From 47f150ba81e353cd1d4128fa63a0d74952b0eae5 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 1 Jun 2016 11:00:44 +0000 Subject: 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 --- .../example/alpha_complex_from_file_example.py | 63 ++++++++++++++++++++++ src/cython/example/cubical_complex_example.py | 40 -------------- .../example/random_cubical_complex_example.py | 57 ++++++++++++++++++++ src/cython/example/rips_persistence_diagram.py | 47 ++++++++++++++++ 4 files changed, 167 insertions(+), 40 deletions(-) create mode 100755 src/cython/example/alpha_complex_from_file_example.py delete mode 100755 src/cython/example/cubical_complex_example.py create mode 100755 src/cython/example/random_cubical_complex_example.py create mode 100755 src/cython/example/rips_persistence_diagram.py (limited to 'src/cython/example') 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 . +""" + +__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/cubical_complex_example.py b/src/cython/example/cubical_complex_example.py deleted file mode 100755 index ec7d2f5f..00000000 --- a/src/cython/example/cubical_complex_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 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 . -""" - -__author__ = "Vincent Rouvreau" -__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("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/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 . +""" + +__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/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py new file mode 100755 index 00000000..3e95f2cc --- /dev/null +++ b/src/cython/example/rips_persistence_diagram.py @@ -0,0 +1,47 @@ +#!/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): Marc Glisse + + 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 . +""" + +__author__ = "Marc Glisse" +__copyright__ = "Copyright (C) 2016 INRIA Saclay (France)" +__license__ = "GPL v3" + +print("#####################################################################") +print("RipsComplex creation from points") +rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]], + max_dimension=1, max_edge_length=42) + +diag = rips.persistence(homology_coeff_field=2, min_persistence=0) +print("diag=", diag) + +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() -- cgit v1.2.3