 100644 index 00000000..6a122b09 --- /dev/null +++ b/src/cython/doc/alpha_complex_ref.rst @@ -0,0 +1,10 @@ +============================== +Alpha complex reference manual +============================== + +.. autoclass:: gudhi.AlphaComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.AlphaComplex.__init__ diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst new file mode 100644 index 00000000..8437e901 --- /dev/null +++ b/src/cython/doc/alpha_complex_sum.rst @@ -0,0 +1,22 @@ +================================================================= =================================== =================================== +:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Requires: CGAL :math:`\geq` 4.7.0 Eigen3 +================================================================= =================================== =================================== + ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| .. figure:: | Alpha_complex is a simplicial complex constructed from the finite | +| img/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 | +| Alpha complex representation | is then said to be Gabriel), and as the minimum of the filtration | +| | values of the codimension 1 cofaces that make it not Gabriel | +| | otherwise. All simplices that have a filtration value strictly | +| | greater than a given alpha squared value are not inserted into the | +| | complex. | +| | | +| | This package requires having CGAL version 4.7 or higher (4.8.1 is | +| | advised for better perfomances). | ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| :doc:`alpha_complex_user` | :doc:`alpha_complex_ref` | ++----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst new file mode 100644 index 00000000..68e53a77 --- /dev/null +++ b/src/cython/doc/alpha_complex_user.rst @@ -0,0 +1,205 @@ +========================= +Alpha complex user manual +========================= +Definition +---------- + +.. include:: alpha_complex_sum.rst + +Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_sum>` using +`Delaunay Triangulation <http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations>`_ +:cite:`cgal:hdj-t-15b` from `CGAL <http://www.cgal.org/>`_ (the Computational Geometry Algorithms Library +:cite:`cgal:eb-15b`). + +Remarks +^^^^^^^ +When Alpha_complex is constructed with an infinite value of :math:`\alpha`, the complex is a Delaunay complex. + +Example from points +------------------- + +This example builds the Delaunay triangulation from the given points, and initializes the alpha complex with it: + +.. testcode:: + + import gudhi + alpha_complex = gudhi.AlphaComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]]) + + simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=60.0) + result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ + repr(simplex_tree.num_simplices()) + ' simplices - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' + print(result_str) + for filtered_value in simplex_tree.get_filtered_tree(): + print(filtered_value) + +The output is: + +.. testoutput:: + + Alpha complex is of dimension 2 - 25 simplices - 7 vertices. + ([0], 0.0) + ([1], 0.0) + ([2], 0.0) + ([3], 0.0) + ([4], 0.0) + ([5], 0.0) + ([6], 0.0) + ([2, 3], 6.25) + ([4, 5], 7.25) + ([0, 2], 8.5) + ([0, 1], 9.25) + ([1, 3], 10.0) + ([1, 2], 11.25) + ([1, 2, 3], 12.5) + ([0, 1, 2], 12.995867768595042) + ([5, 6], 13.25) + ([2, 4], 20.0) + ([4, 6], 22.736686390532547) + ([4, 5, 6], 22.736686390532547) + ([3, 6], 30.25) + ([2, 6], 36.5) + ([2, 3, 6], 36.5) + ([2, 4, 6], 37.24489795918368) + ([0, 4], 59.710743801652896) + ([0, 2, 4], 59.710743801652896) + + +Algorithm +--------- + +Data structure +^^^^^^^^^^^^^^ + +In order to build the alpha complex, first, a Simplex tree is built from the cells of a Delaunay Triangulation. +(The filtration value is set to NaN, which stands for unknown value): + +.. figure:: + img/alpha_complex_doc.png + :figclass: align-center + :alt: Simplex tree structure construction example + + Simplex tree structure construction example + +Filtration value computation algorithm +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + **for** i : dimension :math:`\rightarrow` 0 **do** + **for all** :math:`\sigma` of dimension i + **if** filtration(:math:`\sigma`) is NaN **then** + filtration(:math:`\sigma`) = :math:`\alpha^2(\sigma)` + **end if** + + *//propagate alpha filtration value* + + **for all** :math:`\tau` face of :math:`\sigma` + **if** filtration(:math:`\tau`) is not NaN **then** + filtration(:math:`\tau`) = filtration(:math:`\sigma`) + **end if** + **end for** + **end for** + **end for** + + make_filtration_non_decreasing() + + prune_above_filtration() + +Dimension 2 +^^^^^^^^^^^ + +From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...), +computes the filtration value of the triangle, and then propagates the filtration value as described +here: + +.. figure:: + img/alpha_complex_doc_420.png + :figclass: align-center + :alt: Filtration value propagation example + + Filtration value propagation example + +Dimension 1 +^^^^^^^^^^^ + +Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...), +computes the filtration value of the edge (in this case, propagation will have no effect). + +Dimension 0 +^^^^^^^^^^^ + +Finally, the algorithm looks into each vertex ([0], [1], [2], [3], [4], [5] and [6]) and +sets the filtration value (0 in case of a vertex - propagation will have no effect). + +Non decreasing filtration values +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not +quite define a proper filtration (i.e. non-decreasing with respect to inclusion). +We fix that up by calling `Simplex_tree::make_filtration_non_decreasing()` (cf. +`C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_). + +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 <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_). +In the following example, the value is given by the user as argument of the program. + + +Example from OFF file +^^^^^^^^^^^^^^^^^^^^^ + +This example builds the Delaunay triangulation from the points given by an OFF file, and initializes the alpha complex +with it. + + +Then, it is asked to display information about the alpha complex: + +.. testcode:: + + import gudhi + alpha_complex = gudhi.AlphaComplex(off_file='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 - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' + print(result_str) + for filtered_value in simplex_tree.get_filtered_tree(): + print(filtered_value) + +the program output is: + +.. testoutput:: + + Alpha complex is of dimension 2 - 23 simplices - 7 vertices. + ([0], 0.0) + ([1], 0.0) + ([2], 0.0) + ([3], 0.0) + ([4], 0.0) + ([5], 0.0) + ([6], 0.0) + ([2, 3], 6.25) + ([4, 5], 7.25) + ([0, 2], 8.5) + ([0, 1], 9.25) + ([1, 3], 10.0) + ([1, 2], 11.25) + ([1, 2, 3], 12.5) + ([0, 1, 2], 12.995867768595042) + ([5, 6], 13.25) + ([2, 4], 20.0) + ([4, 6], 22.736686390532547) + ([4, 5, 6], 22.736686390532547) + ([3, 6], 30.25) + ([2, 6], 36.5) + ([2, 3, 6], 36.5) + ([2, 4, 6], 37.24489795918368) + +============== +CGAL citations +============== + +.. bibliography:: 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 new file mode 100644 index 00000000..5c475d0d --- /dev/null +++ b/src/cython/doc/bottleneck_distance_sum.rst @@ -0,0 +1,15 @@ +================================================================= =================================== =================================== +:Author: François Godi :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Requires: CGAL :math:`\geq` 4.8.0 +================================================================= =================================== =================================== + ++-----------------------------------------------------------------+----------------------------------------------------------------------+ +| .. 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 | +| :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. | +| the longest edge | | ++-----------------------------------------------------------------+----------------------------------------------------------------------+ +| :doc:`bottleneck_distance_user` | | ++-----------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst new file mode 100644 index 00000000..3bc170f4 --- /dev/null +++ b/src/cython/doc/bottleneck_distance_user.rst @@ -0,0 +1,37 @@ +=============================== +Bottleneck distance user manual +=============================== +Definition +---------- + +.. include:: bottleneck_distance_sum.rst + +Function +-------- +.. autofunction:: gudhi.bottleneck_distance + + +Basic example +------------- + +This example computes the bottleneck distance from 2 persistence diagrams: + +.. testcode:: + + import gudhi + + diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]] + diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]] + + message = "Bottleneck distance approximation=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0.1)) + print(message) + + message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2)) + print(message) + +The output is: + +.. testoutput:: + + Bottleneck distance approximation=0.8081763781405569 + Bottleneck distance exact value=0.75 diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst new file mode 100644 index 00000000..6cdfb7cc --- /dev/null +++ b/src/cython/doc/citation.rst @@ -0,0 +1,15 @@ +Acknowledging the GUDHI library +############################### + +We kindly ask users to cite the GUDHI library as appropriately as possible in +their papers, and to mention the use of the GUDHI library on the web pages of +their projects using GUDHI and provide us with links to these web pages. Feel +free to contact us in case you have any question or remark on this topic. + +We provide GUDHI bibtex entries for the modules of the User and Reference +Manual, as well as for publications directly related to the GUDHI library. + +GUDHI bibtex +************ + +.. literalinclude:: how_to_cite_gudhi.bib diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py new file mode 100755 index 00000000..42bfd59c --- /dev/null +++ b/src/cython/doc/conf.py @@ -0,0 +1,278 @@ +# -*- coding: utf-8 -*- +# +# GUDHI documentation build configuration file, created by +# sphinx-quickstart on Thu Jun 30 09:55:51 2016. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +# Path to Gudhi.so from source path +sys.path.insert(0, os.path.abspath('..')) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + 'matplotlib.sphinxext.plot_directive', + 'sphinx.ext.autodoc', + 'sphinx.ext.doctest', + 'sphinx.ext.todo', + 'sphinx.ext.mathjax', + 'sphinx.ext.ifconfig', + 'sphinx.ext.viewcode', + 'sphinxcontrib.bibtex', +] + +todo_include_todos = True +# plot option : do not show hyperlinks (Source code, png, hires.png, pdf) +plot_html_show_source_link = False +plot_html_show_formats = False +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'GUDHI' +copyright = u'2016, GUDHI Editorial Board' + +# 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' +# The full version, including alpha/beta/rc tags. +release = '2.0.0' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +#keep_warnings = False + + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'classic' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +html_theme_options = { + "sidebarbgcolor": "#A1ADCD", + "sidebartextcolor": "black", + "sidebarlinkcolor": "#334D5C", +} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# "<project> v<release> documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +#html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {'installation': 'installation.html'} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a <link> tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# 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_ref.rst b/src/cython/doc/cubical_complex_ref.rst new file mode 100644 index 00000000..84aa4223 --- /dev/null +++ b/src/cython/doc/cubical_complex_ref.rst @@ -0,0 +1,9 @@ +Cubical complex reference manual +################################ + +.. autoclass:: gudhi.CubicalComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.CubicalComplex.__init__ diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst new file mode 100644 index 00000000..3ddf6375 --- /dev/null +++ b/src/cython/doc/cubical_complex_sum.rst @@ -0,0 +1,15 @@ +================================================================= =================================== =================================== +: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` | ++-----------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst new file mode 100644 index 00000000..692acdd9 --- /dev/null +++ b/src/cython/doc/cubical_complex_user.rst @@ -0,0 +1,161 @@ +=========================== +Cubical complex user manual +=========================== +Definition +---------- + +===================================== ===================================== ===================================== +:Author: Pawel Dlotko :Introduced in: GUDHI PYTHON 2.0.0 :Copyright: GPL v3 +===================================== ===================================== ===================================== + ++---------------------------------------------+----------------------------------------------------------------------+ +| :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | +| | * :doc:`periodic_cubical_complex_ref` | ++---------------------------------------------+----------------------------------------------------------------------+ + +The cubical complex is an example of a structured complex useful in computational mathematics (specially rigorous +numerics) and image analysis. + +An *elementary interval* is an interval of a form :math:`[n,n+1]`, or :math:`[n,n]`, for :math:`n \in \mathcal{Z}`. +The first one is called *non-degenerate*, while the second one is a *degenerate* interval. A +*boundary of a elementary interval* is a chain :math:`\partial [n,n+1] = [n+1,n+1]-[n,n]` in case of +non-degenerated elementary interval and :math:`\partial [n,n] = 0` in case of degenerate elementary interval. An +*elementary cube* :math:`C` is a product of elementary intervals, :math:`C=I_1 \times \ldots \times I_n`. +*Embedding dimension* of a cube is n, the number of elementary intervals (degenerate or not) in the product. +A *dimension of a cube* :math:`C=I_1 \times ... \times I_n` is the number of non degenerate elementary +intervals in the product. A *boundary of a cube* :math:`C=I_1 \times \ldots \times I_n` is a chain obtained +in the following way: + +.. math:: + + \partial C = (\partial I_1 \times \ldots \times I_n) + (I_1 \times \partial I_2 \times \ldots \times I_n) + + \ldots + (I_1 \times I_2 \times \ldots \times \partial I_n). + +A *cubical complex* :math:`\mathcal{K}` is a collection of cubes closed under operation of taking boundary +(i.e. boundary of every cube from the collection is in the collection). A cube :math:`C` in cubical complex +:math:`\mathcal{K}` is *maximal* if it is not in a boundary of any other cube in :math:`\mathcal{K}`. A +*support* of a cube :math:`C` is the set in :math:`\mathbb{R}^n` occupied by :math:`C` (:math:`n` is the embedding +dimension of :math:`C`). + +Cubes may be equipped with a filtration values in which case we have filtered cubical complex. All the cubical +complexes considered in this implementation are filtered cubical complexes (although, the range of a filtration may +be a set of two elements). + +For further details and theory of cubical complexes, please consult :cite:`kaczynski2004computational` as well as the +following paper :cite:`peikert2012topological`. + +Data structure. +--------------- + +The implementation of Cubical complex provides a representation of complexes that occupy a rectangular region in +:math:`\mathbb{R}^n`. This extra assumption allows for a memory efficient way of storing cubical complexes in a form +of so called bitmaps. Let +:math:`R = [b_1,e_1] \times \ldots \times [b_n,e_n]`, for :math:`b_1,...b_n,e_1,...,e_n \in \mathbb{Z}`, +:math:`b_i \leq d_i` be the considered rectangular region and let :math:`\mathcal{K}` be a filtered +cubical complex having the rectangle :math:`R` as its support. Note that the structure of the coordinate system gives +a way a lexicographical ordering of cells of :math:`\mathcal{K}`. This ordering is a base of the presented +bitmap-based implementation. In this implementation, the whole cubical complex is stored as a vector of the values +of filtration. This, together with dimension of :math:`\mathcal{K}` and the sizes of :math:`\mathcal{K}` in all +directions, allows to determine, dimension, neighborhood, boundary and coboundary of every cube +:math:`C \in \mathcal{K}`. + +.. figure:: + img/Cubical_complex_representation.png + :alt: Cubical complex. + :figclass: align-center + + Cubical complex. + +Note that the cubical complex in the figure above is, in a natural way, a product of one dimensional cubical +complexes in :math:`\mathbb{R}`. The number of all cubes in each direction is equal :math:`2n+1`, where :math:`n` is +the number of maximal cubes in the considered direction. Let us consider a cube at the position :math:`k` in the +bitmap. +Knowing the sizes of the bitmap, by a series of modulo operation, we can determine which elementary intervals are +present in the product that gives the cube :math:`C`. In a similar way, we can compute boundary and the coboundary of +each cube. Further details can be found in the literature. + +Input Format. +------------- + +In the current implantation, filtration is given at the maximal cubes, and it is then extended by the lower star +filtration to all cubes. There are a number of constructors that can be used to construct cubical complex by users +who want to use the code directly. They can be found in the :doc:`cubical_complex_ref`. +Currently one input from a text file is used. It uses a format used already in +`Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda. +Below we are providing a description of the format. The first line contains a number d begin the dimension of the +bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3 +in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8 +20 4 7 6 5 in the example below). + +.. figure:: + img/exampleBitmap.png + :alt: Example of a input data. + :figclass: align-center + + Example of a input data. + +The input file for the following complex is: + +.. literalinclude:: cubicalcomplexdoc.txt + +.. centered:: cubicalcomplexdoc.txt + +.. testcode:: + + import gudhi + cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt') + result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \ + repr(cubical_complex.num_simplices()) + ' simplices.' + print(result_str) + +the program output is: + +.. testoutput:: + + Cubical complex is of dimension 2 - 49 simplices. + +Periodic boundary conditions. +----------------------------- + +Often one would like to impose periodic boundary conditions to the cubical complex (cf. +:doc:`periodic_cubical_complex_ref`). +Let :math:`I_1\times ... \times I_n` be a box that is decomposed with a cubical complex :math:`\mathcal{K}`. +Imposing periodic boundary conditions in the direction i, means that the left and the right side of a complex +:math:`\mathcal{K}` are considered the same. In particular, if for a bitmap :math:`\mathcal{K}` periodic boundary +conditions are imposed in all directions, then complex :math:`\mathcal{K}` became n-dimensional torus. One can use +various constructors from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical +complex with periodic boundary conditions. One can also use Perseus style input files. To indicate periodic boundary +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 + +.. centered:: 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') + result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \ + repr(periodic_cc.num_simplices()) + ' simplices.' + print(result_str) + +the program output is: + +.. testoutput:: + + Periodic cubical complex is of dimension 2 - 42 simplices. + +Examples. +--------- + +End user programs are available in cython/example/ folder. + +Bibliography +************ + +.. bibliography:: bibliography.bib + :filter: docnames + :style: unsrt diff --git a/src/cython/doc/euclidean_strong_witness_complex_ref.rst b/src/cython/doc/euclidean_strong_witness_complex_ref.rst new file mode 100644 index 00000000..bebf0f9a --- /dev/null +++ b/src/cython/doc/euclidean_strong_witness_complex_ref.rst @@ -0,0 +1,10 @@ +================================================= +Euclidean strong witness complex reference manual +================================================= + +.. autoclass:: gudhi.EuclideanStrongWitnessComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.EuclideanStrongWitnessComplex.__init__ diff --git a/src/cython/doc/euclidean_witness_complex_ref.rst b/src/cython/doc/euclidean_witness_complex_ref.rst new file mode 100644 index 00000000..29b8806f --- /dev/null +++ b/src/cython/doc/euclidean_witness_complex_ref.rst @@ -0,0 +1,10 @@ +========================================== +Euclidean witness complex reference manual +========================================== + +.. autoclass:: gudhi.EuclideanWitnessComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.EuclideanWitnessComplex.__init__ diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst new file mode 100644 index 00000000..a89e0596 --- /dev/null +++ b/src/cython/doc/examples.rst @@ -0,0 +1,4 @@ +Examples +######## + +.. include:: examples.inc diff --git a/src/cython/doc/generate_examples.py b/src/cython/doc/generate_examples.py new file mode 100755 index 00000000..d64d506c --- /dev/null +++ b/src/cython/doc/generate_examples.py @@ -0,0 +1,43 @@ +#!/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 <http://www.gnu.org/licenses/>. +""" + +__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/img/graphical_tools_representation.png b/src/cython/doc/img/graphical_tools_representation.png Binary files differnew file mode 100644 index 00000000..9759f7ba --- /dev/null +++ b/src/cython/doc/img/graphical_tools_representation.png diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst new file mode 100644 index 00000000..fca63d65 --- /dev/null +++ b/src/cython/doc/index.rst @@ -0,0 +1,87 @@ +GUDHI documentation +################### + +.. image:: img/Gudhi_banner.png + :align: center + +Introduction +************ + +The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic +open source `C++ library <http://gudhi.gforge.inria.fr/doc/latest/>`_, with a +`Cython interface <http://gudhi.gforge.inria.fr/cython/latest/>`_, for +Computational Topology and Topological Data Analysis +(`TDA <https://en.wikipedia.org/wiki/Topological_data_analysis>`_). +The GUDHI library intends to help the development of new algorithmic solutions +in TDA and their transfer to applications. It provides robust, efficient, +flexible and easy to use implementations of state-of-the-art algorithms and +data structures. + +The current release of the GUDHI library includes: + +* Data structures to represent, construct and manipulate simplicial complexes. +* Algorithms to compute persistent homology and multi-field persistent homology. +* Simplication of simplicial complexes by edge contraction. + +All data-structures are generic and several of their aspects can be +parameterized via template classes. We refer to :cite:`gudhilibrary_ICMS14` +for a detailed description of the design of the library. + +Data structures +*************** + +Alpha complex +============= + +.. include:: alpha_complex_sum.rst + +Cubical complex +=============== + +.. include:: cubical_complex_sum.rst + +Rips complex +============ + +.. include:: rips_complex_sum.rst + +Simplex tree +============ + +.. include:: simplex_tree_sum.rst + +Tangential complex +================== + +.. include:: tangential_complex_sum.rst + +Witness complex +=============== + +.. include:: witness_complex_sum.rst + + +Toolbox +******* + +Bottleneck distance +=================== + +.. include:: bottleneck_distance_sum.rst + +Persistence cohomology +====================== + +.. include:: persistent_cohomology_sum.rst + +Persistence graphical tools +=========================== + +.. include:: persistence_graphical_tools_sum.rst + +Bibliography +************ + +.. bibliography:: bibliography.bib + :filter: docnames + :style: unsrt diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst new file mode 100644 index 00000000..e7d8c210 --- /dev/null +++ b/src/cython/doc/installation.rst @@ -0,0 +1,171 @@ +Installation +############ + +Compiling +********* + +The library uses c++11 and requires `Boost <http://www.boost.org/>`_ with version +1.48.0 or more recent. It is a multi-platform library and compiles on Linux, +Mac OSX and Visual Studio 2015. +It also requires cmake to generate makefiles, and cython to compile the +library. + +GUDHI Cythonization +=================== + +To build the GUDHI cython module, run the following commands in a terminal: + +.. code-block:: bash + + cd /path-to-gudhi/ + mkdir build + cd build/ + cmake .. + make cython + +A list of examples is available here. + +Test suites +=========== + +To test your build, `py.test <http://doc.pytest.org>`_ is required. Run the +following command in a terminal: + +.. code-block:: bash + + cd /path-to-gudhi/build/src/cython + # For windows, you have to set PYTHONPATH environment variable + export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/src/cython' + py.test + +Documentation +============= + +To build the documentation, `sphinx-doc <http://http://www.sphinx-doc.org>`_ is +required. Please refer to *conf.py* file to see which +`sphinx-doc <http://http://www.sphinx-doc.org>`_ modules are required to +generate the documentation. Run the following commands in a terminal: + +.. code-block:: bash + + make sphinx + +Optional third-party library +**************************** + +CGAL +==== + +The :doc:`Alpha complex </alpha_complex_user>`, +:doc:`Tangential complex </tangential_complex_user>` and +:doc:`Witness complex </witness_complex_user>` data structures, and +:doc:`Bottleneck distance </bottleneck_distance_user>` requires CGAL, which is a +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 +`here <http://doc.cgal.org/latest/Manual/installation.html>`_. + +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: + +.. 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: + +.. 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>` + +Eigen3 +====== + +The :doc:`Alpha complex </alpha_complex_user>`, +:doc:`Tangential complex </tangential_complex_user>` and +:doc:`Witness complex </witness_complex_user>` data structures and few +examples requires `Eigen3 <http://eigen.tuxfamily.org/>`_, a C++ template +library for linear algebra: matrices, vectors, numerical solvers, and related +algorithms. + +The following examples require the `Eigen3 <http://eigen.tuxfamily.org/>`_: + +.. 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>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.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>` + +Matplotlib +========== + +The :doc:`persistence graphical tools </persistence_graphical_tools_user>` +module requires `Matplotlib <http://matplotlib.org>`_, a Python 2D plotting +library which produces publication quality figures in a variety of hardcopy +formats and interactive environments across platforms. + +The following examples require the `Matplotlib <http://matplotlib.org>`_: + +.. only:: builder_html + + * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_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:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.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>` + +Numpy +===== + +The :doc:`persistence graphical tools </persistence_graphical_tools_user>` +module requires `NumPy <http://numpy.org>`_, a fundamental package for +scientific computing with Python. + +The following examples require the `NumPy <http://numpy.org>`_: + +.. only:: builder_html + + * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_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:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.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>` + +Threading Building Blocks +========================= + +`Intel® TBB <https://www.threadingbuildingblocks.org/>`_ lets you easily write +parallel C++ programs that take full advantage of multicore performance, that +are portable and composable, and that have future-proof scalability. + +Having Intel® TBB installed is recommended to parallelize and accelerate some +GUDHI computations. + +Bug reports and contributions +***************************** + +Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: + + Contact: gudhi-users@lists.gforge.inria.fr + +GUDHI is open to external contributions. If you want to join our development team, please contact us. diff --git a/src/cython/doc/make.bat b/src/cython/doc/make.bat new file mode 100644 index 00000000..ba009a90 --- /dev/null +++ b/src/cython/doc/make.bat @@ -0,0 +1,246 @@ +@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+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 ^<target^>` where ^<target^> is one of
+ echo. html to make standalone HTML files
+ echo. dirhtml to make HTML files named index.html in directories
+ echo. singlehtml to make a single large HTML file
+ echo. pickle to make pickle files
+ echo. json to make JSON files
+ echo. htmlhelp to make HTML files and a HTML help project
+ echo. qthelp to make HTML files and a qthelp project
+ echo. devhelp to make HTML files and a Devhelp project
+ echo. epub to make an epub
+ echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+ echo. text to make text files
+ echo. man to make manual pages
+ echo. texinfo to make Texinfo files
+ echo. gettext to make PO message catalogs
+ echo. changes to make an overview over all changed/added/deprecated items
+ echo. xml to make Docutils-native XML files
+ echo. pseudoxml to make pseudoxml-XML files for display purposes
+ echo. linkcheck to check all external links for integrity
+ 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" == "dirhtml" (
+ %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+ goto end
+)
+
+if "%1" == "singlehtml" (
+ %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+ goto end
+)
+
+if "%1" == "pickle" (
+ %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the pickle files.
+ goto end
+)
+
+if "%1" == "json" (
+ %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the JSON files.
+ goto end
+)
+
+if "%1" == "htmlhelp" (
+ %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+ goto end
+)
+
+if "%1" == "qthelp" (
+ %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+ echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pouet.qhcp
+ echo.To view the help file:
+ echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pouet.ghc
+ goto end
+)
+
+if "%1" == "devhelp" (
+ %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished.
+ goto end
+)
+
+if "%1" == "epub" (
+ %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The epub file is in %BUILDDIR%/epub.
+ goto end
+)
+
+if "%1" == "latex" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "latexpdf" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ cd %BUILDDIR%/latex
+ make all-pdf
+ cd %BUILDDIR%/..
+ echo.
+ echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "latexpdfja" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ cd %BUILDDIR%/latex
+ make all-pdf-ja
+ cd %BUILDDIR%/..
+ echo.
+ echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "text" (
+ %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The text files are in %BUILDDIR%/text.
+ goto end
+)
+
+if "%1" == "man" (
+ %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The manual pages are in %BUILDDIR%/man.
+ goto end
+)
+
+if "%1" == "texinfo" (
+ %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+ goto end
+)
+
+if "%1" == "gettext" (
+ %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+ goto end
+)
+
+if "%1" == "changes" (
+ %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.The overview file is in %BUILDDIR%/changes.
+ goto end
+)
+
+if "%1" == "linkcheck" (
+ %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+ 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
+)
+
+if "%1" == "xml" (
+ %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The XML files are in %BUILDDIR%/xml.
+ goto end
+)
+
+if "%1" == "pseudoxml" (
+ %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+ goto end
+)
+
+:end
diff --git a/src/cython/doc/periodic_cubical_complex_ref.rst b/src/cython/doc/periodic_cubical_complex_ref.rst new file mode 100644 index 00000000..c6190a1b --- /dev/null +++ b/src/cython/doc/periodic_cubical_complex_ref.rst @@ -0,0 +1,9 @@ +Periodic cubical complex reference manual +######################################### + +.. autoclass:: gudhi.PeriodicCubicalComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.PeriodicCubicalComplex.__init__ diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst new file mode 100644 index 00000000..27c2f68a --- /dev/null +++ b/src/cython/doc/persistence_graphical_tools_ref.rst @@ -0,0 +1,8 @@ +============================================ +Persistence graphical tools reference manual +============================================ + +.. autofunction:: gudhi.__min_birth_max_death +.. autofunction:: gudhi.show_palette_values +.. autofunction:: gudhi.plot_persistence_barcode +.. autofunction:: gudhi.plot_persistence_diagram diff --git a/src/cython/doc/persistence_graphical_tools_sum.rst b/src/cython/doc/persistence_graphical_tools_sum.rst new file mode 100644 index 00000000..d602daa7 --- /dev/null +++ b/src/cython/doc/persistence_graphical_tools_sum.rst @@ -0,0 +1,12 @@ +================================================================= =================================== =================================== +:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Requires: Matplotlib Numpy +================================================================= =================================== =================================== + ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| .. figure:: | These graphical tools comes on top of persistence results and allows | +| img/graphical_tools_representation.png | the user to build easily barcode and persistence diagram. | +| | | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| :doc:`persistence_graphical_tools_user` | :doc:`persistence_graphical_tools_ref` | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst new file mode 100644 index 00000000..f713e971 --- /dev/null +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -0,0 +1,67 @@ +======================================= +Persistence graphical tools user manual +======================================= +Definition +---------- +.. include:: persistence_graphical_tools_sum.rst + + +Show palette values +------------------- + +This function is useful to show the color palette values of dimension: + + +.. testcode:: + + import gudhi + gudhi.show_palette_values(alpha=1.0) + +.. plot:: + + import gudhi + gudhi.show_palette_values(alpha=1.0) + +Show persistence as a barcode +----------------------------- + +This function can display the persistence result as a barcode: + +.. testcode:: + + import gudhi + + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + diag = periodic_cc.persistence() + gudhi.plot_persistence_barcode(diag) + +.. plot:: + + import gudhi + + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + diag = periodic_cc.persistence() + gudhi.plot_persistence_barcode(diag) + +Show persistence as a diagram +----------------------------- + +This function can display the persistence result as a diagram: + +.. testcode:: + + import gudhi + + rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0) + simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) + diag = simplex_tree.persistence() + gudhi.plot_persistence_diagram(diag) + +.. plot:: + + import gudhi + + rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0) + simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) + diag = simplex_tree.persistence() + gudhi.plot_persistence_diagram(diag) diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst new file mode 100644 index 00000000..d1f79cb4 --- /dev/null +++ b/src/cython/doc/persistent_cohomology_sum.rst @@ -0,0 +1,27 @@ +================================================================= =================================== =================================== +:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +================================================================= =================================== =================================== + ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| .. figure:: | The theory of homology consists in attaching to a topological space | +| img/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 | +| Torus | theory is essentially composed of three elements: topological spaces, | +| | their homology groups and an evolution scheme. | +| | | +| | Computation of persistent cohomology using the algorithm of | +| | :cite:`DBLP:journals/dcg/SilvaMV11` and | +| | :cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed | +| | Annotation Matrix implementation of | +| | :cite:`DBLP:conf/esa/BoissonnatDM13`. | +| | | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| :doc:`persistent_cohomology_user` | Please refer to each data structure that contains persistence | +| | feature for reference: | +| | | +| | * :doc:`simplex_tree_ref` | +| | * :doc:`cubical_complex_ref` | +| | * :doc:`periodic_cubical_complex_ref` | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst new file mode 100644 index 00000000..69be3b86 --- /dev/null +++ b/src/cython/doc/persistent_cohomology_user.rst @@ -0,0 +1,115 @@ +================================= +Persistent cohomology user manual +================================= +Definition +---------- +===================================== ===================================== ===================================== +:Author: Clément Maria :Introduced in: GUDHI PYTHON 2.0.0 :Copyright: GPL v3 +===================================== ===================================== ===================================== + ++---------------------------------------------+----------------------------------------------------------------------+ +| :doc:`persistent_cohomology_user` | Please refer to each data structure that contains persistence | +| | feature for reference: | +| | | +| | * :doc:`simplex_tree_ref` | ++---------------------------------------------+----------------------------------------------------------------------+ + + +Computation of persistent cohomology using the algorithm of :cite:`DBLP:journals/dcg/SilvaMV11` and +:cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed Annotation Matrix implementation of +:cite:`DBLP:conf/esa/BoissonnatDM13`. + +The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing global +topological features like connected components, holes, cavities, etc. Persistent homology studies the evolution -- +birth, life and death -- of these features when the topological space is changing. Consequently, the theory is +essentially composed of three elements: + +* topological spaces +* their homology groups +* an evolution scheme. + +Topological Spaces +------------------ + +Topological spaces are represented by simplicial complexes. +Let :math:`V = \{1, \cdots ,|V|\}` be a set of *vertices*. +A *simplex* :math:`\sigma` is a subset of vertices :math:`\sigma \subseteq V`. +A *simplicial complex* :math:`\mathbf{K}` on :math:`V` is a collection of simplices :math:`\{\sigma\}`, +:math:`\sigma \subseteq V`, such that :math:`\tau \subseteq \sigma \in \mathbf{K} \Rightarrow \tau \in \mathbf{K}`. +The dimension :math:`n=|\sigma|-1` of :math:`\sigma` is its number of elements minus 1. +A *filtration* of a simplicial complex is a function :math:`f:\mathbf{K} \rightarrow \mathbb{R}` satisfying +:math:`f(\tau)\leq f(\sigma)` whenever :math:`\tau \subseteq \sigma`. + +Homology +-------- + +For a ring :math:`\mathcal{R}`, the group of *n-chains*, denoted :math:`\mathbf{C}_n(\mathbf{K},\mathcal{R})`, of +:math:`\mathbf{K}` is the group of formal sums of n-simplices with :math:`\mathcal{R}` coefficients. The +*boundary operator* is a linear operator +:math:`\partial_n: \mathbf{C}_n(\mathbf{K},\mathcal{R}) \rightarrow \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R})` +such that :math:`\partial_n \sigma = \partial_n [v_0, \cdots , v_n] = \sum_{i=0}^n (-1)^{i}[v_0,\cdots ,\widehat{v_i}, \cdots,v_n]`, +where :math:`\widehat{v_i}` means :math:`v_i` is omitted from the list. The chain groups form a sequence: + +.. math:: + + \cdots \ \ \mathbf{C}_n(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_n\ } + \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R}) \xrightarrow{\partial_{n-1}} \cdots \xrightarrow{\ \partial_2 \ } + \mathbf{C}_1(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_1 \ } \mathbf{C}_0(\mathbf{K},\mathcal{R}) + +of finitely many groups :math:`\mathbf{C}_n(\mathbf{K},\mathcal{R})` and homomorphisms :math:`\partial_n`, indexed by +the dimension :math:`n \geq 0`. The boundary operators satisfy the property :math:`\partial_n \circ \partial_{n+1}=0` +for every :math:`n > 0` and we define the homology groups: + +.. math:: + + \mathbf{H}_n(\mathbf{K},\mathcal{R}) = \ker \partial_n / \mathrm{im} \ \partial_{n+1} + +We refer to :cite:`Munkres-elementsalgtop1984` for an introduction to homology +theory and to :cite:`DBLP:books/daglib/0025666` for an introduction to persistent homology. + +Indexing Scheme +--------------- + +"Changing" a simplicial complex consists in applying a simplicial map. An *indexing scheme* is a directed graph +together with a traversal order, such that two consecutive nodes in the graph are connected by an arrow (either forward +or backward). +The nodes represent simplicial complexes and the directed edges simplicial maps. + +From the computational point of view, there are two types of indexing schemes of interest in persistent homology: + +* linear ones + :math:`\bullet \longrightarrow \bullet \longrightarrow \cdots \longrightarrow \bullet \longrightarrow \bullet` + in persistent homology :cite:`DBLP:journals/dcg/ZomorodianC05`, +* zigzag ones + :math:`\bullet \longrightarrow \bullet \longleftarrow \cdots \longrightarrow \bullet \longleftarrow \bullet` + in zigzag persistent homology :cite:`DBLP:journals/focm/CarlssonS10`. + +These indexing schemes have a natural left-to-right traversal order, and we describe them with ranges and iterators. +In the current release of the Gudhi library, only the linear case is implemented. + +In the following, we consider the case where the indexing scheme is induced by a filtration. + +Ordering the simplices by increasing filtration values (breaking ties so as a simplex appears after its subsimplices of +same filtration value) provides an indexing scheme. + +Examples +-------- + +We provide several example files: run these examples with -h for details on their use. + +.. only:: builder_html + + * :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:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` + * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` + +Bibliography +************ + +.. bibliography:: bibliography.bib + :filter: docnames + :style: unsrt diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py new file mode 100755 index 00000000..c06ac5a7 --- /dev/null +++ b/src/cython/doc/pyplots/barcode_persistence.py @@ -0,0 +1,5 @@ +import gudhi + +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 new file mode 100755 index 00000000..b4714fe3 --- /dev/null +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -0,0 +1,5 @@ +import gudhi + +alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off') +diag = alpha_complex.persistence() +gudhi.plot_persistence_diagram(diag) diff --git a/src/cython/doc/pyplots/show_palette_values.py b/src/cython/doc/pyplots/show_palette_values.py new file mode 100755 index 00000000..e72a55fd --- /dev/null +++ b/src/cython/doc/pyplots/show_palette_values.py @@ -0,0 +1,2 @@ +import gudhi +gudhi.show_palette_values(alpha=1.0) diff --git a/src/cython/doc/rips_complex_ref.rst b/src/cython/doc/rips_complex_ref.rst new file mode 100644 index 00000000..b17dc4e0 --- /dev/null +++ b/src/cython/doc/rips_complex_ref.rst @@ -0,0 +1,10 @@ +============================= +Rips complex reference manual +============================= + +.. autoclass:: gudhi.RipsComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.RipsComplex.__init__ diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst new file mode 100644 index 00000000..2b65fc19 --- /dev/null +++ b/src/cython/doc/rips_complex_sum.rst @@ -0,0 +1,17 @@ +================================================================= =================================== =================================== +:Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +================================================================= =================================== =================================== + ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton | +| img/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 | +| | value. | +| | | +| | This complex can be built from a point cloud and a distance function, | +| | or from a distance matrix. | ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| :doc:`rips_complex_user` | :doc:`rips_complex_ref` | ++----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst new file mode 100644 index 00000000..027c3bf7 --- /dev/null +++ b/src/cython/doc/rips_complex_user.rst @@ -0,0 +1,237 @@ +========================= +Rips complex user manual +========================= +Definition +---------- + +======================================================= ===================================== ===================================== +:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +======================================================= ===================================== ===================================== + ++-------------------------------------------+----------------------------------------------------------------------+ +| :doc:`rips_complex_user` | :doc:`rips_complex_ref` | ++-------------------------------------------+----------------------------------------------------------------------+ + +`Rips complex <https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex>`_ is a one skeleton graph that allows to +construct a simplicial complex from it. The input can be a point cloud with a given distance function, or a distance +matrix. + +The filtration value of each edge is computed from a user-given distance function, or directly from the distance +matrix. + +All edges that have a filtration value strictly greater than a given threshold value are not inserted into the complex. + +When creating a simplicial complex from this one skeleton graph, Rips inserts the one skeleton graph into the data +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 + :align: center + + Rips-complex one skeleton graph representation + +On this example, as edges (4,5), (4,6) and (5,6) are in the complex, simplex (4,5,6) is added with the filtration value +set with :math:`max(filtration(4,5), filtration(4,6), filtration(5,6))`. And so on for simplex (0,1,2,3). + +If the Rips_complex interfaces are not detailed enough for your need, please refer to rips_persistence_step_by_step.cpp +example, where the graph construction over the Simplex_tree is more detailed. + +Point cloud +----------- + +Example from a point cloud +^^^^^^^^^^^^^^^^^^^^^^^^^^ + +This example builds the one skeleton graph from the given points, and max_edge_length value. +Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it. + +Finally, it is asked to display information about the simplicial complex. + +.. testcode:: + + import gudhi + rips_complex = gudhi.RipsComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]], + 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 - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' + print(result_str) + for filtered_value in simplex_tree.get_filtered_tree(): + print(filtered_value) + +When launching (Rips maximal distance between 2 points is 12.0, is expanded +until dimension 1 - one skeleton graph in other words), the output is: + +.. testoutput:: + + Rips complex is of dimension 1 - 18 simplices - 7 vertices. + ([0], 0.0) + ([1], 0.0) + ([2], 0.0) + ([3], 0.0) + ([4], 0.0) + ([5], 0.0) + ([6], 0.0) + ([2, 3], 5.0) + ([4, 5], 5.385164807134504) + ([0, 2], 5.830951894845301) + ([0, 1], 6.082762530298219) + ([1, 3], 6.324555320336759) + ([1, 2], 6.708203932499369) + ([5, 6], 7.280109889280518) + ([2, 4], 8.94427190999916) + ([0, 3], 9.433981132056603) + ([4, 6], 9.486832980505138) + ([3, 6], 11.0) + +Example from OFF file +^^^^^^^^^^^^^^^^^^^^^ + +This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given +points in an OFF file, and max_edge_length value. +Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it. + +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) + 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 - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' + print(result_str) + for filtered_value in simplex_tree.get_filtered_tree(): + print(filtered_value) + +the program output is: + +.. testoutput:: + + Rips complex is of dimension 1 - 18 simplices - 7 vertices. + ([0], 0.0) + ([1], 0.0) + ([2], 0.0) + ([3], 0.0) + ([4], 0.0) + ([5], 0.0) + ([6], 0.0) + ([2, 3], 5.0) + ([4, 5], 5.385164807134504) + ([0, 2], 5.830951894845301) + ([0, 1], 6.082762530298219) + ([1, 3], 6.324555320336759) + ([1, 2], 6.708203932499369) + ([5, 6], 7.280109889280518) + ([2, 4], 8.94427190999916) + ([0, 3], 9.433981132056603) + ([4, 6], 9.486832980505138) + ([3, 6], 11.0) + +Distance matrix +--------------- + +Example from a distance matrix +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +This example builds the one skeleton graph from the given distance matrix, and max_edge_length value. +Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it. + +Finally, it is asked to display information about the simplicial complex. + +.. testcode:: + + import gudhi + rips_complex = gudhi.RipsComplex(distance_matrix=[[], + [6.0827625303], + [5.8309518948, 6.7082039325], + [9.4339811321, 6.3245553203, 5], + [13.0384048104, 15.6524758425, 8.94427191, 12.0415945788], + [18.0277563773, 19.6468827044, 13.152946438, 14.7648230602, 5.3851648071], + [17.88854382, 17.1172427686, 12.0830459736, 11, 9.4868329805, 7.2801098893]], + 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 - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' + print(result_str) + for filtered_value in simplex_tree.get_filtered_tree(): + print(filtered_value) + +When launching (Rips maximal distance between 2 points is 12.0, is expanded +until dimension 1 - one skeleton graph in other words), the output is: + +.. testoutput:: + + Rips complex is of dimension 1 - 18 simplices - 7 vertices. + ([0], 0.0) + ([1], 0.0) + ([2], 0.0) + ([3], 0.0) + ([4], 0.0) + ([5], 0.0) + ([6], 0.0) + ([2, 3], 5.0) + ([4, 5], 5.3851648071) + ([0, 2], 5.8309518948) + ([0, 1], 6.0827625303) + ([1, 3], 6.3245553203) + ([1, 2], 6.7082039325) + ([5, 6], 7.2801098893) + ([2, 4], 8.94427191) + ([0, 3], 9.4339811321) + ([4, 6], 9.4868329805) + ([3, 6], 11.0) + +Example from csv file +^^^^^^^^^^^^^^^^^^^^^ + +This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given +points in an OFF file, and max_edge_length value. +Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it. + +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) + 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 - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' + print(result_str) + for filtered_value in simplex_tree.get_filtered_tree(): + print(filtered_value) + +the program output is: + +.. testoutput:: + + Rips complex is of dimension 1 - 18 simplices - 7 vertices. + ([0], 0.0) + ([1], 0.0) + ([2], 0.0) + ([3], 0.0) + ([4], 0.0) + ([5], 0.0) + ([6], 0.0) + ([2, 3], 5.0) + ([4, 5], 5.3851648071) + ([0, 2], 5.8309518948) + ([0, 1], 6.0827625303) + ([1, 3], 6.3245553203) + ([1, 2], 6.7082039325) + ([5, 6], 7.2801098893) + ([2, 4], 8.94427191) + ([0, 3], 9.4339811321) + ([4, 6], 9.4868329805) + ([3, 6], 11.0) diff --git a/src/cython/doc/simplex_tree_ref.rst b/src/cython/doc/simplex_tree_ref.rst new file mode 100644 index 00000000..6d196843 --- /dev/null +++ b/src/cython/doc/simplex_tree_ref.rst @@ -0,0 +1,10 @@ +============================= +Simplex tree reference manual +============================= + +.. autoclass:: gudhi.SimplexTree + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.SimplexTree.__init__ diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst new file mode 100644 index 00000000..3174fb62 --- /dev/null +++ b/src/cython/doc/simplex_tree_sum.rst @@ -0,0 +1,14 @@ +================================================================= =================================== =================================== +:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +================================================================= =================================== =================================== + ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| .. figure:: | The simplex tree is an efficient and flexible data structure for | +| img/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | +| :alt: Simplex tree representation | | +| :figclass: align-center | The data structure is described in | +| | :cite:`boissonnatmariasimplextreealgorithmica` | +| Simplex tree representation | | ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| :doc:`simplex_tree_user` | :doc:`simplex_tree_ref` | ++----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst new file mode 100644 index 00000000..6b55c4e7 --- /dev/null +++ b/src/cython/doc/simplex_tree_user.rst @@ -0,0 +1,67 @@ +======================== +Simplex tree user manual +======================== +Definition +---------- + +.. include:: simplex_tree_sum.rst + +A simplicial complex :math:`\mathbf{K}` on a set of vertices :math:`V = \{1, \cdots ,|V|\}` is a collection of +simplices :math:`\{\sigma\}`, :math:`\sigma \subseteq V` such that +:math:`\tau \subseteq \sigma \in \mathbf{K} \rightarrow \tau \in \mathbf{K}`. The dimension :math:`n=|\sigma|-1` of +:math:`\sigma` is its number of elements minus `1`. + +A filtration of a simplicial complex is a function :math:`f:\mathbf{K} \rightarrow \mathbb{R}` satisfying +:math:`f(\tau)\leq f(\sigma)` whenever :math:`\tau \subseteq \sigma`. Ordering the simplices by increasing filtration +values (breaking ties so as a simplex appears after its subsimplices of same filtration value) provides an indexing +scheme. + + +Implementation +-------------- + +There are two implementation of complexes. The first on is the Simplex_tree data structure. +The simplex tree is an efficient and flexible data structure for representing general (filtered) simplicial complexes. +The data structure is described in :cite`boissonnatmariasimplextreealgorithmica`. + +The second one is the Hasse_complex. The Hasse complex is a data structure representing explicitly all co-dimension 1 +incidence relations in a complex. It is consequently faster when accessing the boundary of a simplex, but is less +compact and harder to construct from scratch. + +Example +------- + +.. testcode:: + + import gudhi + st = gudhi.SimplexTree() + if st.insert_simplex([0, 1]): + print("[0, 1] inserted") + if st.insert_simplex_and_subfaces([0, 1, 2], filtration=4.0): + print("[0, 1, 2] inserted") + if st.find([0, 1]): + print("[0, 1] found") + print("num_vertices=", st.num_vertices()) + print("num_simplices=", st.num_simplices()) + print("skeleton_tree(2) =") + for sk_value in st.get_skeleton_tree(2): + print(sk_value) + + +The output is: + +.. testoutput:: + + [0, 1] inserted + [0, 1, 2] inserted + [0, 1] found + ('num_vertices=', 3) + ('num_simplices=', 7) + skeleton_tree(2) = + ([0, 1, 2], 4.0) + ([0, 1], 0.0) + ([0, 2], 4.0) + ([0], 0.0) + ([1, 2], 4.0) + ([1], 4.0) + ([2], 4.0) diff --git a/src/cython/doc/strong_witness_complex_ref.rst b/src/cython/doc/strong_witness_complex_ref.rst new file mode 100644 index 00000000..4ed4fe46 --- /dev/null +++ b/src/cython/doc/strong_witness_complex_ref.rst @@ -0,0 +1,10 @@ +======================================= +Strong witness complex reference manual +======================================= + +.. autoclass:: gudhi.StrongWitnessComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.StrongWitnessComplex.__init__ diff --git a/src/cython/doc/tangential_complex_ref.rst b/src/cython/doc/tangential_complex_ref.rst new file mode 100644 index 00000000..35589475 --- /dev/null +++ b/src/cython/doc/tangential_complex_ref.rst @@ -0,0 +1,10 @@ +=================================== +Tangential complex reference manual +=================================== + +.. autoclass:: gudhi.TangentialComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.TangentialComplex.__init__ diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst new file mode 100644 index 00000000..2b05bc10 --- /dev/null +++ b/src/cython/doc/tangential_complex_sum.rst @@ -0,0 +1,15 @@ +================================================================= =================================== =================================== +:Author: Clément Jamin :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Requires: CGAL :math:`\geq` 4.8.0 Eigen3 +================================================================= =================================== =================================== + ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| .. 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`- | +| :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 | +| | 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 new file mode 100644 index 00000000..6a7e6e41 --- /dev/null +++ b/src/cython/doc/tangential_complex_user.rst @@ -0,0 +1,195 @@ +============================== +Tangential complex user manual +============================== +.. include:: tangential_complex_sum.rst + +Definition +---------- + +A Tangential Delaunay complex is a simplicial complex designed to reconstruct a +:math:`k`-dimensional smooth manifold embedded in :math:`d`-dimensional +Euclidean space. The input is a point sample coming from an unknown manifold, +which means that the points lie close to a structure of "small" intrinsic +dimension. The running time depends only linearly on the extrinsic dimension +:math:`d` and exponentially on the intrinsic dimension :math:`k`. + +An extensive description of the Tangential complex can be found in +:cite:`tangentialcomplex2014`. + +What is a Tangential Complex? +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +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 + :alt: The input + :figclass: align-center + + The input + +For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g. +using PCA). + +.. figure:: img/tc_example_02.png + :alt: The estimated normals + :figclass: align-center + + The estimated normals + + +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 + :alt: The Voronoi diagram + :figclass: align-center + + The Voronoi diagram + +The Tangential Delaunay complex is the union of those stars. + +In practice, neither the ambient Voronoi diagram nor the ambient Delaunay +triangulation is computed. Instead, local :math:`k`-dimensional regular +triangulations are computed with a limited number of points as we only need the +star of each point. More details can be found in :cite:`tangentialcomplex2014`. + +Inconsistencies +^^^^^^^^^^^^^^^ +Inconsistencies between the stars can occur. An inconsistency occurs when a +simplex is not in the star of all its vertices. + +Let us take the same example. + +.. figure:: img/tc_example_07_before.png + :alt: Before + :figclass: align-center + + Before + +Let us slightly move the tangent subspace :math:`T_q` + +.. figure:: img/tc_example_07_after.png + :alt: After + :figclass: align-center + + After + +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 + :alt: After + :figclass: align-center + + After + +One way to solve inconsistencies is to randomly perturb the positions of the +points involved in an inconsistency. In the current implementation, this +perturbation is done in the tangent subspace of each point. The maximum +perturbation radius is given as a parameter to the constructor. + +In most cases, we recommend to provide a point set where the minimum distance +between any two points is not too small. This can be achieved using the +functions provided by the Subsampling module. Then, a good value to start with +for the maximum perturbation radius would be around half the minimum distance +between any two points. The Example with perturbation below shows an example of +such a process. + +In most cases, this process is able to dramatically reduce the number of +inconsistencies, but is not guaranteed to succeed. + +Output +^^^^^^ +The result of the computation is exported as a Simplex_tree. It is the union of +the stars of all the input points. A vertex in the Simplex Tree is the index of +the point in the range provided by the user. The point corresponding to a +vertex can also be obtained through the Tangential_complex::get_point function. +Note that even if the positions of the points are perturbed, their original +positions are kept (e.g. Tangential_complex::get_point returns the original +position of the point). + +The result can be obtained after the computation of the Tangential complex +itself and/or after the perturbation process. + + +Simple example +-------------- + +This example builds the Tangential complex of point set read in an OFF file. + +.. testcode:: + + import gudhi + tc = gudhi.TangentialComplex(off_file='alphacomplexdoc.off') + result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \ + ' simplices - ' + repr(tc.num_vertices()) + ' vertices.' + print(result_str) + + st = tc.create_simplex_tree() + result_str = 'Simplex tree is of dimension ' + repr(st.dimension()) + \ + ' - ' + repr(st.num_simplices()) + ' simplices - ' + \ + repr(st.num_vertices()) + ' vertices.' + print(result_str) + for filtered_value in st.get_filtered_tree(): + print(filtered_value) + +The output is: + +.. testoutput:: + + Tangential contains 12 simplices - 7 vertices. + Simplex tree is of dimension 1 - 15 simplices - 7 vertices. + ([0], 0.0) + ([1], 0.0) + ([0, 1], 0.0) + ([2], 0.0) + ([0, 2], 0.0) + ([1, 2], 0.0) + ([3], 0.0) + ([1, 3], 0.0) + ([4], 0.0) + ([2, 4], 0.0) + ([5], 0.0) + ([4, 5], 0.0) + ([6], 0.0) + ([3, 6], 0.0) + ([5, 6], 0.0) + + +Example with perturbation +------------------------- + +This example builds the Tangential complex of a point set, then tries to solve +inconsistencies by perturbing the positions of points involved in inconsistent +simplices. + +.. testcode:: + + import gudhi + tc = gudhi.TangentialComplex(points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]]) + result_str = 'Tangential contains ' + repr(tc.num_vertices()) + ' vertices.' + print(result_str) + + if tc.num_inconsistent_simplices() > 0: + print('Tangential contains inconsistencies.') + + tc.fix_inconsistencies_using_perturbation(10, 60) + if tc.num_inconsistent_simplices() == 0: + print('Inconsistencies has been fixed.') + +The output is: + +.. testoutput:: + + Tangential contains 4 vertices. + Inconsistencies has been fixed. + +Bibliography +************ + +.. bibliography:: bibliography.bib + :filter: docnames + :style: unsrt diff --git a/src/cython/doc/todos.rst b/src/cython/doc/todos.rst new file mode 100644 index 00000000..78972a4c --- /dev/null +++ b/src/cython/doc/todos.rst @@ -0,0 +1,5 @@ +========== +To be done +========== + +.. todolist:: diff --git a/src/cython/doc/witness_complex_ref.rst b/src/cython/doc/witness_complex_ref.rst new file mode 100644 index 00000000..c78760cb --- /dev/null +++ b/src/cython/doc/witness_complex_ref.rst @@ -0,0 +1,10 @@ +================================ +Witness complex reference manual +================================ + +.. autoclass:: gudhi.WitnessComplex + :members: + :undoc-members: + :show-inheritance: + + .. automethod:: gudhi.WitnessComplex.__init__ diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst new file mode 100644 index 00000000..b65522ba --- /dev/null +++ b/src/cython/doc/witness_complex_sum.rst @@ -0,0 +1,17 @@ +================================================================= =================================== =================================== +:Author: Siargey Kachanovich :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +: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` | ++-----------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst new file mode 100644 index 00000000..07945361 --- /dev/null +++ b/src/cython/doc/witness_complex_user.rst @@ -0,0 +1,135 @@ +=========================== +Witness complex user manual +=========================== +Definition +---------- + +.. include:: witness_complex_sum.rst + + +Definitions +----------- + +Witness complex is a simplicial complex defined on two sets of points in :math:`\mathbb{R}^D`: + +- :math:`W` set of **witnesses** and +- :math:`L` set of **landmarks**. + +Even though often the set of landmarks :math:`L` is a subset of the set of witnesses :math:`W`, it is not a requirement +for the current implementation. + +Landmarks are the vertices of the simplicial complex and witnesses help to decide on which simplices are inserted via a +predicate "is witnessed". + +De Silva and Carlsson in their paper :cite:`de2004topological` differentiate **weak witnessing** and +**strong witnessing**: + +- *weak*: :math:`\sigma \subset L` is witnessed by :math:`w \in W` if :math:`\forall l \in \sigma,\ \forall l' \in \mathbf{L \setminus \sigma},\ d(w,l) \leq d(w,l')` +- *strong*: :math:`\sigma \subset L` is witnessed by :math:`w \in W` if :math:`\forall l \in \sigma,\ \forall l' \in \mathbf{L},\ d(w,l) \leq d(w,l')` + +where :math:`d(.,.)` is a distance function. + +Both definitions can be relaxed by a real value :math:`\alpha`: + +- *weak*: :math:`\sigma \subset L` is :math:`\alpha`-witnessed by :math:`w \in W` if :math:`\forall l \in \sigma,\ \forall l' \in \mathbf{L \setminus \sigma},\ d(w,l)^2 \leq d(w,l')^2 + \alpha^2` +- *strong*: :math:`\sigma \subset L` is :math:`\alpha`-witnessed by :math:`w \in W` if :math:`\forall l \in \sigma,\ \forall l' \in \mathbf{L},\ d(w,l)^2 \leq d(w,l')^2 + \alpha^2` + +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 + :alt: Strongly witnessed simplex + :figclass: align-center + + Strongly witnessed simplex + + +In particular case of 0-relaxation, weak complex corresponds to **witness complex** introduced in +:cite:`de2004topological`, whereas 0-relaxed strong witness complex consists of just vertices and is not very +interesting. Hence for small relaxation weak version is preferable. +However, to capture the homotopy type (for example using Gudhi::persistent_cohomology::Persistent_cohomology) it is +often necessary to work with higher filtration values. In this case strong relaxed witness complex is faster to compute +and offers similar results. + +Implementation +-------------- + +The two complexes described above are implemented in the corresponding classes + +- :doc:`witness_complex_ref` +- :doc:`strong_witness_complex_ref` +- :doc:`euclidean_witness_complex_ref` +- :doc:`euclidean_strong_witness_complex_ref` + +The construction of the Euclidean versions of complexes follow the same scheme: + +1. Construct a search tree on landmarks. +2. Construct lists of nearest landmarks for each witness. +3. Construct the witness complex for nearest landmark lists. + +In the non-Euclidean classes, the lists of nearest landmarks are supposed to be given as input. + +The constructors take on the steps 1 and 2, while the function 'create_complex' executes the step 3. + +Constructing weak relaxed witness complex from an off file +---------------------------------------------------------- + +Let's start with a simple example, which reads an off point file and computes a weak witness complex. + +.. code-block:: python + + import gudhi + import argparse + + parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from ' + 'points read in a OFF file.', + epilog='Example: ' + 'example/witness_complex_diagram_persistence_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' + '- Constructs a alpha complex with the ' + 'points from the given OFF file.') + 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) + + args = parser.parse_args() + + with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("EuclideanWitnessComplex creation from points read in a OFF file") + + witnesses = gudhi.read_off(off_file=args.file) + landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks) + + message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \ + " - Number of landmarks=" + repr(args.number_of_landmarks) + print(message) + + witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses, landmarks=landmarks) + simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square, + limit_dimension=args.limit_dimension) + + message = "Number of simplices=" + repr(simplex_tree.num_simplices()) + print(message) + else: + print(args.file, "is not a valid OFF file") + + f.close() + + +Example2: Computing persistence using strong relaxed witness complex +-------------------------------------------------------------------- + +Here is an example of constructing a strong witness complex filtration and computing persistence on it: + +* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` + +Bibliography +************ + +.. bibliography:: bibliography.bib + :filter: docnames + :style: unsrt 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 new file mode 100755 index 00000000..adedc7d2 --- /dev/null +++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='AlphaComplex creation from ' + 'points read in a OFF file.', + epilog='Example: ' + 'example/alpha_complex_diagram_persistence_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off -a 0.6' + '- Constructs a alpha complex with the ' + '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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("AlphaComplex creation from points read in a OFF file") + + message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square) + print(message) + + alpha_complex = gudhi.AlphaComplex(off_file=args.file) + simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square) + + message = "Number of simplices=" + repr(simplex_tree.num_simplices()) + print(message) + + diag = simplex_tree.persistence() + + print("betti_numbers()=") + print(simplex_tree.betti_numbers()) + + if args.no_diagram == False: + gudhi.plot_persistence_diagram(diag) + else: + print(args.file, "is not a valid OFF file") + + f.close() diff --git a/src/cython/example/alpha_complex_from_points_example.py b/src/cython/example/alpha_complex_from_points_example.py new file mode 100755 index 00000000..688edb65 --- /dev/null +++ b/src/cython/example/alpha_complex_from_points_example.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +from gudhi import AlphaComplex, SimplexTree + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +print("#####################################################################") +print("AlphaComplex creation from points") +alpha_complex = AlphaComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]]) +simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=60.0) + +if simplex_tree.find([0, 1]): + print("[0, 1] Found !!") +else: + print("[0, 1] Not found...") + +if simplex_tree.find([4]): + print("[4] Found !!") +else: + print("[4] Not found...") + +if simplex_tree.insert([0, 1, 2], filtration=4.0): + print("[0, 1, 2] Inserted !!") +else: + print("[0, 1, 2] Not inserted...") + +if simplex_tree.insert([0, 1, 4], filtration=4.0): + print("[0, 1, 4] Inserted !!") +else: + print("[0, 1, 4] Not inserted...") + +if simplex_tree.find([4]): + print("[4] Found !!") +else: + print("[4] Not found...") + +print("dimension=", simplex_tree.dimension()) +print("filtered_tree=", simplex_tree.get_filtered_tree()) +print("star([0])=", simplex_tree.get_star([0])) +print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1)) + +print("point[0]=", alpha_complex.get_point(0)) +print("point[5]=", alpha_complex.get_point(5)) diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py new file mode 100755 index 00000000..ab5fc1e9 --- /dev/null +++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python + +import gudhi +import argparse +import math + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='AlphaComplex and RipsComplex ' + 'persistence creation from points read in ' + 'a OFF file. Bottleneck distance computation' + ' on each dimension', + epilog='Example: ' + 'example/alpha_rips_persistence_bottleneck_distance.py ' + '-f ../data/points/tore3D_1307.off -t 0.15 -d 3') +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-t", "--threshold", type=float, default=0.5) +parser.add_argument("-d", "--max_dimension", type=int, default=1) + +args = parser.parse_args() +with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("RipsComplex creation from points read in a OFF file") + + message = "RipsComplex with max_edge_length=" + repr(args.threshold) + print(message) + + rips_complex = gudhi.RipsComplex(off_file=args.file, + max_edge_length=args.threshold) + + rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) + + message = "Number of simplices=" + repr(rips_stree.num_simplices()) + print(message) + + rips_diag = rips_stree.persistence() + + print("#####################################################################") + print("AlphaComplex creation from points read in a OFF file") + + message = "AlphaComplex with max_edge_length=" + repr(args.threshold) + print(message) + + alpha_complex = gudhi.AlphaComplex(off_file=args.file) + alpha_stree = alpha_complex.create_simplex_tree(max_alpha_square=(args.threshold * args.threshold)) + + message = "Number of simplices=" + repr(alpha_stree.num_simplices()) + print(message) + + alpha_diag = alpha_stree.persistence() + + max_b_distance = 0.0 + for dim in range(args.max_dimension): + # Alpha persistence values needs to be transform because filtration + # values are alpha square values + funcs = [math.sqrt, math.sqrt] + alpha_intervals = [] + for interval in alpha_stree.persistence_intervals_in_dimension(dim): + alpha_intervals.append(map(lambda func,value: func(value), funcs, interval)) + + rips_intervals = rips_stree.persistence_intervals_in_dimension(dim) + bottleneck_distance = gudhi.bottleneck_distance(rips_intervals, alpha_intervals) + message = "In dimension " + repr(dim) + ", bottleneck distance = " + repr(bottleneck_distance) + print(message) + max_b_distance = max(bottleneck_distance, max_b_distance) + + print("================================================================================") + message = "Bottleneck distance is " + repr(max_b_distance) + print(message) + + else: + print(args.file, "is not a valid OFF file") + + f.close() diff --git a/src/cython/example/bottleneck_basic_example.py b/src/cython/example/bottleneck_basic_example.py new file mode 100755 index 00000000..31cecb29 --- /dev/null +++ b/src/cython/example/bottleneck_basic_example.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python + +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): Francois Godi, 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Francois Godi, Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +import gudhi + +diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]] + +diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]] + +message = "diag1=" + repr(diag1) +print(message) + +message = "diag2=" + repr(diag2) +print(message) + +message = "Bottleneck distance approximation=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0.1)) +print(message) + +message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2)) +print(message) + 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 new file mode 100755 index 00000000..2474fc87 --- /dev/null +++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,78 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex creation from ' + 'points read in a OFF file.', + epilog='Example: ' + 'example/witness_complex_diagram_persistence_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' + '- Constructs a strong witness complex with the ' + 'points from the given OFF file.') +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("EuclideanStrongWitnessComplex creation from points read in a OFF file") + + witnesses = gudhi.read_off(off_file=args.file) + landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks) + + message = "EuclideanStrongWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \ + " - Number of landmarks=" + repr(args.number_of_landmarks) + print(message) + + witness_complex = gudhi.EuclideanStrongWitnessComplex(witnesses=witnesses, landmarks=landmarks) + simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square, + limit_dimension=args.limit_dimension) + + message = "Number of simplices=" + repr(simplex_tree.num_simplices()) + print(message) + + diag = simplex_tree.persistence() + + print("betti_numbers()=") + print(simplex_tree.betti_numbers()) + + if args.no_diagram == False: + gudhi.plot_persistence_diagram(diag) + + else: + print(args.file, "is not a valid OFF file") + + f.close() 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 new file mode 100755 index 00000000..5a75417b --- /dev/null +++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,78 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from ' + 'points read in a OFF file.', + epilog='Example: ' + 'example/witness_complex_diagram_persistence_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' + '- Constructs a weak witness complex with the ' + 'points from the given OFF file.') +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("EuclideanWitnessComplex creation from points read in a OFF file") + + witnesses = gudhi.read_off(off_file=args.file) + landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks) + + message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \ + " - Number of landmarks=" + repr(args.number_of_landmarks) + print(message) + + witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses, landmarks=landmarks) + simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square, + limit_dimension=args.limit_dimension) + + message = "Number of simplices=" + repr(simplex_tree.num_simplices()) + print(message) + + diag = simplex_tree.persistence() + + print("betti_numbers()=") + print(simplex_tree.betti_numbers()) + + if args.no_diagram == False: + gudhi.plot_persistence_diagram(diag) + + else: + print(args.file, "is not a valid OFF file") + + f.close() diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py new file mode 100755 index 00000000..bc3b16ec --- /dev/null +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -0,0 +1,47 @@ +#!/usr/bin/env python + +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +print("#####################################################################") +print("Show palette colors values for dimension") + +gudhi.show_palette_values() + +print("#####################################################################") +print("Show barcode persistence example") + +persistence = [(2, (1.0, float('inf'))), (1, (1.4142135623730951, float('inf'))), + (1, (1.4142135623730951, float('inf'))), (0, (0.0, float('inf'))), + (0, (0.0, 1.0)), (0, (0.0, 1.0)), (0, (0.0, 1.0))] +gudhi.plot_persistence_barcode(persistence) + +print("#####################################################################") +print("Show diagram persistence example") + +gudhi.plot_persistence_diagram(persistence) diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py new file mode 100755 index 00000000..db530161 --- /dev/null +++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -0,0 +1,76 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +def is_file_perseus(file): + num_lines = open(file).read().count('\n') + try: + f = open(file) + num_dim = int(f.readline()) + coeff = 1 + for dim in range(0, num_dim): + try: + line = int(f.readline()) + coeff *= abs(line) + except ValueError: + return False + if num_lines == (1 + num_dim + coeff): + return True + else: + return False + except ValueError: + return False + +parser = argparse.ArgumentParser(description='Periodic cubical complex from a ' + 'perseus file style name.', + epilog='Example: ' + './periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py' + ' -f ../data/bitmap/CubicalTwoSphere.txt') + +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument('--no-barcode', default=False, action='store_true' , help='Flag for not to display the barcodes') + +args = parser.parse_args() + +if is_file_perseus(args.file): + print("#####################################################################") + print("PeriodicCubicalComplex creation") + periodic_cubical_complex = gudhi.PeriodicCubicalComplex(perseus_file=args.file) + + print("persistence(homology_coeff_field=3, min_persistence=0)=") + diag = periodic_cubical_complex.persistence(homology_coeff_field=3, min_persistence=0) + print(diag) + + print("betti_numbers()=") + print(periodic_cubical_complex.betti_numbers()) + if args.no_barcode == False: + gudhi.plot_persistence_barcode(diag) +else: + print(args.file, "is not a valid perseus style file") diff --git a/src/cython/example/random_cubical_complex_persistence_example.py b/src/cython/example/random_cubical_complex_persistence_example.py new file mode 100755 index 00000000..1c55f777 --- /dev/null +++ b/src/cython/example/random_cubical_complex_persistence_example.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python + +import gudhi +import numpy +import argparse +import operator + + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='Random cubical complex.', + epilog='Example: ' + './random_cubical_complex_persistence_example.py' + ' 10 10 10 - Constructs a random cubical ' + 'complex in a dimension [10, 10, 10] (aka. ' + '1000 random top dimensional cells).') +parser.add_argument('dimension', type=int, nargs="*", + help='Cubical complex dimensions') + +args = parser.parse_args() +dimension_multiplication = reduce(operator.mul, args.dimension, 1) + +if dimension_multiplication > 1: + print("#####################################################################") + print("CubicalComplex creation") + cubical_complex = gudhi.CubicalComplex(dimensions=args.dimension, + top_dimensional_cells = numpy.random.rand(dimension_multiplication)) + + print("persistence(homology_coeff_field=2, min_persistence=0)=") + print(cubical_complex.persistence(homology_coeff_field=2, min_persistence=0)) + + print("betti_numbers()=") + print(cubical_complex.betti_numbers())
\ No newline at end of file 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 new file mode 100755 index 00000000..664eb5c4 --- /dev/null +++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -0,0 +1,71 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='RipsComplex creation from ' + 'a distance matrix read in a OFF file.', + epilog='Example: ' + 'example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py ' + '-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3' + '- Constructs a Rips complex with the ' + 'points from the given OFF file.') +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("RipsComplex creation from distance matrix read in a csv file") + + message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) + print(message) + + rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length) + simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) + + message = "Number of simplices=" + repr(simplex_tree.num_simplices()) + print(message) + + diag = simplex_tree.persistence() + + print("betti_numbers()=") + print(simplex_tree.betti_numbers()) + + if args.no_diagram == False: + gudhi.plot_persistence_diagram(diag) + else: + print(args.file, "is not a valid OFF file") + + f.close() 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 new file mode 100755 index 00000000..4c21b98e --- /dev/null +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,71 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='RipsComplex creation from ' + 'points read in a OFF file.', + epilog='Example: ' + 'example/rips_complex_diagram_persistence_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off -a 0.6' + '- Constructs a Rips complex with the ' + 'points from the given OFF file.') +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("RipsComplex creation from points read in a OFF file") + + message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) + print(message) + + rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length) + simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) + + message = "Number of simplices=" + repr(simplex_tree.num_simplices()) + print(message) + + diag = simplex_tree.persistence() + + print("betti_numbers()=") + print(simplex_tree.betti_numbers()) + + if args.no_diagram == False: + gudhi.plot_persistence_diagram(diag) + else: + print(args.file, "is not a valid OFF file") + + f.close() diff --git a/src/cython/example/rips_complex_from_points_example.py b/src/cython/example/rips_complex_from_points_example.py new file mode 100755 index 00000000..9b7fc79d --- /dev/null +++ b/src/cython/example/rips_complex_from_points_example.py @@ -0,0 +1,40 @@ +#!/usr/bin/env python + +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +print("#####################################################################") +print("RipsComplex creation from points") +rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]], + max_edge_length=42) + +simplex_tree = rips.create_simplex_tree(max_dimension=1) + +print("filtered_tree=", simplex_tree.get_filtered_tree()) +print("star([0])=", simplex_tree.get_star([0])) +print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1)) diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py new file mode 100755 index 00000000..4e5cd2c8 --- /dev/null +++ b/src/cython/example/rips_persistence_diagram.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python + +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): Marc Glisse + + 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Marc Glisse" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +print("#####################################################################") +print("RipsComplex creation from points") +rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]], + max_edge_length=42) + +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) diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py new file mode 100755 index 00000000..bf5f17a2 --- /dev/null +++ b/src/cython/example/simplex_tree_example.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python + +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +print("#####################################################################") +print("SimplexTree creation from insertion") + +st = gudhi.SimplexTree() + +if st.insert([0, 1]): + print("Inserted !!") +else: + print("Not inserted...") + +if st.find([0, 1]): + print("Found !!") +else: + print("Not found...") + +if st.insert([0, 1, 2], filtration=4.0): + print("Inserted !!") +else: + print("Not inserted...") + +# FIXME: Remove this line +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])) +print("filtration[4, 2]=", st.filtration([4, 2])) + +print("num_simplices=", st.num_simplices()) +print("num_vertices=", st.num_vertices()) + +print("skeleton_tree[2]=", st.get_skeleton_tree(2)) +print("skeleton_tree[1]=", st.get_skeleton_tree(1)) +print("skeleton_tree[0]=", st.get_skeleton_tree(0)) 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 new file mode 100755 index 00000000..4845eb47 --- /dev/null +++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='TangentialComplex creation from ' + 'points read in a OFF file.', + epilog='Example: ' + 'example/tangential_complex_plain_homology_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off' + '- Constructs a tangential complex with the ' + 'points from the given OFF file') +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("TangentialComplex creation from points read in a OFF file") + + tc = gudhi.TangentialComplex(off_file=args.file) + st = tc.create_simplex_tree() + + message = "Number of simplices=" + repr(st.num_simplices()) + print(message) + + diag = st.persistence(persistence_dim_max = True) + + print("betti_numbers()=") + print(st.betti_numbers()) + + if args.no_diagram == False: + gudhi.plot_persistence_diagram(diag) + else: + print(args.file, "is not a valid OFF file") + + f.close() diff --git a/src/cython/example/witness_complex_from_nearest_landmark_table.py b/src/cython/example/witness_complex_from_nearest_landmark_table.py new file mode 100755 index 00000000..92ed970b --- /dev/null +++ b/src/cython/example/witness_complex_from_nearest_landmark_table.py @@ -0,0 +1,46 @@ +#!/usr/bin/env python + +from gudhi import StrongWitnessComplex, SimplexTree + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +print("#####################################################################") +print("WitnessComplex creation from nearest landmark table") +nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]], + [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]], + [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]], + [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]], + [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]] + +witness_complex = StrongWitnessComplex(nearest_landmark_table=nearest_landmark_table) +simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1) + +message = "Number of simplices: " + repr(simplex_tree.num_simplices()) +print(message) + +diag = simplex_tree.persistence(min_persistence=-0.1, homology_coeff_field=11) +print(diag) diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in new file mode 100644 index 00000000..34d7c3b5 --- /dev/null +++ b/src/cython/gudhi.pyx.in @@ -0,0 +1,39 @@ +"""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 <http://www.gnu.org/licenses/>. +""" + +__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/witness_complex.pyx" +include "cython/strong_witness_complex.pyx" +@GUDHI_CYTHON_ALPHA_COMPLEX@ +@GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@ +@GUDHI_CYTHON_SUBSAMPLING@ +@GUDHI_CYTHON_TANGENTIAL_COMPLEX@ +@GUDHI_CYTHON_BOTTLENECK_DISTANCE@ diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h new file mode 100644 index 00000000..d47db71f --- /dev/null +++ b/src/cython/include/Alpha_complex_interface.h @@ -0,0 +1,82 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_ALPHA_COMPLEX_INTERFACE_H_ +#define INCLUDE_ALPHA_COMPLEX_INTERFACE_H_ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Alpha_complex.h> +#include <CGAL/Epick_d.h> + +#include "Simplex_tree_interface.h" + +#include <iostream> +#include <vector> +#include <string> + +namespace Gudhi { + +namespace alpha_complex { + +class Alpha_complex_interface { + using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + using Point_d = Dynamic_kernel::Point_d; + + public: + Alpha_complex_interface(const std::vector<std::vector<double>>& points) { + alpha_complex_ = new Alpha_complex<Dynamic_kernel>(points); + } + + Alpha_complex_interface(const std::string& off_file_name, bool from_file = true) { + alpha_complex_ = new Alpha_complex<Dynamic_kernel>(off_file_name); + } + + ~Alpha_complex_interface() { + delete alpha_complex_; + } + + std::vector<double> get_point(int vh) { + std::vector<double> vd; + try { + Point_d ph = alpha_complex_->get_point(vh); + for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++) + vd.push_back(*coord); + } catch (std::out_of_range outofrange) { + // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown + } + return vd; + } + + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square) { + alpha_complex_->create_complex(*simplex_tree, max_alpha_square); + simplex_tree->initialize_filtration(); + } + + private: + Alpha_complex<Dynamic_kernel>* alpha_complex_; +}; + +} // namespace alpha_complex + +} // namespace Gudhi + +#endif // INCLUDE_ALPHA_COMPLEX_INTERFACE_H_ diff --git a/src/cython/include/Bottleneck_distance_interface.h b/src/cython/include/Bottleneck_distance_interface.h new file mode 100644 index 00000000..d5fbf6ea --- /dev/null +++ b/src/cython/include/Bottleneck_distance_interface.h @@ -0,0 +1,53 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_ +#define INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_ + +#include <gudhi/Bottleneck.h> + +#include <iostream> +#include <vector> +#include <utility> // for std::pair + +namespace Gudhi { + +namespace persistence_diagram { + + // bottleneck_distance function renamed for the python function can be called bottleneck_dstance + double bottleneck(const std::vector<std::pair<double, double>>& diag1, + const std::vector<std::pair<double, double>>& diag2, + double e) { + return bottleneck_distance(diag1, diag2, e); + } + + double bottleneck(const std::vector<std::pair<double, double>>& diag1, + const std::vector<std::pair<double, double>>& diag2) { + return bottleneck_distance(diag1, diag2); + } + +} // namespace persistence_diagram + +} // namespace Gudhi + + +#endif // INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_ diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h new file mode 100644 index 00000000..7c0148f1 --- /dev/null +++ b/src/cython/include/Cubical_complex_interface.h @@ -0,0 +1,56 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_ +#define INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_ + +#include <gudhi/Bitmap_cubical_complex.h> +#include <gudhi/Bitmap_cubical_complex_base.h> +#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h> + +#include <iostream> +#include <vector> +#include <string> + +namespace Gudhi { + +namespace cubical_complex { + +template<typename CubicalComplexOptions = Bitmap_cubical_complex_base<double>> +class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOptions> { + public: + Cubical_complex_interface(const std::vector<unsigned>& dimensions, + const std::vector<double>& top_dimensional_cells) + : Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells) { + } + + Cubical_complex_interface(const std::string& perseus_file) + : Bitmap_cubical_complex<CubicalComplexOptions>(perseus_file.c_str()) { + } +}; + +} // namespace cubical_complex + +} // namespace Gudhi + +#endif // INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_ + diff --git a/src/cython/include/Euclidean_strong_witness_complex_interface.h b/src/cython/include/Euclidean_strong_witness_complex_interface.h new file mode 100644 index 00000000..b9dd8177 --- /dev/null +++ b/src/cython/include/Euclidean_strong_witness_complex_interface.h @@ -0,0 +1,93 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_ +#define INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Euclidean_strong_witness_complex.h> + +#include "Simplex_tree_interface.h" + +#include <CGAL/Epick_d.h> + +#include <vector> +#include <utility> // std::pair +#include <iostream> +#include <cstddef> + +namespace Gudhi { + +namespace witness_complex { + + +class Euclidean_strong_witness_complex_interface { + using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + using Point_d = Dynamic_kernel::Point_d; + + typedef typename Simplex_tree<>::Simplex_key Simplex_key; + + public: + Euclidean_strong_witness_complex_interface(const std::vector<std::vector<double>>& landmarks, + const std::vector<std::vector<double>>& witnesses) { + landmarks_.reserve(landmarks.size()); + for (auto& landmark : landmarks) + landmarks_.emplace_back(landmark.begin(), landmark.end()); + witness_complex_ = new Euclidean_strong_witness_complex<Dynamic_kernel>(landmarks_, witnesses); + } + + ~Euclidean_strong_witness_complex_interface() { + delete witness_complex_; + } + + void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square, + std::size_t limit_dimension) { + witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension); + simplex_tree->initialize_filtration(); + } + + void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square) { + witness_complex_->create_complex(*simplex_tree, max_alpha_square); + simplex_tree->initialize_filtration(); + } + + std::vector<double> get_point(unsigned vh) { + std::vector<double> vd; + if (vh < landmarks_.size()) { + Point_d ph = witness_complex_->get_point(vh); + for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++) + vd.push_back(*coord); + } + return vd; + } + + private: + std::vector<Point_d> landmarks_; + Euclidean_strong_witness_complex<Dynamic_kernel>* witness_complex_; +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif // INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_ + diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/cython/include/Euclidean_witness_complex_interface.h new file mode 100644 index 00000000..2a09b3b5 --- /dev/null +++ b/src/cython/include/Euclidean_witness_complex_interface.h @@ -0,0 +1,92 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_ +#define INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Euclidean_witness_complex.h> + +#include "Simplex_tree_interface.h" + +#include <CGAL/Epick_d.h> + +#include <vector> +#include <utility> // std::pair +#include <iostream> +#include <cstddef> + +namespace Gudhi { + +namespace witness_complex { + + +class Euclidean_witness_complex_interface { + using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + using Point_d = Dynamic_kernel::Point_d; + + typedef typename Simplex_tree<>::Simplex_key Simplex_key; + + public: + Euclidean_witness_complex_interface(const std::vector<std::vector<double>>& landmarks, + const std::vector<std::vector<double>>& witnesses) { + landmarks_.reserve(landmarks.size()); + for (auto& landmark : landmarks) + landmarks_.emplace_back(landmark.begin(), landmark.end()); + witness_complex_ = new Euclidean_witness_complex<Dynamic_kernel>(landmarks_, witnesses); + } + + ~Euclidean_witness_complex_interface() { + delete witness_complex_; + } + + void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square, std::size_t limit_dimension) { + witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension); + simplex_tree->initialize_filtration(); + } + + void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square) { + witness_complex_->create_complex(*simplex_tree, max_alpha_square); + simplex_tree->initialize_filtration(); + } + + std::vector<double> get_point(unsigned vh) { + std::vector<double> vd; + if (vh < landmarks_.size()) { + Point_d ph = witness_complex_->get_point(vh); + for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++) + vd.push_back(*coord); + } + return vd; + } + + private: + std::vector<Point_d> landmarks_; + Euclidean_witness_complex<Dynamic_kernel>* witness_complex_; +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif // INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_ + diff --git a/src/cython/include/Off_reader_interface.h b/src/cython/include/Off_reader_interface.h new file mode 100644 index 00000000..0ca55500 --- /dev/null +++ b/src/cython/include/Off_reader_interface.h @@ -0,0 +1,42 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_OFF_READER_INTERFACE_H_ +#define INCLUDE_OFF_READER_INTERFACE_H_ + +#include <gudhi/Points_off_io.h> + +#include <iostream> +#include <vector> +#include <string> + +namespace Gudhi { + +std::vector<std::vector<double>> read_points_from_OFF_file(const std::string& off_file) { + Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file); + return off_reader.get_point_cloud(); +} + +} // namespace Gudhi + +#endif // INCLUDE_OFF_READER_INTERFACE_H_ + diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h new file mode 100644 index 00000000..55028fd0 --- /dev/null +++ b/src/cython/include/Persistent_cohomology_interface.h @@ -0,0 +1,95 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_ +#define INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_ + +#include <gudhi/Persistent_cohomology.h> + +#include <vector> +#include <utility> // for std::pair +#include <algorithm> // for sort + +namespace Gudhi { + +template<class FilteredComplex> +class Persistent_cohomology_interface : public +persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp> { + private: + /* + * Compare two intervals by dimension, then by length. + */ + struct cmp_intervals_by_dim_then_length { + explicit cmp_intervals_by_dim_then_length(FilteredComplex * sc) + : sc_(sc) { } + + template<typename Persistent_interval> + bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) { + if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2))) + return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1)) + > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2))); + else + return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2))); + } + FilteredComplex* sc_; + }; + + public: + Persistent_cohomology_interface(FilteredComplex* stptr) + : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr), + stptr_(stptr) { } + + Persistent_cohomology_interface(FilteredComplex* stptr, bool persistence_dim_max) + : persistent_cohomology::Persistent_cohomology<FilteredComplex, + persistent_cohomology::Field_Zp>(*stptr, persistence_dim_max), + stptr_(stptr) { } + + std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, + double min_persistence) { + persistent_cohomology::Persistent_cohomology<FilteredComplex, + persistent_cohomology::Field_Zp>::init_coefficients(homology_coeff_field); + persistent_cohomology::Persistent_cohomology<FilteredComplex, + persistent_cohomology::Field_Zp>::compute_persistent_cohomology(min_persistence); + + // Custom sort and output persistence + cmp_intervals_by_dim_then_length cmp(stptr_); + auto persistent_pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex, + persistent_cohomology::Field_Zp>::get_persistent_pairs(); + std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp); + + std::vector<std::pair<int, std::pair<double, double>>> persistence; + for (auto pair : persistent_pairs) { + persistence.push_back(std::make_pair(stptr_->dimension(get<0>(pair)), + std::make_pair(stptr_->filtration(get<0>(pair)), + stptr_->filtration(get<1>(pair))))); + } + return persistence; + } + + private: + // A copy + FilteredComplex* stptr_; +}; + +} // namespace Gudhi + +#endif // INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_ diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h new file mode 100644 index 00000000..1879bd74 --- /dev/null +++ b/src/cython/include/Rips_complex_interface.h @@ -0,0 +1,86 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_RIPS_COMPLEX_INTERFACE_H_ +#define INCLUDE_RIPS_COMPLEX_INTERFACE_H_ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Rips_complex.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/distance_functions.h> +#include <gudhi/reader_utils.h> + +#include "Simplex_tree_interface.h" + +#include <iostream> +#include <vector> +#include <utility> // std::pair +#include <string> + +namespace Gudhi { + +namespace rips_complex { + +class Rips_complex_interface { + using Point_d = std::vector<double>; + using Distance_matrix = std::vector<std::vector<Simplex_tree_interface<>::Filtration_value>>; + + public: + Rips_complex_interface(const std::vector<std::vector<double>>& values, double threshold, bool euclidean) { + if (euclidean) { + // Rips construction where values is a vector of points + rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold, + Euclidean_distance()); + } else { + // Rips construction where values is a distance matrix + rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold); + } + } + + Rips_complex_interface(const std::string& file_name, double threshold, bool euclidean, bool from_file = true) { + if (euclidean) { + // Rips construction where file_name is an OFF file + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(), + threshold, Euclidean_distance()); + } else { + // Rips construction where values is a distance matrix + Distance_matrix distances = + read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name); + rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold); + } + } + + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) { + rips_complex_->create_complex(*simplex_tree, dim_max); + simplex_tree->initialize_filtration(); + } + + private: + Rips_complex<Simplex_tree_interface<>::Filtration_value>* rips_complex_; +}; + +} // namespace rips_complex + +} // namespace Gudhi + +#endif // INCLUDE_RIPS_COMPLEX_INTERFACE_H_ diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h new file mode 100644 index 00000000..4266b3ef --- /dev/null +++ b/src/cython/include/Simplex_tree_interface.h @@ -0,0 +1,149 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_SIMPLEX_TREE_INTERFACE_H_ +#define INCLUDE_SIMPLEX_TREE_INTERFACE_H_ + +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Points_off_io.h> + +#include "Persistent_cohomology_interface.h" + +#include <iostream> +#include <vector> +#include <utility> // std::pair + +namespace Gudhi { + +template<typename SimplexTreeOptions = Simplex_tree_options_full_featured> +class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { + public: + using Base = Simplex_tree<SimplexTreeOptions>; + using Filtration_value = typename Base::Filtration_value; + using Vertex_handle = typename Base::Vertex_handle; + using Simplex_handle = typename Base::Simplex_handle; + using Insertion_result = typename std::pair<Simplex_handle, bool>; + using Simplex = std::vector<Vertex_handle>; + using Complex = std::vector<std::pair<Simplex, Filtration_value>>; + + public: + bool find_simplex(const Simplex& vh) { + return (Base::find(vh) != Base::null_simplex()); + } + + bool insert_simplex(const Simplex& simplex, Filtration_value filtration = 0) { + Insertion_result result = Base::insert_simplex(simplex, filtration); + Base::initialize_filtration(); + return (result.second); + } + + bool insert_simplex_and_subfaces(const Simplex& simplex, Filtration_value filtration = 0) { + Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration); + Base::initialize_filtration(); + return (result.second); + } + + // Do not interface this function, only used in strong witness interface for complex creation + bool insert_simplex(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) { + Insertion_result result = Base::insert_simplex(complex, filtration); + Base::initialize_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<std::size_t>& complex, Filtration_value filtration = 0) { + Insertion_result result = Base::insert_simplex_and_subfaces(complex, filtration); + Base::initialize_filtration(); + return (result.second); + } + + Filtration_value simplex_filtration(const Simplex& simplex) { + return Base::filtration(Base::find(simplex)); + } + + void remove_maximal_simplex(const Simplex& simplex) { + Base::remove_maximal_simplex(Base::find(simplex)); + Base::initialize_filtration(); + } + + Complex get_filtered_tree() { + Complex filtered_tree; + for (auto f_simplex : Base::filtration_simplex_range()) { + Simplex simplex; + for (auto vertex : Base::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + filtered_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex))); + } + return filtered_tree; + } + + Complex get_skeleton_tree(int dimension) { + Complex skeleton_tree; + for (auto f_simplex : Base::skeleton_simplex_range(dimension)) { + Simplex simplex; + for (auto vertex : Base::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + skeleton_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex))); + } + return skeleton_tree; + } + + Complex get_star(const Simplex& simplex) { + Complex star; + for (auto f_simplex : Base::star_simplex_range(Base::find(simplex))) { + Simplex simplex_star; + for (auto vertex : Base::simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + simplex_star.insert(simplex_star.begin(), vertex); + } + std::cout << std::endl; + star.push_back(std::make_pair(simplex_star, Base::filtration(f_simplex))); + } + return star; + } + + Complex get_cofaces(const Simplex& simplex, int dimension) { + Complex cofaces; + for (auto f_simplex : Base::cofaces_simplex_range(Base::find(simplex), dimension)) { + Simplex simplex_coface; + for (auto vertex : Base::simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + simplex_coface.insert(simplex_coface.begin(), vertex); + } + std::cout << std::endl; + cofaces.push_back(std::make_pair(simplex_coface, Base::filtration(f_simplex))); + } + return cofaces; + } + + void create_persistence(Gudhi::Persistent_cohomology_interface<Base>* pcoh) { + pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this); + } +}; + +} // namespace Gudhi + +#endif // INCLUDE_SIMPLEX_TREE_INTERFACE_H_ diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h new file mode 100644 index 00000000..d05eaac5 --- /dev/null +++ b/src/cython/include/Strong_witness_complex_interface.h @@ -0,0 +1,73 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_ +#define INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Strong_witness_complex.h> + +#include "Simplex_tree_interface.h" + +#include <vector> +#include <utility> // std::pair +#include <iostream> +#include <cstddef> + +namespace Gudhi { + +namespace witness_complex { + +class Strong_witness_complex_interface { + using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>; + using Nearest_landmark_table = std::vector<Nearest_landmark_range>; + + public: + Strong_witness_complex_interface(const Nearest_landmark_table& nlt) { + witness_complex_ = new Strong_witness_complex<Nearest_landmark_table>(nlt); + } + + ~Strong_witness_complex_interface() { + delete witness_complex_; + } + + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, + std::size_t limit_dimension) { + witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension); + simplex_tree->initialize_filtration(); + } + + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, + double max_alpha_square) { + witness_complex_->create_complex(*simplex_tree, max_alpha_square); + simplex_tree->initialize_filtration(); + } + + private: + Strong_witness_complex<Nearest_landmark_table>* witness_complex_; +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif // INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_ diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h new file mode 100644 index 00000000..1c6032c0 --- /dev/null +++ b/src/cython/include/Subsampling_interface.h @@ -0,0 +1,119 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_SUBSAMPLING_INTERFACE_H_ +#define INCLUDE_SUBSAMPLING_INTERFACE_H_ + +#include <gudhi/choose_n_farthest_points.h> +#include <gudhi/pick_n_random_points.h> +#include <gudhi/sparsify_point_set.h> +#include <gudhi/Points_off_io.h> +#include <CGAL/Epick_d.h> + +#include <iostream> +#include <vector> +#include <string> + +namespace Gudhi { + +namespace subsampling { + +using Subsampling_dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; +using Subsampling_point_d = Subsampling_dynamic_kernel::Point_d; +using Subsampling_ft = Subsampling_dynamic_kernel::FT; + +// ------ choose_n_farthest_points ------ +std::vector<std::vector<double>> subsampling_n_farthest_points(const std::vector<std::vector<double>>& points, + unsigned nb_points) { + std::vector<std::vector<double>> landmarks; + Subsampling_dynamic_kernel k; + choose_n_farthest_points(k, points, nb_points, std::back_inserter(landmarks)); + + return landmarks; +} + +std::vector<std::vector<double>> subsampling_n_farthest_points(const std::vector<std::vector<double>>& points, + unsigned nb_points, unsigned starting_point) { + std::vector<std::vector<double>> landmarks; + Subsampling_dynamic_kernel k; + choose_n_farthest_points(k, points, nb_points, starting_point, std::back_inserter(landmarks)); + + return landmarks; +} + +std::vector<std::vector<double>> subsampling_n_farthest_points_from_file(const std::string& off_file, + unsigned nb_points) { + Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file); + std::vector<std::vector<double>> points = off_reader.get_point_cloud(); + return subsampling_n_farthest_points(points, nb_points); +} + +std::vector<std::vector<double>> subsampling_n_farthest_points_from_file(const std::string& off_file, + unsigned nb_points, unsigned starting_point) { + Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file); + std::vector<std::vector<double>> points = off_reader.get_point_cloud(); + return subsampling_n_farthest_points(points, nb_points, starting_point); +} + +// ------ pick_n_random_points ------ +std::vector<std::vector<double>> subsampling_n_random_points(const std::vector<std::vector<double>>& points, + unsigned nb_points) { + std::vector<std::vector<double>> landmarks; + pick_n_random_points(points, nb_points, std::back_inserter(landmarks)); + + return landmarks; +} + +std::vector<std::vector<double>> subsampling_n_random_points_from_file(const std::string& off_file, + unsigned nb_points) { + Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file); + std::vector<std::vector<double>> points = off_reader.get_point_cloud(); + return subsampling_n_random_points(points, nb_points); +} + +// ------ sparsify_point_set ------ +std::vector<std::vector<double>> subsampling_sparsify_points(const std::vector<std::vector<double>>& points, + double min_squared_dist) { + std::vector<Subsampling_point_d> input, output; + for (auto point : points) + input.push_back(Subsampling_point_d(point.size(), point.begin(), point.end())); + Subsampling_dynamic_kernel k; + sparsify_point_set(k, input, min_squared_dist, std::back_inserter(output)); + + std::vector<std::vector<double>> landmarks; + for (auto point : output) + landmarks.push_back(std::vector<double>(point.cartesian_begin(), point.cartesian_end())); + return landmarks; +} + +std::vector<std::vector<double>> subsampling_sparsify_points_from_file(const std::string& off_file, + double min_squared_dist) { + Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file); + std::vector<std::vector<double>> points = off_reader.get_point_cloud(); + return subsampling_sparsify_points(points, min_squared_dist); +} + +} // namespace subsampling + +} // namespace Gudhi + +#endif // INCLUDE_SUBSAMPLING_INTERFACE_H_ diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h new file mode 100644 index 00000000..5e9dc0e4 --- /dev/null +++ b/src/cython/include/Tangential_complex_interface.h @@ -0,0 +1,123 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_ +#define INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Tangential_complex.h> +#include <gudhi/Points_off_io.h> +#include <CGAL/Epick_d.h> + +#include "Simplex_tree_interface.h" + +#include <vector> +#include <utility> // std::pair +#include <iostream> +#include <string> + +namespace Gudhi { + +namespace tangential_complex { + +class Tangential_complex_interface { + using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + using Point_d = Dynamic_kernel::Point_d; + using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>; + + public: + Tangential_complex_interface(const std::vector<std::vector<double>>& points) { + Dynamic_kernel k; + unsigned intrisic_dim = 0; + if (points.size() > 0) + intrisic_dim = points[0].size() - 1; + + tangential_complex_ = new TC(points, intrisic_dim, k); + tangential_complex_->compute_tangential_complex(); + num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices(); + } + + Tangential_complex_interface(const std::string& off_file_name, bool from_file = true) { + Gudhi::Points_off_reader<Point_d> off_reader(off_file_name); + Dynamic_kernel k; + unsigned intrisic_dim = 0; + std::vector<Point_d> points = off_reader.get_point_cloud(); + if (points.size() > 0) + intrisic_dim = points[0].size() - 1; + + tangential_complex_ = new TC(points, intrisic_dim, k); + tangential_complex_->compute_tangential_complex(); + num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices(); + } + + ~Tangential_complex_interface() { + delete tangential_complex_; + } + + std::vector<double> get_point(unsigned vh) { + std::vector<double> vd; + if (vh < tangential_complex_->number_of_vertices()) { + Point_d ph = tangential_complex_->get_point(vh); + for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++) + vd.push_back(*coord); + } + return vd; + } + + unsigned number_of_vertices() { + return tangential_complex_->number_of_vertices(); + } + + unsigned number_of_simplices() { + return num_inconsistencies_.num_simplices; + } + + unsigned number_of_inconsistent_simplices() { + return num_inconsistencies_.num_inconsistent_simplices; + } + + unsigned number_of_inconsistent_stars() { + return num_inconsistencies_.num_inconsistent_stars; + } + + void fix_inconsistencies_using_perturbation(double max_perturb, double time_limit) { + tangential_complex_->fix_inconsistencies_using_perturbation(max_perturb, time_limit); + num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices(); + } + + void create_simplex_tree(Simplex_tree<>* simplex_tree) { + int max_dim = tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree); + // FIXME + simplex_tree->set_dimension(max_dim); + simplex_tree->initialize_filtration(); + } + + private: + TC* tangential_complex_; + TC::Num_inconsistencies num_inconsistencies_; +}; + +} // namespace tangential_complex + +} // namespace Gudhi + +#endif // INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_ diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h new file mode 100644 index 00000000..6501cc35 --- /dev/null +++ b/src/cython/include/Witness_complex_interface.h @@ -0,0 +1,74 @@ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef INCLUDE_WITNESS_COMPLEX_INTERFACE_H_ +#define INCLUDE_WITNESS_COMPLEX_INTERFACE_H_ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Witness_complex.h> + +#include "Simplex_tree_interface.h" + +#include <vector> +#include <utility> // std::pair +#include <iostream> +#include <cstddef> + +namespace Gudhi { + +namespace witness_complex { + +class Witness_complex_interface { + using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>; + using Nearest_landmark_table = std::vector<Nearest_landmark_range>; + + public: + Witness_complex_interface(const Nearest_landmark_table& nlt) { + witness_complex_ = new Witness_complex<Nearest_landmark_table>(nlt); + } + + ~Witness_complex_interface() { + delete witness_complex_; + } + + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, + std::size_t limit_dimension) { + witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension); + simplex_tree->initialize_filtration(); + } + + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, + double max_alpha_square) { + witness_complex_->create_complex(*simplex_tree, max_alpha_square); + simplex_tree->initialize_filtration(); + } + + private: + Witness_complex<Nearest_landmark_table>* witness_complex_; +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif // INCLUDE_WITNESS_COMPLEX_INTERFACE_H_ + diff --git a/src/cython/test/test_alpha_complex.py b/src/cython/test/test_alpha_complex.py new file mode 100755 index 00000000..2625d529 --- /dev/null +++ b/src/cython/test/test_alpha_complex.py @@ -0,0 +1,86 @@ +from gudhi import AlphaComplex, SimplexTree + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_empty_alpha(): + alpha_complex = AlphaComplex(points=[[0,0]]) + assert alpha_complex.__is_defined() == True + +def test_infinite_alpha(): + point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] + alpha_complex = AlphaComplex(points=point_list) + assert alpha_complex.__is_defined() == True + + simplex_tree = alpha_complex.create_simplex_tree() + assert simplex_tree.__is_persistence_defined() == False + + assert simplex_tree.num_simplices() == 11 + assert simplex_tree.num_vertices() == 4 + + assert simplex_tree.get_filtered_tree() == \ + [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0), + ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25), + ([2, 3], 0.25), ([1, 2], 0.5), ([0, 1, 2], 0.5), + ([1, 2, 3], 0.5)] + assert simplex_tree.get_star([0]) == \ + [([0], 0.0), ([0, 1], 0.25), ([0, 1, 2], 0.5), + ([0, 2], 0.25)] + assert simplex_tree.get_cofaces([0], 1) == \ + [([0, 1], 0.25), ([0, 2], 0.25)] + + assert point_list[0] == alpha_complex.get_point(0) + assert point_list[1] == alpha_complex.get_point(1) + assert point_list[2] == alpha_complex.get_point(2) + assert point_list[3] == alpha_complex.get_point(3) + assert alpha_complex.get_point(4) == [] + assert alpha_complex.get_point(125) == [] + +def test_filtered_alpha(): + point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] + filtered_alpha = AlphaComplex(points=point_list) + + simplex_tree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25) + + assert simplex_tree.num_simplices() == 8 + assert simplex_tree.num_vertices() == 4 + + assert point_list[0] == filtered_alpha.get_point(0) + assert point_list[1] == filtered_alpha.get_point(1) + assert point_list[2] == filtered_alpha.get_point(2) + assert point_list[3] == filtered_alpha.get_point(3) + assert filtered_alpha.get_point(4) == [] + assert filtered_alpha.get_point(125) == [] + + assert simplex_tree.get_filtered_tree() == \ + [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0), + ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25), + ([2, 3], 0.25)] + assert simplex_tree.get_star([0]) == \ + [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)] + assert simplex_tree.get_cofaces([0], 1) == \ + [([0, 1], 0.25), ([0, 2], 0.25)] diff --git a/src/cython/test/test_bottleneck_distance.py b/src/cython/test/test_bottleneck_distance.py new file mode 100755 index 00000000..3d982d34 --- /dev/null +++ b/src/cython/test/test_bottleneck_distance.py @@ -0,0 +1,35 @@ +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_basic_bottleneck(): + diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]] + diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]] + + assert(gudhi.bottleneck_distance(diag1, diag2, 0.1) == 0.8081763781405569) + assert(gudhi.bottleneck_distance(diag1, diag2) == 0.75) diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py new file mode 100755 index 00000000..c8df8089 --- /dev/null +++ b/src/cython/test/test_cubical_complex.py @@ -0,0 +1,86 @@ +from gudhi import CubicalComplex + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_empty_constructor(): + # Try to create an empty CubicalComplex + cub = CubicalComplex() + assert cub.__is_defined() == False + assert cub.__is_persistence_defined() == False + +def test_non_existing_perseus_file_constructor(): + # Try to open a non existing file + cub = CubicalComplex(perseus_file='pouetpouettralala.toubiloubabdou') + assert cub.__is_defined() == False + assert cub.__is_persistence_defined() == False + +def test_dimension_or_perseus_file_constructor(): + # Create test file + test_file = open('CubicalOneSphere.txt', 'w') + test_file.write('2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n') + test_file.close() + # CubicalComplex can be constructed from dimensions and + # top_dimensional_cells OR from a perseus file style name. + cub = CubicalComplex(dimensions=[3, 3], + top_dimensional_cells = [1,2,3,4,5,6,7,8,9], + perseus_file='CubicalOneSphere.txt') + assert cub.__is_defined() == False + assert cub.__is_persistence_defined() == False + + cub = CubicalComplex(top_dimensional_cells = [1,2,3,4,5,6,7,8,9], + perseus_file='CubicalOneSphere.txt') + assert cub.__is_defined() == False + assert cub.__is_persistence_defined() == False + + cub = CubicalComplex(dimensions=[3, 3], + perseus_file='CubicalOneSphere.txt') + assert cub.__is_defined() == False + assert cub.__is_persistence_defined() == False + +def test_dimension_constructor(): + cub = CubicalComplex(dimensions=[3, 3], + 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.__is_persistence_defined() == True + assert cub.betti_numbers() == [1, 0] + assert cub.persistent_betti_numbers(0, 1000) == [0, 0] + +def test_dimension_constructor(): + # Create test file + test_file = open('CubicalOneSphere.txt', 'w') + test_file.write('2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n') + test_file.close() + 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.__is_persistence_defined() == True + assert cub.betti_numbers() == [1, 0, 0] + assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0] diff --git a/src/cython/test/test_euclidean_witness_complex.py b/src/cython/test/test_euclidean_witness_complex.py new file mode 100755 index 00000000..0947cc09 --- /dev/null +++ b/src/cython/test/test_euclidean_witness_complex.py @@ -0,0 +1,71 @@ +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_empty_euclidean_witness_complex(): + euclidean_witness = gudhi.EuclideanWitnessComplex() + assert euclidean_witness.__is_defined() == False + +def test_witness_complex(): + point_cloud = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0], [9.0, 6.0], + [0.0, 14.0], [2.0, 19.0], [9.0, 17.0]] + landmarks = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0]] + euclidean_witness_complex = gudhi.EuclideanWitnessComplex(landmarks=landmarks, witnesses = point_cloud) + simplex_tree = euclidean_witness_complex.create_simplex_tree(max_alpha_square=4.1) + + assert landmarks[0] == euclidean_witness_complex.get_point(0) + assert landmarks[1] == euclidean_witness_complex.get_point(1) + assert landmarks[2] == euclidean_witness_complex.get_point(2) + + assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0), + ([0, 1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([1, 2], 0.0), + ([0, 1, 2], 0.0)] + +def test_empty_euclidean_strong_witness_complex(): + euclidean_strong_witness = gudhi.EuclideanStrongWitnessComplex() + assert euclidean_strong_witness.__is_defined() == False + +def test_strong_witness_complex(): + point_cloud = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0], [9.0, 6.0], + [0.0, 14.0], [2.0, 19.0], [9.0, 17.0]] + landmarks = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0]] + euclidean_strong_witness_complex = gudhi.EuclideanStrongWitnessComplex(landmarks=landmarks, witnesses = point_cloud) + simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(max_alpha_square=14.9) + + assert landmarks[0] == euclidean_strong_witness_complex.get_point(0) + assert landmarks[1] == euclidean_strong_witness_complex.get_point(1) + assert landmarks[2] == euclidean_strong_witness_complex.get_point(2) + + assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0), ([2], 0.0)] + + simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(max_alpha_square=100.0) + + assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0), + ([2], 0.0), ([1, 2], 15.0), ([0, 2], 34.0), ([0, 1], 37.0), + ([0, 1, 2], 37.0)] + diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py new file mode 100755 index 00000000..286a645b --- /dev/null +++ b/src/cython/test/test_rips_complex.py @@ -0,0 +1,111 @@ +from gudhi import RipsComplex +from math import sqrt + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_empty_rips(): + rips_complex = RipsComplex() + assert rips_complex.__is_defined() == True + +def test_rips_from_points(): + point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] + rips_complex = RipsComplex(points=point_list, max_edge_length=42) + + simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) + + assert simplex_tree.__is_defined() == True + assert simplex_tree.__is_persistence_defined() == False + + assert simplex_tree.num_simplices() == 10 + assert simplex_tree.num_vertices() == 4 + + assert simplex_tree.get_filtered_tree() == \ + [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0), + ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0), + ([2, 3], 1.0), ([1, 2], 1.4142135623730951), + ([0, 3], 1.4142135623730951)] + assert simplex_tree.get_star([0]) == \ + [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0), + ([0, 3], 1.4142135623730951)] + assert simplex_tree.get_cofaces([0], 1) == \ + [([0, 1], 1.0), ([0, 2], 1.0), + ([0, 3], 1.4142135623730951)] + +def test_filtered_rips_from_points(): + point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] + filtered_rips = RipsComplex(points=point_list, max_edge_length=1.0) + + simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1) + + assert simplex_tree.__is_defined() == True + assert simplex_tree.__is_persistence_defined() == False + + assert simplex_tree.num_simplices() == 8 + assert simplex_tree.num_vertices() == 4 + +def test_rips_from_distance_matrix(): + distance_matrix = [[0], + [1, 0], + [1, sqrt(2), 0], + [sqrt(2), 1, 1, 0]] + rips_complex = RipsComplex(distance_matrix=distance_matrix, max_edge_length=42) + + simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) + + assert simplex_tree.__is_defined() == True + assert simplex_tree.__is_persistence_defined() == False + + assert simplex_tree.num_simplices() == 10 + assert simplex_tree.num_vertices() == 4 + + assert simplex_tree.get_filtered_tree() == \ + [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0), + ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0), + ([2, 3], 1.0), ([1, 2], 1.4142135623730951), + ([0, 3], 1.4142135623730951)] + assert simplex_tree.get_star([0]) == \ + [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0), + ([0, 3], 1.4142135623730951)] + assert simplex_tree.get_cofaces([0], 1) == \ + [([0, 1], 1.0), ([0, 2], 1.0), + ([0, 3], 1.4142135623730951)] + +def test_filtered_rips_from_distance_matrix(): + distance_matrix = [[0], + [1, 0], + [1, sqrt(2), 0], + [sqrt(2), 1, 1, 0]] + filtered_rips = RipsComplex(distance_matrix=distance_matrix, max_edge_length=1.0) + + simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1) + + assert simplex_tree.__is_defined() == True + assert simplex_tree.__is_persistence_defined() == False + + assert simplex_tree.num_simplices() == 8 + assert simplex_tree.num_vertices() == 4 diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py new file mode 100755 index 00000000..af5b639a --- /dev/null +++ b/src/cython/test/test_simplex_tree.py @@ -0,0 +1,133 @@ +from gudhi import SimplexTree + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_insertion(): + st = SimplexTree() + assert st.__is_defined() == True + assert st.__is_persistence_defined() == False + + # insert test + assert st.insert_simplex([0, 1]) == True + assert st.insert_simplex_and_subfaces([0, 1, 2], filtration=4.0) == True + # FIXME: Remove this line + st.set_dimension(2) + assert st.num_simplices() == 7 + assert st.num_vertices() == 3 + + # find test + assert st.find([0, 1, 2]) == True + assert st.find([0, 1]) == True + assert st.find([0, 2]) == True + assert st.find([0]) == True + assert st.find([1]) == True + assert st.find([2]) == True + assert st.find([3]) == False + assert st.find([0, 3]) == False + assert st.find([1, 3]) == False + assert st.find([2, 3]) == False + + # filtration test + st.set_filtration(5.0) + st.initialize_filtration() + assert st.get_filtration() == 5.0 + assert st.filtration([0, 1, 2]) == 4.0 + assert st.filtration([0, 2]) == 4.0 + assert st.filtration([1, 2]) == 4.0 + assert st.filtration([2]) == 4.0 + assert st.filtration([0, 1]) == 0.0 + assert st.filtration([0]) == 0.0 + assert st.filtration([1]) == 4.0 + + # skeleton_tree test + assert st.get_skeleton_tree(2) == \ + [([0, 1, 2], 4.0), ([0, 1], 0.0), ([0, 2], 4.0), + ([0], 0.0), ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)] + assert st.get_skeleton_tree(1) == \ + [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0), + ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)] + assert st.get_skeleton_tree(0) == \ + [([0], 0.0), ([1], 4.0), ([2], 4.0)] + + # remove_maximal_simplex test + assert st.get_cofaces([0, 1, 2], 1) == [] + st.remove_maximal_simplex([0, 1, 2]) + assert st.get_skeleton_tree(2) == \ + [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0), + ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)] + assert st.find([0, 1, 2]) == False + assert st.find([0, 1]) == True + assert st.find([0, 2]) == True + assert st.find([0]) == True + assert st.find([1]) == True + assert st.find([2]) == True + + st.initialize_filtration() + assert st.persistence() == [(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] + +def test_expansion(): + st = SimplexTree() + assert st.__is_defined() == True + assert st.__is_persistence_defined() == False + + # insert test + assert st.insert_simplex_and_subfaces([3, 2], 0.1) == True + assert st.insert_simplex_and_subfaces([2, 0], 0.2) == True + assert st.insert_simplex_and_subfaces([1, 0], 0.3) == True + assert st.insert_simplex_and_subfaces([3, 1], 0.4) == True + assert st.insert_simplex_and_subfaces([2, 1], 0.5) == True + assert st.insert_simplex_and_subfaces([6, 5], 0.6) == True + assert st.insert_simplex_and_subfaces([4, 2], 0.7) == True + assert st.insert_simplex_and_subfaces([3, 0], 0.8) == True + assert st.insert_simplex_and_subfaces([6, 4], 0.9) == True + assert st.insert_simplex_and_subfaces([6, 3], 1.0) == True + + assert st.num_vertices() == 7 + assert st.num_simplices() == 17 + assert st.get_filtered_tree() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1), + ([0], 0.2), ([0, 2], 0.2), ([1], 0.3), ([0, 1], 0.3), ([1, 3], 0.4), + ([1, 2], 0.5), ([5], 0.6), ([6], 0.6), ([5, 6], 0.6), ([4], 0.7), + ([2, 4], 0.7), ([0, 3], 0.8), ([4, 6], 0.9), ([3, 6], 1.0)] + + st.expansion(3) + assert st.num_vertices() == 7 + assert st.num_simplices() == 22 + st.initialize_filtration() + + assert st.get_filtered_tree() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1), + ([0], 0.2), ([0, 2], 0.2), ([1], 0.3), ([0, 1], 0.3), ([1, 3], 0.4), + ([1, 2], 0.5), ([0, 1, 2], 0.5), ([1, 2, 3], 0.5), ([5], 0.6), ([6], 0.6), + ([5, 6], 0.6), ([4], 0.7), ([2, 4], 0.7), ([0, 3], 0.8), ([0, 1, 3], 0.8), + ([0, 2, 3], 0.8), ([0, 1, 2, 3], 0.8), ([4, 6], 0.9), ([3, 6], 1.0)] diff --git a/src/cython/test/test_subsampling.py b/src/cython/test/test_subsampling.py new file mode 100755 index 00000000..2caf4ddb --- /dev/null +++ b/src/cython/test/test_subsampling.py @@ -0,0 +1,133 @@ +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) 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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_write_off_file_for_tests(): + file = open("subsample.off", "w") + file.write("nOFF\n") + file.write("2 7 0 0\n") + file.write("1.0 1.0\n") + file.write("7.0 0.0\n") + file.write("4.0 6.0\n") + file.write("9.0 6.0\n") + file.write("0.0 14.0\n") + file.write("2.0 19.0\n") + file.write("9.0 17.0\n") + file.close() + +def test_simple_choose_n_farthest_points_with_a_starting_point(): + point_set = [[0,1], [0,0], [1,0], [1,1]] + i = 0 + for point in point_set: + # The iteration starts with the given starting point + sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 1, starting_point = i) + assert sub_set[0] == point_set[i] + i = i + 1 + + # The iteration finds then the farthest + sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 1) + assert sub_set[1] == point_set[3] + sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 3) + assert sub_set[1] == point_set[1] + sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 0) + assert sub_set[1] == point_set[2] + sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 2) + assert sub_set[1] == point_set[0] + + # Test the limits + assert gudhi.choose_n_farthest_points(points = [], nb_points = 0, starting_point = 0) == [] + assert gudhi.choose_n_farthest_points(points = [], nb_points = 1, starting_point = 0) == [] + assert gudhi.choose_n_farthest_points(points = [], nb_points = 0, starting_point = 1) == [] + assert gudhi.choose_n_farthest_points(points = [], nb_points = 1, starting_point = 1) == [] + + # From off file test + for i in range (0, 7): + assert len(gudhi.choose_n_farthest_points(off_file = 'subsample.off', nb_points = i, starting_point = i)) == i + +def test_simple_choose_n_farthest_points_randomed(): + point_set = [[0,1], [0,0], [1,0], [1,1]] + # Test the limits + assert gudhi.choose_n_farthest_points(points = [], nb_points = 0) == [] + assert gudhi.choose_n_farthest_points(points = [], nb_points = 1) == [] + assert gudhi.choose_n_farthest_points(points = point_set, nb_points = 0) == [] + + # Go furter than point set on purpose + for iter in range(1,10): + sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = iter) + for sub in sub_set: + found = False + for point in point_set: + if point == sub: + found = True + # Check each sub set point is existing in the point set + assert found == True + + # From off file test + for i in range (0, 7): + assert len(gudhi.choose_n_farthest_points(off_file = 'subsample.off', nb_points = i)) == i + +def test_simple_pick_n_random_points(): + point_set = [[0,1], [0,0], [1,0], [1,1]] + # Test the limits + assert gudhi.pick_n_random_points(points = [], nb_points = 0) == [] + assert gudhi.pick_n_random_points(points = [], nb_points = 1) == [] + assert gudhi.pick_n_random_points(points = point_set, nb_points = 0) == [] + + # Go furter than point set on purpose + for iter in range(1,10): + sub_set = gudhi.pick_n_random_points(points = point_set, nb_points = iter) + print(5) + for sub in sub_set: + found = False + for point in point_set: + if point == sub: + found = True + # Check each sub set point is existing in the point set + assert found == True + + # From off file test + for i in range (0, 7): + assert len(gudhi.pick_n_random_points(off_file = 'subsample.off', nb_points = i)) == i + +def test_simple_sparsify_points(): + point_set = [[0,1], [0,0], [1,0], [1,1]] + # Test the limits + # assert gudhi.sparsify_point_set(points = [], min_squared_dist = 0.0) == [] + # assert gudhi.sparsify_point_set(points = [], min_squared_dist = 10.0) == [] + assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 0.0) == point_set + assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 1.0) == point_set + assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 2.0) == [[0,1], [1,0]] + assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 2.01) == [[0,1]] + + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 0.0)) == 7 + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 30.0)) == 5 + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 40.0)) == 4 + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 90.0)) == 3 + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 100.0)) == 2 + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 325.0)) == 2 + assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 325.01)) == 1 diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py new file mode 100755 index 00000000..c191baa4 --- /dev/null +++ b/src/cython/test/test_tangential_complex.py @@ -0,0 +1,52 @@ +from gudhi import TangentialComplex, SimplexTree + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_tangential(): + point_list = [[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]] + tc = TangentialComplex(points=point_list) + assert tc.__is_defined() == True + assert tc.num_vertices() == 4 + + st = tc.create_simplex_tree() + assert st.__is_defined() == True + assert st.__is_persistence_defined() == False + + assert st.num_simplices() == 6 + assert st.num_vertices() == 4 + + assert st.get_filtered_tree() == \ + [([0], 0.0), ([1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([3], 0.0), ([1, 3], 0.0)] + assert st.get_cofaces([0], 1) == [([0, 2], 0.0)] + + assert point_list[0] == tc.get_point(0) + assert point_list[1] == tc.get_point(1) + assert point_list[2] == tc.get_point(2) + assert point_list[3] == tc.get_point(3) + assert tc.get_point(4) == [] + assert tc.get_point(125) == [] diff --git a/src/cython/test/test_witness_complex.py b/src/cython/test/test_witness_complex.py new file mode 100755 index 00000000..7d1fb6be --- /dev/null +++ b/src/cython/test/test_witness_complex.py @@ -0,0 +1,62 @@ +from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree + +"""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 <http://www.gnu.org/licenses/>. +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + + +def test_empty_witness_complex(): + witness = WitnessComplex() + assert witness.__is_defined() == False + +def test_witness_complex(): + nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]], + [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]], + [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]], + [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]], + [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]] + + witness_complex = WitnessComplex(nearest_landmark_table=nearest_landmark_table) + simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1) + assert simplex_tree.num_vertices() == 5 + assert simplex_tree.num_simplices() == 31 + simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1, limit_dimension=2) + assert simplex_tree.num_vertices() == 5 + assert simplex_tree.num_simplices() == 25 + +def test_strong_witness_complex(): + nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]], + [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]], + [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]], + [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]], + [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]] + + strong_witness_complex = StrongWitnessComplex(nearest_landmark_table=nearest_landmark_table) + simplex_tree = strong_witness_complex.create_simplex_tree(max_alpha_square=4.1) + assert simplex_tree.num_vertices() == 5 + assert simplex_tree.num_simplices() == 31 + simplex_tree = strong_witness_complex.create_simplex_tree(max_alpha_square=4.1, limit_dimension=2) + assert simplex_tree.num_vertices() == 5 + assert simplex_tree.num_simplices() == 25 diff --git a/src/debian/changelog b/src/debian/changelog deleted file mode 100644 index 32b3f6f9..00000000 --- a/src/debian/changelog +++ /dev/null @@ -1,5 +0,0 @@ -gudhi (1.3.0-1) unstable; urgency=low - - * Initial release. - - -- Marc Glisse <marc.glisse@inria.fr> Sat, 26 Mar 2016 10:51:01 +0100 diff --git a/src/debian/compat b/src/debian/compat deleted file mode 100644 index ec635144..00000000 --- a/src/debian/compat +++ /dev/null @@ -1 +0,0 @@ -9 diff --git a/src/debian/control b/src/debian/control deleted file mode 100644 index 838234a9..00000000 --- a/src/debian/control +++ /dev/null @@ -1,26 +0,0 @@ -Source: gudhi -Priority: optional -Maintainer: Marc Glisse <marc.glisse@normalesup.org> -Build-Depends: debhelper (>= 9), cmake, libboost-dev -Standards-Version: 3.9.6 -Section: libs -Homepage: http://gudhi.gforge.inria.fr/ -#Vcs-Git: git://anonscm.debian.org/collab-maint/gudhi.git -#Vcs-Browser: https://anonscm.debian.org/gitweb/?p=collab-maint/gudhi.git;a=summary - -Package: libgudhi-dev -Section: libdevel -Architecture: all -Depends: libboost-dev, ${misc:Depends} -Recommends: libcgal-dev -Description: Gudhi library for topological data analysis - The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic - open source C++ library for Computational Topology and Topological Data - Analysis (TDA). - . - The current release of the GUDHI library includes: - * Data structures to represent, construct and manipulate simplicial and - cubical complexes, including alpha-complex, witness complex, Rips complex. - * Algorithms to compute persistent homology and multi-field persistent - homology. - * Simplication of simplicial complexes by edge contraction. diff --git a/src/debian/copyright b/src/debian/copyright deleted file mode 100644 index 2e1f88cd..00000000 --- a/src/debian/copyright +++ /dev/null @@ -1,28 +0,0 @@ -Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: gudhi -Upstream-Contact: gudhi-users@lists.gforge.inria.fr -Source: <url://http://gudhi.gforge.inria.fr/> - -Files: * -Copyright: 2014-2016 Inria Sophia Antipolis-Méditerranée - 2014-2016 Inria Saclay - Ile de France - 2014-2016 Université Nice Sophia Antipolis -License: GPL-3.0+ - -License: GPL-3.0+ - 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 package 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 <https://www.gnu.org/licenses/>. - . - On Debian systems, the complete text of the GNU General - Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". - diff --git a/src/debian/docs b/src/debian/docs deleted file mode 100644 index 878a2ba1..00000000 --- a/src/debian/docs +++ /dev/null @@ -1,2 +0,0 @@ -Conventions.txt -README diff --git a/src/debian/rules b/src/debian/rules deleted file mode 100755 index c9b049af..00000000 --- a/src/debian/rules +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/make -f -# See debhelper(7) (uncomment to enable) -# output every command that modifies files on the build system. -#export DH_VERBOSE = 1 - -# see EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/* -DPKG_EXPORT_BUILDFLAGS = 1 -include /usr/share/dpkg/default.mk - -# see FEATURE AREAS in dpkg-buildflags(1) -#export DEB_BUILD_MAINT_OPTIONS = hardening=+all - -# see ENVIRONMENT in dpkg-buildflags(1) -# package maintainers to append CFLAGS -#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic -# package maintainers to append LDFLAGS -#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed - - -# main packaging script based on dh7 syntax -%: - dh $@ - -# dh_make generated override targets -# This is example for Cmake (See https://bugs.debian.org/641051 ) -#override_dh_auto_configure: -# dh_auto_configure -- \ -# -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) diff --git a/src/debian/source/format b/src/debian/source/format deleted file mode 100644 index 163aaf8d..00000000 --- a/src/debian/source/format +++ /dev/null @@ -1 +0,0 @@ -3.0 (quilt) |
