Remove pandas examples and use of OFF files interfaces to be more consistent (pandas interface is not that hard to be done)

Add of distance matrix in Rips


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2081 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3a3b24f0824eed2710edb5bf17d120039973bf62

1 files changed, 71 insertions, 0 deletions

diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
new file mode 100755
index 00000000..eb1c4ed5
--- /dev/null
+++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+
+import gudhi
+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"
+
+parser = argparse.ArgumentParser(description='RipsComplex creation from '
+                                 'points read in a OFF file.',
+                                 epilog='Example: '
+                                 'example/rips_complex_diagram_persistence_from_off_file_example.py '
+                                 '-f ../data/points/tore3D_300.off -a 0.6'
+                                 '- Constructs a Rips complex with the '
+                                 'points from the given OFF file.')
+parser.add_argument("-f", "--file", 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('--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("RipsComplex creation from points read in a OFF file")
+        
+        message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+        print(message)
+        
+        rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length)
+        simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_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.diagram_persistence(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()