From af46c40bec8ae03cdf5a1e5a37ede198f910e3ea Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 14 Mar 2017 22:08:43 +0000 Subject: Add Windows and CGAL_HEADER_ONLY cythonization support Add OFF reader interfaces (required by Euclidean witness complex) Add Euclidean_witness_complex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2186 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4d780f05c3409bea47a81e4377dbaf509b9e718c --- ...ex_diagram_persistence_from_off_file_example.py | 78 ++++++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100755 src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py (limited to 'src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py') 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 new file mode 100755 index 00000000..7f04a98e --- /dev/null +++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,78 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""This file is part of the Gudhi Library. The Gudhi library + (Geometric Understanding in Higher Dimensions) is a generic C++ + library for computational topology. + + Author(s): Vincent Rouvreau + + Copyright (C) 2016 INRIA + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from ' + 'points read in a OFF file.', + epilog='Example: ' + 'example/witness_complex_diagram_persistence_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' + '- Constructs a alpha complex with the ' + 'points from the given OFF file.') +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +with open(args.file, 'r') as f: + first_line = f.readline() + if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + print("#####################################################################") + print("EuclideanWitnessComplex creation from points read in a OFF file") + + witnesses = gudhi.read_off(off_file=args.file) + landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks) + + message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \ + " - Number of landmarks=" + repr(args.number_of_landmarks) + print(message) + + witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses, landmarks=landmarks) + simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square, + limit_dimension=args.limit_dimension) + + message = "Number of simplices=" + repr(simplex_tree.num_simplices()) + print(message) + + diag = simplex_tree.persistence() + + print("betti_numbers()=") + print(simplex_tree.betti_numbers()) + + if args.no_diagram == False: + gudhi.diagram_persistence(diag) + + else: + print(args.file, "is not a valid OFF file") + + f.close() -- cgit v1.2.3 From 30374ed5154610dc63198742220153aa9387139c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 20 Mar 2017 15:48:04 +0000 Subject: Rename barcode_persistence and diagram_persistence functions git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2204 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f91e283fa6b6b02198ae28a44f41bd761c1c1f48 --- src/cython/cython/persistence_graphical_tools.py | 4 ++-- src/cython/doc/persistence_graphical_tools_ref.rst | 4 ++-- src/cython/doc/persistence_graphical_tools_user.rst | 8 ++++---- src/cython/doc/pyplots/barcode_persistence.py | 2 +- src/cython/doc/pyplots/diagram_persistence.py | 2 +- .../alpha_complex_diagram_persistence_from_off_file_example.py | 2 +- src/cython/example/alpha_rips_persistence_bottleneck_distance.py | 2 -- ...g_witness_complex_diagram_persistence_from_off_file_example.py | 4 ++-- ...n_witness_complex_diagram_persistence_from_off_file_example.py | 4 ++-- src/cython/example/gudhi_graphical_tools_example.py | 4 ++-- ...bical_complex_barcode_persistence_from_perseus_file_example.py | 2 +- ...mplex_diagram_persistence_from_distance_matrix_file_example.py | 2 +- .../rips_complex_diagram_persistence_from_off_file_example.py | 2 +- src/cython/example/rips_persistence_diagram.py | 2 +- .../tangential_complex_plain_homology_from_off_file_example.py | 2 +- 15 files changed, 22 insertions(+), 24 deletions(-) (limited to 'src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 2a3d9f63..d7287a66 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -73,7 +73,7 @@ def show_palette_values(alpha=0.6): plt.show() -def barcode_persistence(persistence, alpha=0.6): +def plot_barcode_persistence(persistence, alpha=0.6): """This function plots the persistence bar code. :param persistence: The persistence to plot. @@ -108,7 +108,7 @@ def barcode_persistence(persistence, alpha=0.6): plt.axis([axis_start, infinity, 0, ind]) plt.show() -def diagram_persistence(persistence, alpha=0.6): +def plot_diagram_persistence(persistence, alpha=0.6): """This function plots the persistence diagram. :param persistence: The persistence to plot. diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst index a12021c4..3d7e4fc7 100644 --- a/src/cython/doc/persistence_graphical_tools_ref.rst +++ b/src/cython/doc/persistence_graphical_tools_ref.rst @@ -4,5 +4,5 @@ Persistence graphical tools reference manual .. autofunction:: gudhi.__min_birth_max_death .. autofunction:: gudhi.show_palette_values -.. autofunction:: gudhi.barcode_persistence -.. autofunction:: gudhi.diagram_persistence +.. autofunction:: gudhi.plot_barcode_persistence +.. autofunction:: gudhi.plot_diagram_persistence diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 1a5195c5..2644aa11 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -33,7 +33,7 @@ This function can display the persistence result as a barcode: periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') diag = periodic_cc.persistence() - gudhi.barcode_persistence(diag) + gudhi.plot_barcode_persistence(diag) .. plot:: @@ -41,7 +41,7 @@ This function can display the persistence result as a barcode: periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') diag = periodic_cc.persistence() - gudhi.barcode_persistence(diag) + gudhi.plot_barcode_persistence(diag) Show persistence as a diagram ----------------------------- @@ -55,7 +55,7 @@ This function can display the persistence result as a diagram: 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) + gudhi.plot_diagram_persistence(diag) .. plot:: @@ -64,4 +64,4 @@ This function can display the persistence result as a diagram: 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) + gudhi.plot_diagram_persistence(diag) diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py index 95bbd343..9fcb33d0 100755 --- a/src/cython/doc/pyplots/barcode_persistence.py +++ b/src/cython/doc/pyplots/barcode_persistence.py @@ -2,4 +2,4 @@ import gudhi periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt') diag = periodic_cc.persistence() -gudhi.barcode_persistence(diag) +gudhi.plot_barcode_persistence(diag) diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py index b006b0bf..fbb6e60b 100755 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -2,4 +2,4 @@ import gudhi alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off') diag = alpha_complex.persistence() -gudhi.diagram_persistence(diag) +gudhi.plot_diagram_persistence(diag) 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 ae03aa67..9714b382 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 @@ -63,7 +63,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.diagram_persistence(diag) + gudhi.plot_diagram_persistence(diag) else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py index 04a59b44..cd64704b 100755 --- a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py @@ -42,8 +42,6 @@ parser.add_argument("-t", "--threshold", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) args = parser.parse_args() -print(repr(float('inf'))) -print(repr(math.sqrt(float('inf')))) with open(args.file, 'r') as f: first_line = f.readline() if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): 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 6c3e3a8a..3addf708 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 @@ -34,7 +34,7 @@ parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex crea epilog='Example: ' 'example/witness_complex_diagram_persistence_from_off_file_example.py ' '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' - '- Constructs a alpha complex with the ' + '- Constructs a strong witness complex with the ' 'points from the given OFF file.') parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, required=True) @@ -70,7 +70,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.diagram_persistence(diag) + gudhi.plot_diagram_persistence(diag) 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 7f04a98e..1e7d788a 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 @@ -34,7 +34,7 @@ parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation f epilog='Example: ' 'example/witness_complex_diagram_persistence_from_off_file_example.py ' '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' - '- Constructs a alpha complex with the ' + '- Constructs a weak witness complex with the ' 'points from the given OFF file.') parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, required=True) @@ -70,7 +70,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.diagram_persistence(diag) + gudhi.plot_diagram_persistence(diag) 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 40558bee..f1aa5d73 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -39,9 +39,9 @@ print("Show barcode persistence example") persistence = [(2, (1.0, float('inf'))), (1, (1.4142135623730951, float('inf'))), (1, (1.4142135623730951, float('inf'))), (0, (0.0, float('inf'))), (0, (0.0, 1.0)), (0, (0.0, 1.0)), (0, (0.0, 1.0))] -gudhi.barcode_persistence(persistence) +gudhi.plot_barcode_persistence(persistence) print("#####################################################################") print("Show diagram persistence example") -gudhi.diagram_persistence(persistence) +gudhi.plot_diagram_persistence(persistence) diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index a9545ee9..128706b2 100755 --- a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -71,6 +71,6 @@ if is_file_perseus(args.file): print("betti_numbers()=") print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: - gudhi.barcode_persistence(diag) + gudhi.plot_barcode_persistence(diag) else: print(args.file, "is not a valid perseus style file") 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 2b726f90..5f1416be 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 @@ -64,7 +64,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.diagram_persistence(diag) + gudhi.plot_diagram_persistence(diag) else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index eb1c4ed5..4f888e77 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -64,7 +64,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.diagram_persistence(diag) + gudhi.plot_diagram_persistence(diag) else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py index e485b2f5..3d51f379 100755 --- a/src/cython/example/rips_persistence_diagram.py +++ b/src/cython/example/rips_persistence_diagram.py @@ -39,4 +39,4 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1) diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0) print("diag=", diag) -gudhi.diagram_persistence(diag) +gudhi.plot_diagram_persistence(diag) 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 be4c40be..a3fc9911 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 @@ -59,7 +59,7 @@ with open(args.file, 'r') as f: print(st.betti_numbers()) if args.no_diagram == False: - gudhi.diagram_persistence(diag) + gudhi.plot_diagram_persistence(diag) else: print(args.file, "is not a valid OFF file") -- cgit v1.2.3 From 0724c2bcab0fa444ecf8178c27f59ca788a0aa03 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 22 Mar 2017 21:19:15 +0000 Subject: Rename plot_persistence_diagram and barcode git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2220 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 66a06ffdc62d5284119df80c3f104a48568cd241 --- src/cython/cython/persistence_graphical_tools.py | 4 ++-- src/cython/doc/persistence_graphical_tools_ref.rst | 4 ++-- src/cython/doc/persistence_graphical_tools_user.rst | 8 ++++---- src/cython/doc/pyplots/barcode_persistence.py | 2 +- src/cython/doc/pyplots/diagram_persistence.py | 2 +- .../alpha_complex_diagram_persistence_from_off_file_example.py | 2 +- ...g_witness_complex_diagram_persistence_from_off_file_example.py | 2 +- ...n_witness_complex_diagram_persistence_from_off_file_example.py | 2 +- src/cython/example/gudhi_graphical_tools_example.py | 4 ++-- ...bical_complex_barcode_persistence_from_perseus_file_example.py | 2 +- ...mplex_diagram_persistence_from_distance_matrix_file_example.py | 2 +- .../rips_complex_diagram_persistence_from_off_file_example.py | 2 +- src/cython/example/rips_persistence_diagram.py | 2 +- .../tangential_complex_plain_homology_from_off_file_example.py | 2 +- 14 files changed, 20 insertions(+), 20 deletions(-) (limited to 'src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index d7287a66..a984633e 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -73,7 +73,7 @@ def show_palette_values(alpha=0.6): plt.show() -def plot_barcode_persistence(persistence, alpha=0.6): +def plot_persistence_barcode(persistence, alpha=0.6): """This function plots the persistence bar code. :param persistence: The persistence to plot. @@ -108,7 +108,7 @@ def plot_barcode_persistence(persistence, alpha=0.6): plt.axis([axis_start, infinity, 0, ind]) plt.show() -def plot_diagram_persistence(persistence, alpha=0.6): +def plot_persistence_diagram(persistence, alpha=0.6): """This function plots the persistence diagram. :param persistence: The persistence to plot. diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst index 3d7e4fc7..27c2f68a 100644 --- a/src/cython/doc/persistence_graphical_tools_ref.rst +++ b/src/cython/doc/persistence_graphical_tools_ref.rst @@ -4,5 +4,5 @@ Persistence graphical tools reference manual .. autofunction:: gudhi.__min_birth_max_death .. autofunction:: gudhi.show_palette_values -.. autofunction:: gudhi.plot_barcode_persistence -.. autofunction:: gudhi.plot_diagram_persistence +.. autofunction:: gudhi.plot_persistence_barcode +.. autofunction:: gudhi.plot_persistence_diagram diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 2644aa11..f713e971 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -33,7 +33,7 @@ This function can display the persistence result as a barcode: periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') diag = periodic_cc.persistence() - gudhi.plot_barcode_persistence(diag) + gudhi.plot_persistence_barcode(diag) .. plot:: @@ -41,7 +41,7 @@ This function can display the persistence result as a barcode: periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') diag = periodic_cc.persistence() - gudhi.plot_barcode_persistence(diag) + gudhi.plot_persistence_barcode(diag) Show persistence as a diagram ----------------------------- @@ -55,7 +55,7 @@ This function can display the persistence result as a diagram: 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.plot_diagram_persistence(diag) + gudhi.plot_persistence_diagram(diag) .. plot:: @@ -64,4 +64,4 @@ This function can display the persistence result as a diagram: 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.plot_diagram_persistence(diag) + gudhi.plot_persistence_diagram(diag) diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py index 9fcb33d0..c06ac5a7 100755 --- a/src/cython/doc/pyplots/barcode_persistence.py +++ b/src/cython/doc/pyplots/barcode_persistence.py @@ -2,4 +2,4 @@ import gudhi periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt') diag = periodic_cc.persistence() -gudhi.plot_barcode_persistence(diag) +gudhi.plot_persistence_barcode(diag) diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py index fbb6e60b..b4714fe3 100755 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -2,4 +2,4 @@ import gudhi alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off') diag = alpha_complex.persistence() -gudhi.plot_diagram_persistence(diag) +gudhi.plot_persistence_diagram(diag) 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 9714b382..adedc7d2 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 @@ -63,7 +63,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_diagram_persistence(diag) + gudhi.plot_persistence_diagram(diag) 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 3addf708..2474fc87 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 @@ -70,7 +70,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_diagram_persistence(diag) + gudhi.plot_persistence_diagram(diag) 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 1e7d788a..5a75417b 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 @@ -70,7 +70,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_diagram_persistence(diag) + gudhi.plot_persistence_diagram(diag) 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 f1aa5d73..bc3b16ec 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -39,9 +39,9 @@ print("Show barcode persistence example") persistence = [(2, (1.0, float('inf'))), (1, (1.4142135623730951, float('inf'))), (1, (1.4142135623730951, float('inf'))), (0, (0.0, float('inf'))), (0, (0.0, 1.0)), (0, (0.0, 1.0)), (0, (0.0, 1.0))] -gudhi.plot_barcode_persistence(persistence) +gudhi.plot_persistence_barcode(persistence) print("#####################################################################") print("Show diagram persistence example") -gudhi.plot_diagram_persistence(persistence) +gudhi.plot_persistence_diagram(persistence) diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 128706b2..db530161 100755 --- a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -71,6 +71,6 @@ if is_file_perseus(args.file): print("betti_numbers()=") print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: - gudhi.plot_barcode_persistence(diag) + gudhi.plot_persistence_barcode(diag) else: print(args.file, "is not a valid perseus style file") 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 5f1416be..664eb5c4 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 @@ -64,7 +64,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_diagram_persistence(diag) + gudhi.plot_persistence_diagram(diag) else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index 4f888e77..4c21b98e 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -64,7 +64,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - gudhi.plot_diagram_persistence(diag) + gudhi.plot_persistence_diagram(diag) else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py index 3d51f379..4e5cd2c8 100755 --- a/src/cython/example/rips_persistence_diagram.py +++ b/src/cython/example/rips_persistence_diagram.py @@ -39,4 +39,4 @@ 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_diagram_persistence(diag) +gudhi.plot_persistence_diagram(diag) 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 a3fc9911..4845eb47 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 @@ -59,7 +59,7 @@ with open(args.file, 'r') as f: print(st.betti_numbers()) if args.no_diagram == False: - gudhi.plot_diagram_persistence(diag) + gudhi.plot_persistence_diagram(diag) else: print(args.file, "is not a valid OFF file") -- cgit v1.2.3