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Diffstat (limited to 'src/python/example')
22 files changed, 1330 insertions, 0 deletions
diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py new file mode 100755 index 00000000..b8f283b3 --- /dev/null +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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=0.0) +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/src/python/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py new file mode 100755 index 00000000..a746998c --- /dev/null +++ b/src/python/example/alpha_complex_from_points_example.py @@ -0,0 +1,55 @@ +#!/usr/bin/env python + +from gudhi import AlphaComplex, SimplexTree + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py new file mode 100755 index 00000000..086307ee --- /dev/null +++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py @@ -0,0 +1,105 @@ +#!/usr/bin/env python + +import gudhi +import argparse +import math + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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/src/python/example/bottleneck_basic_example.py b/src/python/example/bottleneck_basic_example.py new file mode 100755 index 00000000..392d2a6e --- /dev/null +++ b/src/python/example/bottleneck_basic_example.py @@ -0,0 +1,37 @@ +#!/usr/bin/env python + +import gudhi + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Francois Godi, Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +diag1 = [[2.7, 3.7], [9.6, 14.0], [34.2, 34.974], [3.0, 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/src/python/example/coordinate_graph_induced_complex.py b/src/python/example/coordinate_graph_induced_complex.py new file mode 100755 index 00000000..e32141b4 --- /dev/null +++ b/src/python/example/coordinate_graph_induced_complex.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2018 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2018 Inria" +__license__ = "MIT" + +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/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py new file mode 100755 index 00000000..610ba44f --- /dev/null +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,83 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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=0.0) +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/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py new file mode 100755 index 00000000..7587b732 --- /dev/null +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,82 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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=0.0) +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/src/python/example/functional_graph_induced_complex.py b/src/python/example/functional_graph_induced_complex.py new file mode 100755 index 00000000..8b645040 --- /dev/null +++ b/src/python/example/functional_graph_induced_complex.py @@ -0,0 +1,69 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2018 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2018 Inria" +__license__ = "MIT" + +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/src/python/example/gudhi_graphical_tools_example.py b/src/python/example/gudhi_graphical_tools_example.py new file mode 100755 index 00000000..3b0ca54d --- /dev/null +++ b/src/python/example/gudhi_graphical_tools_example.py @@ -0,0 +1,43 @@ +#!/usr/bin/env python + +import gudhi + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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/src/python/example/nerve_of_a_covering.py b/src/python/example/nerve_of_a_covering.py new file mode 100755 index 00000000..3c8e0f90 --- /dev/null +++ b/src/python/example/nerve_of_a_covering.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2018 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2018 Inria" +__license__ = "MIT" + +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/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py new file mode 100755 index 00000000..9cb855cd --- /dev/null +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -0,0 +1,74 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + + +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/src/python/example/random_cubical_complex_persistence_example.py b/src/python/example/random_cubical_complex_persistence_example.py new file mode 100755 index 00000000..da0eb177 --- /dev/null +++ b/src/python/example/random_cubical_complex_persistence_example.py @@ -0,0 +1,49 @@ +#!/usr/bin/env python + +import gudhi +import numpy +from functools import reduce +import argparse +import operator + + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py new file mode 100755 index 00000000..3571580b --- /dev/null +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +import gudhi +import sys +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2017 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2017 Inria" +__license__ = "MIT" + +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=0.0) +parser.add_argument( + "--no-diagram", + default=False, + action="store_true", + help="Flag for not to display the diagrams", +) + +args = parser.parse_args() + +if not (-1.0 < args.min_edge_correlation < 1.0): + 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 = [ + [1.0 - 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=1.0 - 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], (1.0 - diag[pers][1][0], 1.0 - 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/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py new file mode 100755 index 00000000..0b9a9ba9 --- /dev/null +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -0,0 +1,63 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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=0.0) +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/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py new file mode 100755 index 00000000..2b335bba --- /dev/null +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,72 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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=0.0) +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/src/python/example/rips_complex_from_points_example.py b/src/python/example/rips_complex_from_points_example.py new file mode 100755 index 00000000..59d8a261 --- /dev/null +++ b/src/python/example/rips_complex_from_points_example.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python + +import gudhi + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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/src/python/example/rips_persistence_diagram.py b/src/python/example/rips_persistence_diagram.py new file mode 100755 index 00000000..f5897d7b --- /dev/null +++ b/src/python/example/rips_persistence_diagram.py @@ -0,0 +1,30 @@ +#!/usr/bin/env python + +import gudhi + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Marc Glisse" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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/src/python/example/simplex_tree_example.py b/src/python/example/simplex_tree_example.py new file mode 100755 index 00000000..30de00da --- /dev/null +++ b/src/python/example/simplex_tree_example.py @@ -0,0 +1,51 @@ +#!/usr/bin/env python + +import gudhi + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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/src/python/example/sparse_rips_persistence_diagram.py b/src/python/example/sparse_rips_persistence_diagram.py new file mode 100755 index 00000000..671d5e34 --- /dev/null +++ b/src/python/example/sparse_rips_persistence_diagram.py @@ -0,0 +1,32 @@ +#!/usr/bin/env python + +import gudhi + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2018 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Marc Glisse" +__copyright__ = "Copyright (C) 2018 Inria" +__license__ = "MIT" + +print("#####################################################################") +print("Sparse RipsComplex creation from points") +rips = gudhi.RipsComplex( + points=[[0, 0], [0, 0.1], [1, 0], [0, 1], [1, 1]], max_edge_length=42, sparse=0.5 +) + +simplex_tree = rips.create_simplex_tree(max_dimension=2) + + +diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0) +print("diag=", diag) + +pplot = gudhi.plot_persistence_diagram(diag) +pplot.show() diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py new file mode 100755 index 00000000..456bc9eb --- /dev/null +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -0,0 +1,64 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +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=0.0) +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) + tc.compute_tangential_complex() + 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/src/python/example/voronoi_graph_induced_complex.py b/src/python/example/voronoi_graph_induced_complex.py new file mode 100755 index 00000000..38be6c92 --- /dev/null +++ b/src/python/example/voronoi_graph_induced_complex.py @@ -0,0 +1,65 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2018 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2018 Inria" +__license__ = "MIT" + +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/src/python/example/witness_complex_from_nearest_landmark_table.py b/src/python/example/witness_complex_from_nearest_landmark_table.py new file mode 100755 index 00000000..c04a82b2 --- /dev/null +++ b/src/python/example/witness_complex_from_nearest_landmark_table.py @@ -0,0 +1,36 @@ +#!/usr/bin/env python + +from gudhi import StrongWitnessComplex, SimplexTree + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +print("#####################################################################") +print("WitnessComplex creation from nearest landmark table") +nearest_landmark_table = [ + [[0, 0.0], [1, 0.1], [2, 0.2], [3, 0.3], [4, 0.4]], + [[1, 0.0], [2, 0.1], [3, 0.2], [4, 0.3], [0, 0.4]], + [[2, 0.0], [3, 0.1], [4, 0.2], [0, 0.3], [1, 0.4]], + [[3, 0.0], [4, 0.1], [0, 0.2], [1, 0.3], [2, 0.4]], + [[4, 0.0], [0, 0.1], [1, 0.2], [2, 0.3], [3, 0.4]], +] + +witness_complex = StrongWitnessComplex(nearest_landmark_table=nearest_landmark_table) +simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=0.41) + +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) |