diff options
9 files changed, 50 insertions, 42 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 1f101d87..c09996fe 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -345,27 +345,29 @@ 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) - # 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) + 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 - 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) + # 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() # Subsampling add_gudhi_py_test(test_subsampling) @@ -420,11 +422,13 @@ 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") - add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + 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_gudhi_py_test(test_alpha_complex) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) @@ -441,26 +445,30 @@ 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) - 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) + 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_gudhi_py_test(test_cubical_complex) # Rips - 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) + 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_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_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_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 1e0273b3..727af4fa 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 @@ -3,6 +3,7 @@ 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/ - @@ -64,7 +65,6 @@ 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 4e97cfe3..e1e572df 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 @@ -3,6 +3,7 @@ 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/ - @@ -81,7 +82,6 @@ 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 29076c74..58cb2bb5 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 @@ -3,6 +3,7 @@ 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/ - @@ -78,7 +79,6 @@ 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 ee3290c6..499171df 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 @@ -1,6 +1,7 @@ #!/usr/bin/env python import argparse +import matplotlib.pyplot as plot import errno import os import gudhi @@ -74,7 +75,6 @@ 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 ea2eb7e1..1acb187c 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 @@ -2,6 +2,7 @@ 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. @@ -83,6 +84,5 @@ 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 236d085d..79ccca96 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 @@ -1,6 +1,7 @@ #!/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. @@ -59,6 +60,5 @@ 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 e80233a9..6f992508 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 @@ -3,6 +3,7 @@ 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/ - @@ -69,7 +70,6 @@ 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 a4b4e9f5..85bade4a 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 @@ -3,6 +3,7 @@ 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/ - @@ -61,7 +62,6 @@ 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: |