diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-07-06 15:38:44 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-07-06 15:38:44 +0000 |
commit | 4832d865981bb74c8afc7240e953adc8f54c52b0 (patch) | |
tree | bbbf138e27985a1c7b8a5f11d3fe5cba6c51d5e0 /src/cython/example | |
parent | a4b7d528893f992115711225c7d4396de55c6c58 (diff) |
Plot functions now returns a plot that can be modified before to be shown
Add confidence band in plot_persistence_diagram
Cythonization of read_lower_triangular_matrix_from_csv_file and read_persistence_intervals functions
Add Python tests of read functions
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2590 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 522ec31e9ad3a9a688875612d246114704b8c74e
Diffstat (limited to 'src/cython/example')
7 files changed, 25 insertions, 9 deletions
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 index adedc7d2..b4487be4 100755 --- 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 @@ -38,6 +38,7 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from ' '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("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -63,7 +64,8 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") 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 index 2371c36c..e3f362dc 100755 --- 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 @@ -40,6 +40,7 @@ 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("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -70,8 +71,8 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) - + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") 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 index 5748aa8a..c236d992 100755 --- 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 @@ -40,6 +40,7 @@ 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("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -70,8 +71,8 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) - + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py index bc3b16ec..ed87806b 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -44,4 +44,11 @@ gudhi.plot_persistence_barcode(persistence) print("#####################################################################") print("Show diagram persistence example") -gudhi.plot_persistence_diagram(persistence) +pplot = gudhi.plot_persistence_diagram(persistence) +pplot.show() + +print("#####################################################################") +print("Show diagram persistence example with a confidence band") + +pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2) +pplot.show() 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 index 984dbf1b..3baebd17 100755 --- 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 @@ -39,6 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' 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("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -61,4 +62,5 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py index 4e5cd2c8..9bfea41c 100755 --- a/src/cython/example/rips_persistence_diagram.py +++ b/src/cython/example/rips_persistence_diagram.py @@ -39,4 +39,5 @@ 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) +pplot = gudhi.plot_persistence_diagram(diag) +pplot.show() 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 index 4845eb47..6145e7f2 100755 --- 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 @@ -37,6 +37,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from ' '- Constructs a tangential complex with the ' 'points from the given OFF file') parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -59,7 +60,8 @@ with open(args.file, 'r') as f: print(st.betti_numbers()) if args.no_diagram == False: - gudhi.plot_persistence_diagram(diag) + pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot.show() else: print(args.file, "is not a valid OFF file") |