From 6bc1f27bbab03139718db674f98d748a7aeaced3 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 20 Nov 2019 14:12:01 +0100 Subject: Use matplotlib axes to be able to subplot persistence graphical tools --- ...omplex_diagram_persistence_from_off_file_example.py | 7 ++++--- ...omplex_diagram_persistence_from_off_file_example.py | 7 ++++--- ...omplex_diagram_persistence_from_off_file_example.py | 7 ++++--- src/python/example/gudhi_graphical_tools_example.py | 18 ++++++++++++++---- ...ex_barcode_persistence_from_perseus_file_example.py | 4 +++- ...persistence_from_correlation_matrix_file_example.py | 7 ++++--- ...am_persistence_from_distance_matrix_file_example.py | 7 ++++--- ...omplex_diagram_persistence_from_off_file_example.py | 7 ++++--- src/python/example/rips_persistence_diagram.py | 5 +++-- src/python/example/sparse_rips_persistence_diagram.py | 5 +++-- ...ial_complex_plain_homology_from_off_file_example.py | 7 ++++--- 11 files changed, 51 insertions(+), 30 deletions(-) (limited to 'src/python/example') 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 b8f283b3..4079a469 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 @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi 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. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -60,8 +61,8 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") 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 610ba44f..0eedd140 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 @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi 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. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -75,8 +76,8 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") 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 7587b732..1fe55737 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 @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi 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. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -74,8 +75,8 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/python/example/gudhi_graphical_tools_example.py b/src/python/example/gudhi_graphical_tools_example.py index 3b0ca54d..37ecbf53 100755 --- a/src/python/example/gudhi_graphical_tools_example.py +++ b/src/python/example/gudhi_graphical_tools_example.py @@ -1,5 +1,6 @@ #!/usr/bin/env python +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -29,15 +30,24 @@ persistence = [ (0, (0.0, 1.0)), ] gudhi.plot_persistence_barcode(persistence) +plot.show() print("#####################################################################") print("Show diagram persistence example") -pplot = gudhi.plot_persistence_diagram(persistence) -pplot.show() +gudhi.plot_persistence_diagram(persistence) +plot.show() print("#####################################################################") print("Show diagram persistence example with a confidence band") -pplot = gudhi.plot_persistence_diagram(persistence, band=0.2) -pplot.show() +gudhi.plot_persistence_diagram(persistence, band=0.2) +plot.show() + +print("#####################################################################") +print("Show barcode and diagram persistence side by side example") +fig, axes = plot.subplots(nrows=1, ncols=2) +gudhi.plot_persistence_barcode(persistence, axes = axes[0]) +gudhi.plot_persistence_diagram(persistence, axes = axes[1]) +fig.suptitle("barcode versus diagram") +plot.show() 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 9cb855cd..c692e66f 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 +1,8 @@ #!/usr/bin/env python -import gudhi 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. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -70,5 +71,6 @@ if is_file_perseus(args.file): print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: gudhi.plot_persistence_barcode(diag) + plot.show() else: print(args.file, "is not a valid perseus style file") 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 3571580b..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 @@ -1,8 +1,9 @@ #!/usr/bin/env python -import gudhi 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. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -83,5 +84,5 @@ invert_diag = [ ] if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band) - pplot.show() + 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 0b9a9ba9..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 @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi 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. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -59,5 +60,5 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + 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 2b335bba..b9074cf9 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 @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi 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. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -64,8 +65,8 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/python/example/rips_persistence_diagram.py b/src/python/example/rips_persistence_diagram.py index f5897d7b..2a90b4bc 100755 --- a/src/python/example/rips_persistence_diagram.py +++ b/src/python/example/rips_persistence_diagram.py @@ -1,5 +1,6 @@ #!/usr/bin/env python +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -26,5 +27,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1) diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0) print("diag=", diag) -pplot = gudhi.plot_persistence_diagram(diag) -pplot.show() +gudhi.plot_persistence_diagram(diag) +plot.show() diff --git a/src/python/example/sparse_rips_persistence_diagram.py b/src/python/example/sparse_rips_persistence_diagram.py index 671d5e34..410a6a86 100755 --- a/src/python/example/sparse_rips_persistence_diagram.py +++ b/src/python/example/sparse_rips_persistence_diagram.py @@ -1,5 +1,6 @@ #!/usr/bin/env python +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -28,5 +29,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=2) diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0) print("diag=", diag) -pplot = gudhi.plot_persistence_diagram(diag) -pplot.show() +gudhi.plot_persistence_diagram(diag) +plot.show() 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 456bc9eb..f0df2189 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 @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi 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. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -56,8 +57,8 @@ with open(args.file, "r") as f: print(st.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") -- cgit v1.2.3