diff options
Diffstat (limited to 'src/python/example')
14 files changed, 197 insertions, 115 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 index 727af4fa..c96121a6 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -1,10 +1,7 @@ #!/usr/bin/env python import argparse -import errno -import os -import matplotlib.pyplot as plot -import gudhi +import gudhi as gd """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -26,12 +23,12 @@ 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" + "-f ../data/points/tore3D_300.off" "- 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("-a", "--max_alpha_square", type=float, required=False) parser.add_argument("-b", "--band", type=float, default=0.0) parser.add_argument( "--no-diagram", @@ -42,33 +39,24 @@ parser.add_argument( 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: - gudhi.plot_persistence_diagram(diag, band=args.band) - plot.show() - else: - raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), - args.file) - - f.close() +print("##############################################################") +print("AlphaComplex creation from points read in a OFF file") + +points = gd.read_points_from_off_file(off_file = args.file) +alpha_complex = gd.AlphaComplex(points = points) +if args.max_alpha_square is not None: + print("with max_edge_length=", args.max_alpha_square) + simplex_tree = alpha_complex.create_simplex_tree( + max_alpha_square=args.max_alpha_square + ) +else: + simplex_tree = alpha_complex.create_simplex_tree() + +print("Number of simplices=", simplex_tree.num_simplices()) + +diag = simplex_tree.persistence() +print("betti_numbers()=", simplex_tree.betti_numbers()) +if args.no_diagram == False: + import matplotlib.pyplot as plot + gd.plot_persistence_diagram(diag, band=args.band) + plot.show() diff --git a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py new file mode 100644 index 00000000..3558077e --- /dev/null +++ b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py @@ -0,0 +1,35 @@ +#!/usr/bin/env python + +from gudhi.datasets.generators import _points +from gudhi import AlphaComplex + + +""" 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): Hind Montassif + + Copyright (C) 2021 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Hind Montassif" +__copyright__ = "Copyright (C) 2021 Inria" +__license__ = "MIT" + +print("#####################################################################") +print("AlphaComplex creation from generated points on sphere") + + +gen_points = _points.sphere(n_samples = 50, ambient_dim = 2, radius = 1, sample = "random") + +# Create an alpha complex +alpha_complex = AlphaComplex(points = gen_points) +simplex_tree = alpha_complex.create_simplex_tree() + +result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ + repr(simplex_tree.num_simplices()) + ' simplices - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' +print(result_str) + diff --git a/src/python/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py index 465632eb..5d5ca66a 100755 --- a/src/python/example/alpha_complex_from_points_example.py +++ b/src/python/example/alpha_complex_from_points_example.py @@ -19,7 +19,7 @@ __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) +simplex_tree = alpha_complex.create_simplex_tree() if simplex_tree.find([0, 1]): print("[0, 1] Found !!") diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py index 3e12b0d5..6b97fb3b 100755 --- a/src/python/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py @@ -1,10 +1,8 @@ #!/usr/bin/env python -import gudhi +import gudhi as gd import argparse import math -import errno -import os import numpy as np """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -37,70 +35,60 @@ 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_points_from_off_file(off_file=args.file) - print("##############################################################") - print("RipsComplex creation from points read in a OFF file") +point_cloud = gd.read_points_from_off_file(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) +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_stree.compute_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) +rips_complex = gd.RipsComplex( + points=point_cloud, max_edge_length=args.threshold +) - alpha_stree.compute_persistence() +rips_stree = rips_complex.create_simplex_tree( + max_dimension=args.max_dimension) - 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 - alpha_intervals = np.sqrt(alpha_stree.persistence_intervals_in_dimension(dim)) +message = "Number of simplices=" + repr(rips_stree.num_simplices()) +print(message) - 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) +rips_stree.compute_persistence() - print("==============================================================") - message = "Bottleneck distance is " + repr(max_b_distance) - print(message) +print("##############################################################") +print("AlphaComplex creation from points read in a OFF file") - else: - raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), - args.file) +message = "AlphaComplex with max_edge_length=" + repr(args.threshold) +print(message) +alpha_complex = gd.AlphaComplex(points=point_cloud) +alpha_stree = alpha_complex.create_simplex_tree( + max_alpha_square=(args.threshold * args.threshold) +) - f.close() +message = "Number of simplices=" + repr(alpha_stree.num_simplices()) +print(message) + +alpha_stree.compute_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 + alpha_intervals = np.sqrt(alpha_stree.persistence_intervals_in_dimension(dim)) + + rips_intervals = rips_stree.persistence_intervals_in_dimension(dim) + bottleneck_distance = gd.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) diff --git a/src/python/example/diagram_vectorizations_distances_kernels.py b/src/python/example/diagram_vectorizations_distances_kernels.py index c4a71a7a..2801576e 100755 --- a/src/python/example/diagram_vectorizations_distances_kernels.py +++ b/src/python/example/diagram_vectorizations_distances_kernels.py @@ -5,11 +5,11 @@ import numpy as np from sklearn.kernel_approximation import RBFSampler from sklearn.preprocessing import MinMaxScaler -from gudhi.representations import DiagramSelector, Clamping, Landscape, Silhouette, BettiCurve, ComplexPolynomial,\ +from gudhi.representations import (DiagramSelector, Clamping, Landscape, Silhouette, BettiCurve, ComplexPolynomial,\ TopologicalVector, DiagramScaler, BirthPersistenceTransform,\ PersistenceImage, PersistenceWeightedGaussianKernel, Entropy, \ PersistenceScaleSpaceKernel, SlicedWassersteinDistance,\ - SlicedWassersteinKernel, BottleneckDistance, PersistenceFisherKernel, WassersteinDistance + SlicedWassersteinKernel, PersistenceFisherKernel, WassersteinDistance) D1 = np.array([[0.,4.],[1.,2.],[3.,8.],[6.,8.], [0., np.inf], [5., np.inf]]) @@ -93,14 +93,21 @@ print("SW distance is " + str(sW(D1, D2))) SW = SlicedWassersteinKernel(num_directions=100, bandwidth=1.) print("SW kernel is " + str(SW(D1, D2))) -W = WassersteinDistance(order=2, internal_p=2, mode="pot") -print("Wasserstein distance (POT) is " + str(W(D1, D2))) +try: + W = WassersteinDistance(order=2, internal_p=2, mode="pot") + print("Wasserstein distance (POT) is " + str(W(D1, D2))) +except ImportError: + print("WassersteinDistance (POT) is not available, you may be missing pot.") W = WassersteinDistance(order=2, internal_p=2, mode="hera", delta=0.0001) print("Wasserstein distance (hera) is " + str(W(D1, D2))) -W = BottleneckDistance(epsilon=.001) -print("Bottleneck distance is " + str(W(D1, D2))) +try: + from gudhi.representations import BottleneckDistance + W = BottleneckDistance(epsilon=.001) + print("Bottleneck distance is " + str(W(D1, D2))) +except ImportError: + print("BottleneckDistance is not available, you may be missing CGAL.") PF = PersistenceFisherKernel(bandwidth_fisher=1., bandwidth=1.) print("PF kernel is " + str(PF(D1, D2))) diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index e1e572df..4e97cfe3 100755 --- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -82,6 +81,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 58cb2bb5..29076c74 100755 --- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -79,6 +78,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 499171df..ee3290c6 100755 --- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import errno import os import gudhi @@ -75,6 +74,7 @@ if is_file_perseus(args.file): print("betti_numbers()=") print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_barcode(diag) plot.show() else: diff --git a/src/python/example/plot_alpha_complex.py b/src/python/example/plot_alpha_complex.py index 99c18a7c..0924619b 100755 --- a/src/python/example/plot_alpha_complex.py +++ b/src/python/example/plot_alpha_complex.py @@ -1,8 +1,9 @@ #!/usr/bin/env python import numpy as np -import gudhi -ac = gudhi.AlphaComplex(off_file='../../data/points/tore3D_1307.off') +import gudhi as gd +points = gd.read_points_from_off_file(off_file = '../../data/points/tore3D_1307.off') +ac = gd.AlphaComplex(points = points) st = ac.create_simplex_tree() points = np.array([ac.get_point(i) for i in range(st.num_vertices())]) # We want to plot the alpha-complex with alpha=0.1. diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 1acb187c..ea2eb7e1 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -2,7 +2,6 @@ import sys import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -84,5 +83,6 @@ invert_diag = [ ] if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(invert_diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 79ccca96..8a9cc857 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -22,11 +21,12 @@ 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" + "-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -s , -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("-s", "--separator", 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) @@ -45,7 +45,7 @@ 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) +distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file, separator=args.separator) rips_complex = gudhi.RipsComplex( distance_matrix=distance_matrix, max_edge_length=args.max_edge_length ) @@ -60,5 +60,6 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index 6f992508..e80233a9 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -70,6 +69,7 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: diff --git a/src/python/example/rips_complex_edge_collapse_example.py b/src/python/example/rips_complex_edge_collapse_example.py new file mode 100755 index 00000000..b26eb9fc --- /dev/null +++ b/src/python/example/rips_complex_edge_collapse_example.py @@ -0,0 +1,62 @@ +#!/usr/bin/env python + +import gudhi +import matplotlib.pyplot as plt +import time + +""" 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) 2020 Inria" +__license__ = "MIT" + + +print("#####################################################################") +print("RipsComplex (only the one-skeleton) creation from tore3D_300.off file") + +off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' +point_cloud = gudhi.read_points_from_off_file(off_file = off_file) +rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=12.0) +simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) +print('1. Rips complex is of dimension ', simplex_tree.dimension(), ' - ', + simplex_tree.num_simplices(), ' simplices - ', + simplex_tree.num_vertices(), ' vertices.') + +# Expansion of this one-skeleton would require a lot of memory. Let's collapse it +start = time.process_time() +simplex_tree.collapse_edges() +print('2. Rips complex is of dimension ', simplex_tree.dimension(), ' - ', + simplex_tree.num_simplices(), ' simplices - ', + simplex_tree.num_vertices(), ' vertices.') +simplex_tree.expansion(3) +diag = simplex_tree.persistence() +print("Collapse, expansion and persistence computation took ", time.process_time() - start, " sec.") + +# Use subplots to display diagram and density side by side +fig, axes = plt.subplots(nrows=1, ncols=2, figsize=(12, 5)) +gudhi.plot_persistence_diagram(diag, axes=axes[0]) +axes[0].set_title("Persistence after 1 collapse") + +# Collapse can be performed several times. Let's collapse it 3 times +start = time.process_time() +simplex_tree.collapse_edges(nb_iterations = 3) +print('3. Rips complex is of dimension ', simplex_tree.dimension(), ' - ', + simplex_tree.num_simplices(), ' simplices - ', + simplex_tree.num_vertices(), ' vertices.') +simplex_tree.expansion(3) +diag = simplex_tree.persistence() +print("Collapse, expansion and persistence computation took ", time.process_time() - start, " sec.") + +gudhi.plot_persistence_diagram(diag, axes=axes[1]) +axes[1].set_title("Persistence after 3 more collapses") + +# Plot the 2 persistence diagrams side to side to check the persistence is the same +plt.show()
\ No newline at end of file diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index 85bade4a..a4b4e9f5 100755 --- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -3,7 +3,6 @@ import argparse import errno import os -import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -62,6 +61,7 @@ with open(args.file, "r") as f: print(st.betti_numbers()) if args.no_diagram == False: + import matplotlib.pyplot as plot gudhi.plot_persistence_diagram(diag, band=args.band) plot.show() else: |