Witness complex cythonization

Review of graphical tools


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1264 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 35d1204190e4324cb9f9e4f8679c13c8ad080f51

4 files changed, 79 insertions, 4 deletions

diff --git a/src/cython/example/alpha_complex_from_file_example.py b/src/cython/example/alpha_complex_from_file_example.py
index d1040e83..beb5d101 100755
--- a/src/cython/example/alpha_complex_from_file_example.py
+++ b/src/cython/example/alpha_complex_from_file_example.py
@@ -59,4 +59,4 @@ print(alpha_complex.betti_numbers())
 
 gudhi.diagram_persistence(diag)
 
-gudhi.bar_code_persistence(diag)
+gudhi.barcode_persistence(diag)
diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py
index c43b2338..40558bee 100755
--- a/src/cython/example/gudhi_graphical_tools_example.py
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -34,9 +34,14 @@ print("Show palette colors values for dimension")
 gudhi.show_palette_values()
 
 print("#####################################################################")
-print("Show bar code persistence example")
+print("Show barcode persistence example")
 
 persistence = [(2, (1.0, float('inf'))), (1, (1.4142135623730951, float('inf'))),
                (1, (1.4142135623730951, float('inf'))), (0, (0.0, float('inf'))),
                (0, (0.0, 1.0)), (0, (0.0, 1.0)), (0, (0.0, 1.0))]
-gudhi.bar_code_persistence(persistence)
+gudhi.barcode_persistence(persistence)
+
+print("#####################################################################")
+print("Show diagram persistence example")
+
+gudhi.diagram_persistence(persistence)
diff --git a/src/cython/example/rips_complex_from_file_example.py b/src/cython/example/rips_complex_from_file_example.py
index 1831a5e9..9385aba0 100755
--- a/src/cython/example/rips_complex_from_file_example.py
+++ b/src/cython/example/rips_complex_from_file_example.py
@@ -59,4 +59,4 @@ print(rips_complex.betti_numbers())
 
 gudhi.diagram_persistence(diag)
 
-gudhi.bar_code_persistence(diag)
+gudhi.barcode_persistence(diag)
diff --git a/src/cython/example/witness_complex_from_file_example.py b/src/cython/example/witness_complex_from_file_example.py
new file mode 100755
index 00000000..9d1a940f
--- /dev/null
+++ b/src/cython/example/witness_complex_from_file_example.py
@@ -0,0 +1,70 @@
+#!/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("WitnessComplex creation from points read in a file")
+
+parser = argparse.ArgumentParser(description='WitnessComplex creation from '
+                                 'points read in a file.',
+                                 epilog='Example: '
+                                 'example/witness_complex_from_file_example.py'
+                                 ' data/500_random_points_on_3D_Torus.csv '
+                                 '- Constructs a witness 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)
+
+print("WitnessComplex with number_of_landmarks=5")
+
+witness_complex = gudhi.WitnessComplex(points=points.values,
+                                     number_of_landmarks=200)
+
+print("filtered_tree=", witness_complex.get_filtered_tree())
+
+witness_complex.initialize_filtration()
+diag = witness_complex.persistence(homology_coeff_field=2, min_persistence=0.1)
+
+print("diag=", diag)
+
+gudhi.diagram_persistence(diag)
+
+"""
+print("betti_numbers()=")
+print(witness_complex.betti_numbers())
+
+gudhi.diagram_persistence(diag)
+
+gudhi.barcode_persistence(diag)
+"""
\ No newline at end of file