diff options
Diffstat (limited to 'cython/example')
21 files changed, 0 insertions, 1385 deletions
diff --git a/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py deleted file mode 100755 index 4abe22d4..00000000 --- a/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ /dev/null @@ -1,72 +0,0 @@ -#!/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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='AlphaComplex creation from ' - 'points read in a OFF file.', - epilog='Example: ' - 'example/alpha_complex_diagram_persistence_from_off_file_example.py ' - '-f ../data/points/tore3D_300.off -a 0.6' - '- 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, default=0.5) -parser.add_argument("-b", "--band", 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() - -with open(args.file, 'r') as f: - first_line = f.readline() - if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): - print("#####################################################################") - print("AlphaComplex creation from points read in a OFF file") - - message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square) - print(message) - - alpha_complex = gudhi.AlphaComplex(off_file=args.file) - simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square) - - 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: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() - else: - print(args.file, "is not a valid OFF file") - - f.close() diff --git a/cython/example/alpha_complex_from_points_example.py b/cython/example/alpha_complex_from_points_example.py deleted file mode 100755 index ad73c744..00000000 --- a/cython/example/alpha_complex_from_points_example.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env python - -from gudhi import AlphaComplex, SimplexTree - -"""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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -print("#####################################################################") -print("AlphaComplex creation from points") -alpha_complex = AlphaComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]]) -simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=60.0) - -if simplex_tree.find([0, 1]): - print("[0, 1] Found !!") -else: - print("[0, 1] Not found...") - -if simplex_tree.find([4]): - print("[4] Found !!") -else: - print("[4] Not found...") - -if simplex_tree.insert([0, 1, 2], filtration=4.0): - print("[0, 1, 2] Inserted !!") -else: - print("[0, 1, 2] Not inserted...") - -if simplex_tree.insert([0, 1, 4], filtration=4.0): - print("[0, 1, 4] Inserted !!") -else: - print("[0, 1, 4] Not inserted...") - -if simplex_tree.find([4]): - print("[4] Found !!") -else: - print("[4] Not found...") - -print("dimension=", simplex_tree.dimension()) -print("filtrations=", simplex_tree.get_filtration()) -print("star([0])=", simplex_tree.get_star([0])) -print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1)) - -print("point[0]=", alpha_complex.get_point(0)) -print("point[5]=", alpha_complex.get_point(5)) diff --git a/cython/example/alpha_rips_persistence_bottleneck_distance.py b/cython/example/alpha_rips_persistence_bottleneck_distance.py deleted file mode 100755 index b51fa7a8..00000000 --- a/cython/example/alpha_rips_persistence_bottleneck_distance.py +++ /dev/null @@ -1,101 +0,0 @@ -#!/usr/bin/env python - -import gudhi -import argparse -import math - -"""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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='AlphaComplex and RipsComplex ' - 'persistence creation from points read in ' - 'a OFF file. Bottleneck distance computation' - ' on each dimension', - epilog='Example: ' - 'example/alpha_rips_persistence_bottleneck_distance.py ' - '-f ../data/points/tore3D_1307.off -t 0.15 -d 3') -parser.add_argument("-f", "--file", type=str, required=True) -parser.add_argument("-t", "--threshold", type=float, default=0.5) -parser.add_argument("-d", "--max_dimension", type=int, default=1) - -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'): - point_cloud = gudhi.read_off(off_file=args.file) - print("#####################################################################") - print("RipsComplex creation from points read in a OFF file") - - message = "RipsComplex with max_edge_length=" + repr(args.threshold) - print(message) - - rips_complex = gudhi.RipsComplex(points=point_cloud, - max_edge_length=args.threshold) - - rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) - - message = "Number of simplices=" + repr(rips_stree.num_simplices()) - print(message) - - rips_diag = rips_stree.persistence() - - print("#####################################################################") - print("AlphaComplex creation from points read in a OFF file") - - message = "AlphaComplex with max_edge_length=" + repr(args.threshold) - print(message) - - alpha_complex = gudhi.AlphaComplex(points=point_cloud) - alpha_stree = alpha_complex.create_simplex_tree(max_alpha_square=(args.threshold * args.threshold)) - - message = "Number of simplices=" + repr(alpha_stree.num_simplices()) - print(message) - - alpha_diag = alpha_stree.persistence() - - max_b_distance = 0.0 - for dim in range(args.max_dimension): - # Alpha persistence values needs to be transform because filtration - # values are alpha square values - funcs = [math.sqrt, math.sqrt] - alpha_intervals = [] - for interval in alpha_stree.persistence_intervals_in_dimension(dim): - alpha_intervals.append(map(lambda func,value: func(value), funcs, interval)) - - rips_intervals = rips_stree.persistence_intervals_in_dimension(dim) - bottleneck_distance = gudhi.bottleneck_distance(rips_intervals, alpha_intervals) - message = "In dimension " + repr(dim) + ", bottleneck distance = " + repr(bottleneck_distance) - print(message) - max_b_distance = max(bottleneck_distance, max_b_distance) - - print("================================================================================") - message = "Bottleneck distance is " + repr(max_b_distance) - print(message) - - else: - print(args.file, "is not a valid OFF file") - - f.close() diff --git a/cython/example/bottleneck_basic_example.py b/cython/example/bottleneck_basic_example.py deleted file mode 100755 index 287956e7..00000000 --- a/cython/example/bottleneck_basic_example.py +++ /dev/null @@ -1,46 +0,0 @@ -#!/usr/bin/env python - -import gudhi - -"""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): Francois Godi, 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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Francois Godi, Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]] - -diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]] - -message = "diag1=" + repr(diag1) -print(message) - -message = "diag2=" + repr(diag2) -print(message) - -message = "Bottleneck distance approximation=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0.1)) -print(message) - -message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2)) -print(message) - diff --git a/cython/example/coordinate_graph_induced_complex.py b/cython/example/coordinate_graph_induced_complex.py deleted file mode 100755 index 9e93109a..00000000 --- a/cython/example/coordinate_graph_induced_complex.py +++ /dev/null @@ -1,68 +0,0 @@ -#!/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) 2018 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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2018 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='Coordinate GIC ' - 'from points read in a OFF file.', - epilog='Example: ' - 'example/coordinate_graph_induced_complex.py ' - '-f ../data/points/KleinBottle5D.off -c 0 -v' - '- Constructs the coordinate GIC with the ' - 'points from the given OFF file.') -parser.add_argument("-f", "--file", type=str, required=True) -parser.add_argument("-c", "--coordinate", type=int, default=0) -parser.add_argument("-v", "--verbose", default=False, action='store_true' , help='Flag for program verbosity') - -args = parser.parse_args() - -nerve_complex = gudhi.CoverComplex() -nerve_complex.set_verbose(args.verbose) - -if (nerve_complex.read_point_cloud(args.file)): - nerve_complex.set_type('GIC') - nerve_complex.set_color_from_coordinate(args.coordinate) - nerve_complex.set_function_from_coordinate(args.coordinate) - nerve_complex.set_graph_from_automatic_rips() - nerve_complex.set_automatic_resolution() - nerve_complex.set_gain() - nerve_complex.set_cover_from_function() - nerve_complex.find_simplices() - nerve_complex.plot_dot() - simplex_tree = nerve_complex.create_simplex_tree() - nerve_complex.compute_PD() - if (args.verbose): - print('Iterator on coordinate GIC simplices') - result_str = 'Coordinate GIC is of dimension ' + \ - repr(simplex_tree.dimension()) + ' - ' + \ - repr(simplex_tree.num_simplices()) + ' simplices - ' + \ - repr(simplex_tree.num_vertices()) + ' vertices.' - print(result_str) - for filtered_value in simplex_tree.get_filtration(): - print(filtered_value[0]) diff --git a/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py deleted file mode 100755 index 3b29781f..00000000 --- a/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ /dev/null @@ -1,79 +0,0 @@ -#!/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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex creation from ' - 'points read in a OFF file.', - epilog='Example: ' - 'example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py ' - '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' - '- 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) -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", 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() - -with open(args.file, 'r') as f: - first_line = f.readline() - if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): - print("#####################################################################") - print("EuclideanStrongWitnessComplex 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 = "EuclideanStrongWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \ - " - Number of landmarks=" + repr(args.number_of_landmarks) - print(message) - - witness_complex = gudhi.EuclideanStrongWitnessComplex(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: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() - else: - print(args.file, "is not a valid OFF file") - - f.close() diff --git a/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py deleted file mode 100755 index db34962d..00000000 --- a/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ /dev/null @@ -1,79 +0,0 @@ -#!/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 <http://www.gnu.org/licenses/>. -""" - -__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/euclidean_witness_complex_diagram_persistence_from_off_file_example.py ' - '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' - '- 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) -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", 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() - -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: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() - else: - print(args.file, "is not a valid OFF file") - - f.close() diff --git a/cython/example/functional_graph_induced_complex.py b/cython/example/functional_graph_induced_complex.py deleted file mode 100755 index 6ad7c2ec..00000000 --- a/cython/example/functional_graph_induced_complex.py +++ /dev/null @@ -1,69 +0,0 @@ -#!/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) 2018 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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2018 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='Functional GIC ' - 'from points read in a OFF file.', - epilog='Example: ' - 'example/functional_graph_induced_complex.py ' - '-o ../data/points/COIL_database/lucky_cat.off ' - '-f ../data/points/COIL_database/lucky_cat_PCA1' - '- Constructs the functional GIC with the ' - 'points from the given OFF and function files.') -parser.add_argument("-o", "--off-file", type=str, required=True) -parser.add_argument("-f", "--function-file", type=str, required=True) -parser.add_argument("-v", "--verbose", default=False, action='store_true' , help='Flag for program verbosity') - -args = parser.parse_args() - -nerve_complex = gudhi.CoverComplex() -nerve_complex.set_verbose(args.verbose) - -if (nerve_complex.read_point_cloud(args.off_file)): - nerve_complex.set_type('GIC') - nerve_complex.set_color_from_file(args.function_file) - nerve_complex.set_function_from_file(args.function_file) - nerve_complex.set_graph_from_automatic_rips() - nerve_complex.set_automatic_resolution() - nerve_complex.set_gain() - nerve_complex.set_cover_from_function() - nerve_complex.find_simplices() - nerve_complex.plot_dot() - simplex_tree = nerve_complex.create_simplex_tree() - nerve_complex.compute_PD() - if (args.verbose): - print('Iterator on functional GIC simplices') - result_str = 'Functional GIC is of dimension ' + \ - repr(simplex_tree.dimension()) + ' - ' + \ - repr(simplex_tree.num_simplices()) + ' simplices - ' + \ - repr(simplex_tree.num_vertices()) + ' vertices.' - print(result_str) - for filtered_value in simplex_tree.get_filtration(): - print(filtered_value[0]) diff --git a/cython/example/gudhi_graphical_tools_example.py b/cython/example/gudhi_graphical_tools_example.py deleted file mode 100755 index ac3d146c..00000000 --- a/cython/example/gudhi_graphical_tools_example.py +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env python - -import gudhi - -"""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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -print("#####################################################################") -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_persistence_barcode(persistence) - -print("#####################################################################") -print("Show diagram persistence example") - -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=0.2) -pplot.show() diff --git a/cython/example/nerve_of_a_covering.py b/cython/example/nerve_of_a_covering.py deleted file mode 100755 index c5577cb1..00000000 --- a/cython/example/nerve_of_a_covering.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/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) 2018 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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2018 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='Nerve of a covering creation ' - 'from points read in a OFF file.', - epilog='Example: ' - 'example/nerve_of_a_covering.py ' - '-f ../data/points/human.off -c 2 -r 10 -g 0.3' - '- Constructs Nerve of a covering with the ' - 'points from the given OFF file.') -parser.add_argument("-f", "--file", type=str, required=True) -parser.add_argument("-c", "--coordinate", type=int, default=0) -parser.add_argument("-r", "--resolution", type=int, default=10) -parser.add_argument("-g", "--gain", type=float, default=0.3) -parser.add_argument("-v", "--verbose", default=False, action='store_true' , help='Flag for program verbosity') - -args = parser.parse_args() - -nerve_complex = gudhi.CoverComplex() -nerve_complex.set_verbose(args.verbose) - -if (nerve_complex.read_point_cloud(args.file)): - nerve_complex.set_type('Nerve') - nerve_complex.set_color_from_coordinate(args.coordinate) - nerve_complex.set_function_from_coordinate(args.coordinate) - nerve_complex.set_graph_from_OFF() - nerve_complex.set_resolution_with_interval_number(args.resolution) - nerve_complex.set_gain(args.gain) - nerve_complex.set_cover_from_function() - nerve_complex.find_simplices() - nerve_complex.write_info() - simplex_tree = nerve_complex.create_simplex_tree() - nerve_complex.compute_PD() - if (args.verbose): - print('Iterator on graph induced complex simplices') - result_str = 'Nerve is of dimension ' + \ - repr(simplex_tree.dimension()) + ' - ' + \ - repr(simplex_tree.num_simplices()) + ' simplices - ' + \ - repr(simplex_tree.num_vertices()) + ' vertices.' - print(result_str) - for filtered_value in simplex_tree.get_filtration(): - print(filtered_value[0]) diff --git a/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py deleted file mode 100755 index 5f968bf1..00000000 --- a/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ /dev/null @@ -1,76 +0,0 @@ -#!/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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -def is_file_perseus(file): - num_lines = open(file).read().count('\n') - try: - f = open(file) - num_dim = int(f.readline()) - coeff = 1 - for dim in range(0, num_dim): - try: - line = int(f.readline()) - coeff *= abs(line) - except ValueError: - return False - if num_lines == (1 + num_dim + coeff): - return True - else: - return False - except ValueError: - return False - -parser = argparse.ArgumentParser(description='Periodic cubical complex from a ' - 'Perseus-style file name.', - epilog='Example: ' - './periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py' - ' -f ../data/bitmap/CubicalTwoSphere.txt') - -parser.add_argument("-f", "--file", type=str, required=True) -parser.add_argument('--no-barcode', default=False, action='store_true' , help='Flag for not to display the barcodes') - -args = parser.parse_args() - -if is_file_perseus(args.file): - print("#####################################################################") - print("PeriodicCubicalComplex creation") - periodic_cubical_complex = gudhi.PeriodicCubicalComplex(perseus_file=args.file) - - print("persistence(homology_coeff_field=3, min_persistence=0)=") - diag = periodic_cubical_complex.persistence(homology_coeff_field=3, min_persistence=0) - print(diag) - - print("betti_numbers()=") - print(periodic_cubical_complex.betti_numbers()) - if args.no_barcode == False: - gudhi.plot_persistence_barcode(diag) -else: - print(args.file, "is not a valid perseus style file") diff --git a/cython/example/random_cubical_complex_persistence_example.py b/cython/example/random_cubical_complex_persistence_example.py deleted file mode 100755 index 80ff2452..00000000 --- a/cython/example/random_cubical_complex_persistence_example.py +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/env python - -import gudhi -import numpy -from functools import reduce -import argparse -import operator - - -"""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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='Random cubical complex.', - epilog='Example: ' - './random_cubical_complex_persistence_example.py' - ' 10 10 10 - Constructs a random cubical ' - 'complex in a dimension [10, 10, 10] (aka. ' - '1000 random top dimensional cells).') -parser.add_argument('dimension', type=int, nargs="*", - help='Cubical complex dimensions') - -args = parser.parse_args() -dimension_multiplication = reduce(operator.mul, args.dimension, 1) - -if dimension_multiplication > 1: - print("#####################################################################") - print("CubicalComplex creation") - cubical_complex = gudhi.CubicalComplex(dimensions=args.dimension, - top_dimensional_cells = numpy.random.rand(dimension_multiplication)) - - print("persistence(homology_coeff_field=2, min_persistence=0)=") - print(cubical_complex.persistence(homology_coeff_field=2, min_persistence=0)) - - print("betti_numbers()=") - print(cubical_complex.betti_numbers()) diff --git a/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py deleted file mode 100755 index 0c9dfc43..00000000 --- a/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ /dev/null @@ -1,84 +0,0 @@ -#!/usr/bin/env python - -import gudhi -import sys -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) 2017 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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='RipsComplex creation from ' - 'a correlation matrix read in a csv file.', - epilog='Example: ' - 'example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py ' - '-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3' - '- Constructs a Rips complex with the ' - 'correlation matrix from the given csv file.') -parser.add_argument("-f", "--file", type=str, required=True) -parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5) -parser.add_argument("-d", "--max_dimension", type=int, default=1) -parser.add_argument("-b", "--band", 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() - -if not (-1. < args.min_edge_correlation < 1.): - print("Wrong value of the treshold corelation (should be between -1 and 1).") - sys.exit(1) - -print("#####################################################################") -print("Caution: as persistence diagrams points will be under the diagonal,") -print("bottleneck distance and persistence graphical tool will not work") -print("properly, this is a known issue.") - -print("#####################################################################") -print("RipsComplex creation from correlation matrix read in a csv file") - -message = "RipsComplex with min_edge_correlation=" + repr(args.min_edge_correlation) -print(message) - -correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file) -# Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix: -distance_matrix = [[1.-correlation_matrix[i][j] for j in range(len(correlation_matrix[i]))] for i in range(len(correlation_matrix))] - -rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, - max_edge_length=1.-args.min_edge_correlation) -simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) - -message = "Number of simplices=" + repr(simplex_tree.num_simplices()) -print(message) - -diag = simplex_tree.persistence() - -print("betti_numbers()=") -print(simplex_tree.betti_numbers()) - -# invert the persistence diagram -invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))] - -if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band) - pplot.show() diff --git a/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py deleted file mode 100755 index 4d2ed577..00000000 --- a/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='RipsComplex creation from ' - 'a distance matrix read in a csv file.', - epilog='Example: ' - 'example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py ' - '-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3' - '- Constructs a Rips complex with the ' - 'distance matrix from the given csv file.') -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", 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() - -print("#####################################################################") -print("RipsComplex creation from distance matrix read in a csv file") - -message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) -print(message) - -distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file) -rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, max_edge_length=args.max_edge_length) -simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_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: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() diff --git a/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/cython/example/rips_complex_diagram_persistence_from_off_file_example.py deleted file mode 100755 index d15d5eb0..00000000 --- a/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ /dev/null @@ -1,74 +0,0 @@ -#!/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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='RipsComplex creation from ' - 'points read in a OFF file.', - epilog='Example: ' - 'example/rips_complex_diagram_persistence_from_off_file_example.py ' - '-f ../data/points/tore3D_300.off -a 0.6' - '- Constructs a Rips complex with the ' - 'points from the given OFF file.') -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", 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() - -with open(args.file, 'r') as f: - first_line = f.readline() - if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): - print("#####################################################################") - print("RipsComplex creation from points read in a OFF file") - - message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) - print(message) - - point_cloud = gudhi.read_off(off_file=args.file) - rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=args.max_edge_length) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_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: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() - else: - print(args.file, "is not a valid OFF file") - - f.close() diff --git a/cython/example/rips_complex_from_points_example.py b/cython/example/rips_complex_from_points_example.py deleted file mode 100755 index ffa9d91f..00000000 --- a/cython/example/rips_complex_from_points_example.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -import gudhi - -"""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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -print("#####################################################################") -print("RipsComplex creation from points") -rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]], - max_edge_length=42) - -simplex_tree = rips.create_simplex_tree(max_dimension=1) - -print("filtrations=", simplex_tree.get_filtration()) -print("star([0])=", simplex_tree.get_star([0])) -print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1)) diff --git a/cython/example/rips_persistence_diagram.py b/cython/example/rips_persistence_diagram.py deleted file mode 100755 index 7a6a9f46..00000000 --- a/cython/example/rips_persistence_diagram.py +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env python - -import gudhi - -"""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): Marc Glisse - - 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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Marc Glisse" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -print("#####################################################################") -print("RipsComplex creation from points") -rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]], - max_edge_length=42) - -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() diff --git a/cython/example/simplex_tree_example.py b/cython/example/simplex_tree_example.py deleted file mode 100755 index 28679015..00000000 --- a/cython/example/simplex_tree_example.py +++ /dev/null @@ -1,63 +0,0 @@ -#!/usr/bin/env python - -import gudhi - -"""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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -print("#####################################################################") -print("SimplexTree creation from insertion") - -st = gudhi.SimplexTree() - -if st.insert([0, 1]): - print("Inserted !!") -else: - print("Not inserted...") - -if st.find([0, 1]): - print("Found !!") -else: - print("Not found...") - -if st.insert([0, 1, 2], filtration=4.0): - print("Inserted !!") -else: - print("Not inserted...") - -print("dimension=", st.dimension()) - -st.initialize_filtration() -print("filtration=", st.get_filtration()) -print("filtration[1, 2]=", st.filtration([1, 2])) -print("filtration[4, 2]=", st.filtration([4, 2])) - -print("num_simplices=", st.num_simplices()) -print("num_vertices=", st.num_vertices()) - -print("skeleton[2]=", st.get_skeleton(2)) -print("skeleton[1]=", st.get_skeleton(1)) -print("skeleton[0]=", st.get_skeleton(0)) diff --git a/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/cython/example/tangential_complex_plain_homology_from_off_file_example.py deleted file mode 100755 index 0f8f5e80..00000000 --- a/cython/example/tangential_complex_plain_homology_from_off_file_example.py +++ /dev/null @@ -1,69 +0,0 @@ -#!/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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='TangentialComplex creation from ' - 'points read in a OFF file.', - epilog='Example: ' - 'example/tangential_complex_plain_homology_from_off_file_example.py ' - '-f ../data/points/tore3D_300.off -i 3' - '- Constructs a tangential complex with the ' - 'points from the given OFF file') -parser.add_argument("-f", "--file", type=str, required=True) -parser.add_argument("-i", "--intrisic_dim", type=int, required=True) -parser.add_argument("-b", "--band", 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() - -with open(args.file, 'r') as f: - first_line = f.readline() - if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): - print("#####################################################################") - print("TangentialComplex creation from points read in a OFF file") - - tc = gudhi.TangentialComplex(intrisic_dim = args.intrisic_dim, off_file=args.file) - st = tc.create_simplex_tree() - - message = "Number of simplices=" + repr(st.num_simplices()) - print(message) - - diag = st.persistence(persistence_dim_max = True) - - print("betti_numbers()=") - print(st.betti_numbers()) - - if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() - else: - print(args.file, "is not a valid OFF file") - - f.close() diff --git a/cython/example/voronoi_graph_induced_complex.py b/cython/example/voronoi_graph_induced_complex.py deleted file mode 100755 index 8266a0e4..00000000 --- a/cython/example/voronoi_graph_induced_complex.py +++ /dev/null @@ -1,65 +0,0 @@ -#!/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) 2018 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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2018 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='Voronoi GIC ' - 'from points read in a OFF file.', - epilog='Example: ' - 'example/voronoi_graph_induced_complex.py ' - '-f ../data/points/human.off -n 700 -v' - '- Constructs the Voronoi GIC with the ' - 'points from the given OFF file.') -parser.add_argument("-f", "--file", type=str, required=True) -parser.add_argument("-n", "--subsample-nb-points", type=int, default=100) -parser.add_argument("-v", "--verbose", default=False, action='store_true' , help='Flag for program verbosity') - -args = parser.parse_args() - -nerve_complex = gudhi.CoverComplex() -nerve_complex.set_verbose(args.verbose) - -if (nerve_complex.read_point_cloud(args.file)): - nerve_complex.set_type('GIC') - nerve_complex.set_color_from_coordinate() - nerve_complex.set_graph_from_OFF() - nerve_complex.set_cover_from_Voronoi(args.subsample_nb_points) - nerve_complex.find_simplices() - nerve_complex.plot_off() - simplex_tree = nerve_complex.create_simplex_tree() - nerve_complex.compute_PD() - if (args.verbose): - print('Iterator on graph induced complex simplices') - result_str = 'Graph induced complex is of dimension ' + \ - repr(simplex_tree.dimension()) + ' - ' + \ - repr(simplex_tree.num_simplices()) + ' simplices - ' + \ - repr(simplex_tree.num_vertices()) + ' vertices.' - print(result_str) - for filtered_value in simplex_tree.get_filtration(): - print(filtered_value[0]) diff --git a/cython/example/witness_complex_from_nearest_landmark_table.py b/cython/example/witness_complex_from_nearest_landmark_table.py deleted file mode 100755 index e6b295ee..00000000 --- a/cython/example/witness_complex_from_nearest_landmark_table.py +++ /dev/null @@ -1,46 +0,0 @@ -#!/usr/bin/env python - -from gudhi import StrongWitnessComplex, SimplexTree - -"""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 <http://www.gnu.org/licenses/>. -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -print("#####################################################################") -print("WitnessComplex creation from nearest landmark table") -nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]], - [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]], - [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]], - [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]], - [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]] - -witness_complex = StrongWitnessComplex(nearest_landmark_table=nearest_landmark_table) -simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1) - -message = "Number of simplices: " + repr(simplex_tree.num_simplices()) -print(message) - -diag = simplex_tree.persistence(min_persistence=-0.1, homology_coeff_field=11) -print(diag) |