diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-06-01 11:00:44 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-06-01 11:00:44 +0000 |
commit | 47f150ba81e353cd1d4128fa63a0d74952b0eae5 (patch) | |
tree | dffa0bd10165d9e368e91788f42b2c6d191e4c3b /src/cython/example | |
parent | 64bb1fe71e6e9e745e473aea456aef29df9cf6d0 (diff) |
Add interfaces with pandas, numpy and matplotlib
new examples : rips_persistence_diagram.py, random_cubical_complex_example & alpha_complex_from_file_example
new data files for alpha_complex_from_file_example
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1235 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 901cc5eb791633f7bfcd86c0b7b8733cb6eb054c
Diffstat (limited to 'src/cython/example')
-rwxr-xr-x | src/cython/example/alpha_complex_from_file_example.py | 63 | ||||
-rwxr-xr-x | src/cython/example/random_cubical_complex_example.py | 57 | ||||
-rwxr-xr-x | src/cython/example/rips_persistence_diagram.py (renamed from src/cython/example/cubical_complex_example.py) | 25 |
3 files changed, 136 insertions, 9 deletions
diff --git a/src/cython/example/alpha_complex_from_file_example.py b/src/cython/example/alpha_complex_from_file_example.py new file mode 100755 index 00000000..9ceb82b1 --- /dev/null +++ b/src/cython/example/alpha_complex_from_file_example.py @@ -0,0 +1,63 @@ +#!/usr/bin/env python + +import gudhi +import pandas +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 Saclay (France) + + 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 Saclay (France)" +__license__ = "GPL v3" + +print("#####################################################################") +print("AlphaComplex creation from points read in a file") + +parser = argparse.ArgumentParser(description='AlphaComplex creation from ' + 'points read in a file.', + epilog='Example: ' + 'example/alpha_complex_from_file_example.py ' + 'data/500_random_points_on_3D_Torus.csv ' + '- Constructs a alpha complex with the ' + 'points from the given file. File format ' + 'is X1, X2, ..., Xn') +parser.add_argument('file', type=argparse.FileType('r')) +args = parser.parse_args() + +points = pandas.read_csv(args.file, header=None) + +alpha_complex = gudhi.AlphaComplex(points=points.values, + max_alpha_square=0.5) + +print("dimension=", alpha_complex.dimension()) +print("point[0]=", alpha_complex.get_point(0)) +print("point[5]=", alpha_complex.get_point(5)) + +alpha_complex.initialize_filtration() +diag = alpha_complex.persistence(homology_coeff_field=2, min_persistence=0.1) + +print("betti_numbers()=") +print(alpha_complex.betti_numbers()) + +print("star([0])=", alpha_complex.get_star_tree([0])) +print("coface([0], 1)=", alpha_complex.get_coface_tree([0], 1)) diff --git a/src/cython/example/random_cubical_complex_example.py b/src/cython/example/random_cubical_complex_example.py new file mode 100755 index 00000000..b479e2e6 --- /dev/null +++ b/src/cython/example/random_cubical_complex_example.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python + +import gudhi +import numpy +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 Saclay (France) + + 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 Saclay (France)" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='Random cubical complex.', + epilog='Example: ' + './random_cubical_complex_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())
\ No newline at end of file diff --git a/src/cython/example/cubical_complex_example.py b/src/cython/example/rips_persistence_diagram.py index ec7d2f5f..3e95f2cc 100755 --- a/src/cython/example/cubical_complex_example.py +++ b/src/cython/example/rips_persistence_diagram.py @@ -1,12 +1,13 @@ #!/usr/bin/env python import gudhi +import matplotlib.pyplot as plt """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 + Author(s): Marc Glisse Copyright (C) 2016 INRIA Saclay (France) @@ -24,17 +25,23 @@ import gudhi along with this program. If not, see <http://www.gnu.org/licenses/>. """ -__author__ = "Vincent Rouvreau" +__author__ = "Marc Glisse" __copyright__ = "Copyright (C) 2016 INRIA Saclay (France)" __license__ = "GPL v3" print("#####################################################################") -print("CubicalComplex creation") -cubical_complex = gudhi.CubicalComplex(dimensions=[3, 3], - top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9]) +print("RipsComplex creation from points") +rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]], + max_dimension=1, max_edge_length=42) -print("persistence(homology_coeff_field=2, min_persistence=0)=") -print(cubical_complex.persistence(homology_coeff_field=2, min_persistence=0)) +diag = rips.persistence(homology_coeff_field=2, min_persistence=0) +print("diag=", diag) -print("betti_numbers()=") -print(cubical_complex.betti_numbers()) +diag0=[i[1] for i in diag if i[0]==0] +diag1=[i[1] for i in diag if i[0]==1] + +plt.plot([i[0] for i in diag0],[min(i[1],1.5) for i in diag0],'ro', + [i[0] for i in diag1],[i[1] for i in diag1],'bs',[-.2,1.5],[-.2,1.5], + '-') +plt.axis([-.2,1.5,-.2,1.5]) +plt.show() |