diff options
author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2020-11-04 08:26:01 +0100 |
---|---|---|
committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2020-11-04 08:26:01 +0100 |
commit | daa3b08931e830212bc09130f7040d98d257b08f (patch) | |
tree | a4ad2e1f2a186a78aae05d8ca37c2da2bce1b75e | |
parent | a07430764c57c195c9260fc1b301ba0aeb77dcc7 (diff) | |
parent | 56dc7eb47cce596ee345dd7c6605dbee2f412f5e (diff) |
Merge branch 'master' into weighted_alpha_complex_dD
21 files changed, 59 insertions, 107 deletions
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index dc659f2d..0ff290ef 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -6,5 +6,3 @@ if (TBB_FOUND) endif() add_test(NAME Bitmap_cubical_complex_example_random COMMAND $<TARGET_FILE:Random_bitmap_cubical_complex> "2" "100" "100") - -install(TARGETS Random_bitmap_cubical_complex DESTINATION bin) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index cc230531..79ec42c1 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -50,6 +50,14 @@ include_directories(include) # Include module CMake subdirectories # GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake +if (WITH_GUDHI_PYTHON) + # specific for cython module + add_subdirectory(${GUDHI_PYTHON_PATH}) +else() + message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") +endif() + foreach(GUDHI_MODULE ${GUDHI_MODULES}) foreach(GUDHI_SUB_DIRECTORY ${GUDHI_SUB_DIRECTORIES}) if(EXISTS ${CMAKE_SOURCE_DIR}/${GUDHI_SUB_DIRECTORY}/${GUDHI_MODULE}/CMakeLists.txt) @@ -60,14 +68,6 @@ endforeach() add_subdirectory(GudhUI) -if (WITH_GUDHI_PYTHON) - # specific for cython module - add_subdirectory(${GUDHI_PYTHON_PATH}) -else() - message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") - set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") -endif() - message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"") diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 1667472f..4b0f4677 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -22,7 +22,4 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") - install(TARGETS CoordGIC DESTINATION bin) - install(TARGETS FuncGIC DESTINATION bin) - endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index a7c6ef39..997f85dc 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -3,30 +3,24 @@ project(Persistence_representations_example) add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) add_test(NAME Persistence_representations_example_landscape_on_grid COMMAND $<TARGET_FILE:Persistence_representations_example_landscape_on_grid>) -install(TARGETS Persistence_representations_example_landscape_on_grid DESTINATION bin) add_executable ( Persistence_representations_example_landscape persistence_landscape.cpp ) add_test(NAME Persistence_representations_example_landscape COMMAND $<TARGET_FILE:Persistence_representations_example_landscape>) -install(TARGETS Persistence_representations_example_landscape DESTINATION bin) add_executable ( Persistence_representations_example_intervals persistence_intervals.cpp ) add_test(NAME Persistence_representations_example_intervals COMMAND $<TARGET_FILE:Persistence_representations_example_intervals> "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers") -install(TARGETS Persistence_representations_example_intervals DESTINATION bin) add_executable ( Persistence_representations_example_vectors persistence_vectors.cpp ) add_test(NAME Persistence_representations_example_vectors COMMAND $<TARGET_FILE:Persistence_representations_example_vectors>) -install(TARGETS Persistence_representations_example_vectors DESTINATION bin) add_executable ( Persistence_representations_example_heat_maps persistence_heat_maps.cpp ) add_test(NAME Persistence_representations_example_heat_maps COMMAND $<TARGET_FILE:Persistence_representations_example_heat_maps>) -install(TARGETS Persistence_representations_example_heat_maps DESTINATION bin) add_executable ( Sliced_Wasserstein sliced_wasserstein.cpp ) add_test(NAME Sliced_Wasserstein COMMAND $<TARGET_FILE:Sliced_Wasserstein>) -install(TARGETS Sliced_Wasserstein DESTINATION bin) diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index d6a92ed6..c68c6524 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -5,7 +5,6 @@ if (TBB_FOUND) target_link_libraries(plain_homology ${TBB_LIBRARIES}) endif() add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $<TARGET_FILE:plain_homology>) -install(TARGETS plain_homology DESTINATION bin) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) if (TBB_FOUND) @@ -13,7 +12,6 @@ if (TBB_FOUND) endif() add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<TARGET_FILE:persistence_from_simple_simplex_tree> "1" "0") -install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin) if(TARGET Boost::program_options) add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) @@ -23,7 +21,6 @@ if(TARGET Boost::program_options) endif() add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") - install(TARGETS rips_persistence_step_by_step DESTINATION bin) endif() if(TARGET Boost::program_options) @@ -34,7 +31,6 @@ if(TARGET Boost::program_options) endif() add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix> "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") - install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin) endif() if(TARGET Boost::program_options) @@ -47,7 +43,6 @@ if(TARGET Boost::program_options) "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0") add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file> "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") - install(TARGETS persistence_from_file DESTINATION bin) endif() if(GMP_FOUND) @@ -61,7 +56,6 @@ if(GMP_FOUND) endif(TBB_FOUND) add_test(NAME Persistent_cohomology_example_multifield_2_71 COMMAND $<TARGET_FILE:rips_multifield_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "2" "-q" "71") - install(TARGETS rips_multifield_persistence DESTINATION bin) endif() endif(GMPXX_FOUND) endif(GMP_FOUND) @@ -73,5 +67,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $<TARGET_FILE:custom_persistence_sort>) - install(TARGETS custom_persistence_sort DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index 244a93ec..206f4c11 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -72,8 +72,3 @@ if (DIFF_PATH) endif() -install(TARGETS Rips_complex_example_from_off DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_from_points DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_from_distance_matrix DESTINATION bin) -install(TARGETS Rips_complex_example_from_csv_distance_matrix DESTINATION bin) -install(TARGETS Rips_complex_example_one_skeleton_rips_from_correlation_matrix DESTINATION bin) diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt index 0e5d2f11..456612df 100644 --- a/src/Skeleton_blocker/example/CMakeLists.txt +++ b/src/Skeleton_blocker/example/CMakeLists.txt @@ -7,7 +7,3 @@ add_executable(Skeleton_blocker_example_link Skeleton_blocker_link.cpp) add_test(NAME Skeleton_blocker_example_from_simplices COMMAND $<TARGET_FILE:Skeleton_blocker_example_from_simplices>) add_test(NAME Skeleton_blocker_example_iteration COMMAND $<TARGET_FILE:Skeleton_blocker_example_iteration>) add_test(NAME Skeleton_blocker_example_link COMMAND $<TARGET_FILE:Skeleton_blocker_example_link>) - -install(TARGETS Skeleton_blocker_example_from_simplices DESTINATION bin) -install(TARGETS Skeleton_blocker_example_iteration DESTINATION bin) -install(TARGETS Skeleton_blocker_example_link DESTINATION bin) diff --git a/src/Spatial_searching/example/CMakeLists.txt b/src/Spatial_searching/example/CMakeLists.txt index eeb3e85f..308afa00 100644 --- a/src/Spatial_searching/example/CMakeLists.txt +++ b/src/Spatial_searching/example/CMakeLists.txt @@ -5,5 +5,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Spatial_searching_example_spatial_searching ${CGAL_LIBRARY}) add_test(NAME Spatial_searching_example_spatial_searching COMMAND $<TARGET_FILE:Spatial_searching_example_spatial_searching>) - install(TARGETS Spatial_searching_example_spatial_searching DESTINATION bin) endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index 28aab103..dfac055c 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -14,9 +14,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Subsampling_example_sparsify_point_set COMMAND $<TARGET_FILE:Subsampling_example_sparsify_point_set>) - install(TARGETS Subsampling_example_pick_n_random_points DESTINATION bin) - install(TARGETS Subsampling_example_choose_n_farthest_points DESTINATION bin) - install(TARGETS Subsampling_example_custom_kernel DESTINATION bin) - install(TARGETS Subsampling_example_sparsify_point_set DESTINATION bin) - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index cb1486a4..b66b5f39 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -15,6 +15,4 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Tangential_complex_example_with_perturb COMMAND $<TARGET_FILE:Tangential_complex_example_with_perturb>) - install(TARGETS Tangential_complex_example_basic DESTINATION bin) - install(TARGETS Tangential_complex_example_with_perturb DESTINATION bin) endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 2659798e..5e9736ed 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -7,8 +7,6 @@ endif() add_test(NAME Witness_complex_example_nearest_landmark_table COMMAND $<TARGET_FILE:Witness_complex_example_nearest_landmark_table>) -install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) - # CGAL and Eigen3 are required for Euclidean version of Witness if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) @@ -33,10 +31,5 @@ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Witness_complex_example_strong_off_test_torus COMMAND $<TARGET_FILE:Witness_complex_example_strong_off> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") - - install(TARGETS Witness_complex_example_off DESTINATION bin) - install(TARGETS Witness_complex_example_sphere DESTINATION bin) - install(TARGETS Witness_complex_example_strong_off DESTINATION bin) - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index c09996fe..56b6876c 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -345,29 +345,27 @@ if(PYTHONINTERP_FOUND) COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - # Tangential - add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" - --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - - add_gudhi_py_test(test_tangential_complex) - - # Witness complex AND Subsampling - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - endif() + # Tangential + add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + + add_gudhi_py_test(test_tangential_complex) + + # Witness complex + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) # Subsampling add_gudhi_py_test(test_subsampling) @@ -422,13 +420,11 @@ if(PYTHONINTERP_FOUND) WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) - endif() + add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) add_gudhi_py_test(test_alpha_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) @@ -445,30 +441,26 @@ if(PYTHONINTERP_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - if(NUMPY_FOUND) - add_test(NAME random_cubical_complex_persistence_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" - 10 10 10) - endif() + add_test(NAME random_cubical_complex_persistence_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" + 10 10 10) add_gudhi_py_test(test_cubical_complex) # Rips - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) + add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) - endif() + add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index 727af4fa..1e0273b3 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -65,6 +64,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index e1e572df..4e97cfe3 100755 --- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -82,6 +81,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 58cb2bb5..29076c74 100755 --- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -79,6 +78,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 499171df..ee3290c6 100755 --- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import errno import os import gudhi @@ -75,6 +74,7 @@ if is_file_perseus(args.file): print("betti_numbers()=") print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_barcode(diag) plot.show() else: diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 1acb187c..ea2eb7e1 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -2,7 +2,6 @@ import sys import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -84,5 +83,6 @@ invert_diag = [ ] if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(invert_diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 79ccca96..236d085d 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -60,5 +59,6 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index 6f992508..e80233a9 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -70,6 +69,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index 85bade4a..a4b4e9f5 100755 --- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -62,6 +61,7 @@ with open(args.file, "r") as f: print(st.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index c671da56..813dc5c2 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -287,6 +287,8 @@ cdef class SimplexTree: def get_boundaries(self, simplex): """This function returns a generator with the boundaries of a given N-simplex. + If you do not need the filtration values, the boundary can also be obtained as + :code:`itertools.combinations(simplex,len(simplex)-1)`. :param simplex: The N-simplex, represented by a list of vertex. :type simplex: list of int. |