summaryrefslogtreecommitdiff
path: root/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py
diff options
context:
space:
mode:
Diffstat (limited to 'src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py')
-rwxr-xr-xsrc/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py68
1 files changed, 68 insertions, 0 deletions
diff --git a/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py b/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py
new file mode 100755
index 00000000..bcf2fbcb
--- /dev/null
+++ b/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py
@@ -0,0 +1,68 @@
+#!/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
+
+ 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"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("RipsComplex creation from points read in a file")
+
+parser = argparse.ArgumentParser(description='RipsComplex creation from '
+ 'points read in a file.',
+ epilog='Example: '
+ 'example/rips_complex_diagram_persistence_with_pandas_interface_example.py '
+ '../data/2000_random_points_on_3D_Torus.csv '
+ '- Constructs a rips complex with the '
+ 'points from the given file. File format '
+ 'is X1, X2, ..., Xn')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-e", "--max-edge-length", type=float, default=0.5)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+args = parser.parse_args()
+
+points = pandas.read_csv(args.file, header=None)
+
+message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+print(message)
+
+rips_complex = gudhi.RipsComplex(points=points.values,
+ max_dimension=len(points.values[0]), max_edge_length=args.max_edge_length)
+
+message = "Number of simplices=" + repr(rips_complex.num_simplices())
+print(message)
+
+rips_complex.initialize_filtration()
+diag = rips_complex.persistence()
+
+print("betti_numbers()=")
+print(rips_complex.betti_numbers())
+
+if args.no_diagram == False:
+ gudhi.diagram_persistence(diag)