From d357b3bf12430d5d1ccd03fed58966155bd8826c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 27 Feb 2017 16:17:08 +0000 Subject: Add TBB compilation support and documentation Add Matplotlib results in GUDHI persistence graphical tools git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2112 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e9fe1111d3a7d82c004a390cee77197221f117ec --- src/cython/CMakeLists.txt | 54 +++++++++++++--------- src/cython/doc/installation.rst | 19 ++++++++ .../doc/persistence_graphical_tools_user.rst | 25 +++++++++- 3 files changed, 75 insertions(+), 23 deletions(-) (limited to 'src') diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 449a980c..9e107500 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -40,12 +40,30 @@ if(PYTHON_PATH AND CYTHON_PATH) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") endif (EIGEN3_FOUND) - # Copy recursively include, cython, example and test repositories before packages finding - # Some tests files are removed in case some packages are not 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") + # 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") + # 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 @@ -54,6 +72,9 @@ if(PYTHON_PATH AND CYTHON_PATH) else (NOT CGAL_VERSION VERSION_LESS 4.8.1) # Remove alpha complex 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") endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) if (NOT CGAL_VERSION VERSION_LESS 4.8.0) # If CGAL_VERSION >= 4.8.0, include tangential complex @@ -63,6 +84,12 @@ if(PYTHON_PATH AND CYTHON_PATH) # 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 4.8.0) if (NOT CGAL_VERSION VERSION_LESS 4.7.0) # If CGAL_VERSION >= 4.7.0, include alpha @@ -70,6 +97,9 @@ if(PYTHON_PATH AND CYTHON_PATH) 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(CGAL_FOUND) @@ -139,28 +169,10 @@ if(PYTHON_PATH AND CYTHON_PATH) # Documentation generation is available through sphinx find_program( SPHINX_PATH sphinx-build ) if(SPHINX_PATH) - file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) - # Developper version - file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png") - file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") - # User version - file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png") - 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 (UNIX) add_custom_target(sphinx WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc - COMMAND make html && make doctest) + COMMAND make html doctest) else (UNIX) add_custom_target(sphinx WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index 0a715b34..c47802b9 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -135,3 +135,22 @@ The following examples require the `NumPy `_: * :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>` + +Threading Building Blocks +========================= + +`Intel® TBB `_ lets you easily write +parallel C++ programs that take full advantage of multicore performance, that +are portable and composable, and that have 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/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 43c695bf..1a5195c5 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -17,6 +17,11 @@ This function is useful to show the color palette values of dimension: import gudhi gudhi.show_palette_values(alpha=1.0) +.. plot:: + + import gudhi + gudhi.show_palette_values(alpha=1.0) + Show persistence as a barcode ----------------------------- @@ -30,6 +35,13 @@ This function can display the persistence result as a barcode: diag = periodic_cc.persistence() gudhi.barcode_persistence(diag) +.. plot:: + + import gudhi + + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + diag = periodic_cc.persistence() + gudhi.barcode_persistence(diag) Show persistence as a diagram ----------------------------- @@ -40,7 +52,16 @@ This function can display the persistence result as a diagram: import gudhi - alpha_complex = gudhi.AlphaComplex(off_file='tore3D_300.off') - simplex_tree = alpha_complex.create_simplex_tree() + 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.diagram_persistence(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.diagram_persistence(diag) -- cgit v1.2.3