Commit 12b28171 authored by Cas Spaans's avatar Cas Spaans

Start of implementation, Distance matrix!=landmark for gudhi

parent b0ee488f
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#!/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.
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_points_from_off_file(off_file=args.file)
landmarks = gudhi.pick_n_random_points(
points=witnesses, nb_points=args.number_of_landmarks
)
message = (
"EuclideanWitnessComplex with max_edge_length="
+ repr(args.max_alpha_square)
+ " - Number of landmarks="
+ repr(args.number_of_landmarks)
)
print(message)
witness_complex = gudhi.EuclideanWitnessComplex(
witnesses=witnesses, landmarks=landmarks
)
simplex_tree = witness_complex.create_simplex_tree(
max_alpha_square=args.max_alpha_square, limit_dimension=args.limit_dimension
)
message = "Number of simplices=" + repr(simplex_tree.num_simplices())
print(message)
diag = simplex_tree.persistence()
print("betti_numbers()=")
print(simplex_tree.betti_numbers())
if args.no_diagram == False:
gudhi.plot_persistence_diagram(diag, band=args.band)
plot.show()
else:
print(args.file, "is not a valid OFF file")
f.close()
#!/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)
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#!/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.
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_points_from_off_file(off_file=args.file)
landmarks = gudhi.pick_n_random_points(
points=witnesses, nb_points=args.number_of_landmarks
)
message = (
"EuclideanWitnessComplex with max_edge_length="
+ repr(args.max_alpha_square)
+ " - Number of landmarks="
+ repr(args.number_of_landmarks)
)
print(message)
witness_complex = gudhi.EuclideanWitnessComplex(
witnesses=witnesses, landmarks=landmarks
)
simplex_tree = witness_complex.create_simplex_tree(
max_alpha_square=args.max_alpha_square, limit_dimension=args.limit_dimension
)
message = "Number of simplices=" + repr(simplex_tree.num_simplices())
print(message)
diag = simplex_tree.persistence()
print("betti_numbers()=")
print(simplex_tree.betti_numbers())
if args.no_diagram == False:
gudhi.plot_persistence_diagram(diag, band=args.band)
plot.show()
else:
print(args.file, "is not a valid OFF file")
f.close()
#!/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)
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