Fix rips complex with the new interface

Remove mini simplex tree
Fix persistent cohomology doc - only simplex tree used
Remove useless type definition in Cython C++ interfaces


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2003 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fff43192b00df1c70d59109a6c14932013992ff1

4 files changed, 17 insertions, 84 deletions

diff --git a/src/cython/example/mini_simplex_tree_example.py b/src/cython/example/mini_simplex_tree_example.py
deleted file mode 100755
index 7b65a9d6..00000000
--- a/src/cython/example/mini_simplex_tree_example.py
+++ /dev/null
@@ -1,73 +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
-
-   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("MiniSimplexTree creation from insertion")
-
-""" Complex to build.
-     1   3
-     o---o
-    /X\ /
-   o---o   o
-   2   0   4
-"""
-
-triangle012 = [0, 1, 2]
-edge03 = [0, 3]
-edge13 = [1, 3]
-vertex4 = [4]
-mini_st = gudhi.MiniSimplexTree()
-mini_st.insert(triangle012)
-mini_st.insert(edge03)
-mini_st.insert(edge13)
-mini_st.insert(vertex4)
-
-# FIXME: Remove this line
-mini_st.set_dimension(2)
-
-# initialize_filtration required before plain_homology
-mini_st.initialize_filtration()
-
-print("persistence(homology_coeff_field=2)=")
-print(mini_st.persistence(homology_coeff_field=2))
-
-edge02 = [0, 2]
-if mini_st.find(edge02):
-    # Only coface is 012
-    print("coface(edge02,1)=", mini_st.get_coface_tree(edge02, 1))
-
-if mini_st.get_coface_tree(triangle012, 1) == []:
-    # Precondition: Check the simplex has no coface before removing it.
-    mini_st.remove_maximal_simplex(triangle012)
-
-# initialize_filtration required after removing
-mini_st.initialize_filtration()
-
-print("filtered_tree after triangle012 removal =", mini_st.get_filtered_tree())
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
index bcf2fbcb..8af1b767 100755
--- 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
@@ -53,16 +53,17 @@ 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)
+                                 max_edge_length=args.max_edge_length)
 
-message = "Number of simplices=" + repr(rips_complex.num_simplices())
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=len(points.values[0]))
+
+message = "Number of simplices=" + repr(simplex_tree.num_simplices())
 print(message)
 
-rips_complex.initialize_filtration()
-diag = rips_complex.persistence()
+diag = simplex_tree.persistence()
 
 print("betti_numbers()=")
-print(rips_complex.betti_numbers())
+print(simplex_tree.betti_numbers())
 
 if args.no_diagram == False:
     gudhi.diagram_persistence(diag)
diff --git a/src/cython/example/rips_complex_from_points_example.py b/src/cython/example/rips_complex_from_points_example.py
index 1a22d8e3..df6252cd 100755
--- a/src/cython/example/rips_complex_from_points_example.py
+++ b/src/cython/example/rips_complex_from_points_example.py
@@ -31,8 +31,10 @@ __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)
+                         max_edge_length=42)
 
-print("filtered_tree=", rips.get_filtered_tree())
-print("star([0])=", rips.get_star_tree([0]))
-print("coface([0], 1)=", rips.get_coface_tree([0], 1))
+simplex_tree = rips.create_simplex_tree(max_dimension=1)
+
+print("filtered_tree=", simplex_tree.get_filtered_tree())
+print("star([0])=", simplex_tree.get_star_tree([0]))
+print("coface([0], 1)=", simplex_tree.get_coface_tree([0], 1))
diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py
index fddea298..e485b2f5 100755
--- a/src/cython/example/rips_persistence_diagram.py
+++ b/src/cython/example/rips_persistence_diagram.py
@@ -31,9 +31,12 @@ __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)
+                         max_edge_length=42)
 
-diag = rips.persistence(homology_coeff_field=2, min_persistence=0)
+simplex_tree = rips.create_simplex_tree(max_dimension=1)
+
+
+diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0)
 print("diag=", diag)
 
 gudhi.diagram_persistence(diag)