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, 45 insertions, 2 deletions

diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py
index 687e8529..464c69e5 100755
--- a/src/cython/test/test_rips_complex.py
+++ b/src/cython/test/test_rips_complex.py
@@ -1,4 +1,5 @@
 from gudhi import RipsComplex
+from math import sqrt
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -31,7 +32,7 @@ def test_empty_rips():
     rips_complex = RipsComplex()
     assert rips_complex.__is_defined() == True
 
-def test_rips():
+def test_rips_from_points():
     point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
     rips_complex = RipsComplex(points=point_list, max_edge_length=42)
 
@@ -55,7 +56,7 @@ def test_rips():
            [([0, 1], 1.0), ([0, 2], 1.0),
             ([0, 3], 1.4142135623730951)]
 
-def test_filtered_rips():
+def test_filtered_rips_from_points():
     point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
     filtered_rips = RipsComplex(points=point_list, max_edge_length=1.0)
 
@@ -66,3 +67,45 @@ def test_filtered_rips():
 
     assert simplex_tree.num_simplices() == 8
     assert simplex_tree.num_vertices() == 4
+
+def test_rips_from_distance_matrix():
+    distance_matrix = [[0],
+                       [1, 0],
+                       [1, sqrt(2), 0],
+                       [sqrt(2), 1, 1, 0]]
+    rips_complex = RipsComplex(distance_matrix=distance_matrix, max_edge_length=42)
+
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+
+    assert simplex_tree.__is_defined() == True
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 10
+    assert simplex_tree.num_vertices() == 4
+
+    assert simplex_tree.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
+            ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
+            ([0, 3], 1.4142135623730951)]
+    assert simplex_tree.get_star_tree([0]) == \
+           [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+    assert simplex_tree.get_coface_tree([0], 1) == \
+           [([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+
+def test_filtered_rips_from_distance_matrix():
+    distance_matrix = [[0],
+                       [1, 0],
+                       [1, sqrt(2), 0],
+                       [sqrt(2), 1, 1, 0]]
+    filtered_rips = RipsComplex(distance_matrix=distance_matrix, max_edge_length=1.0)
+
+    simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1)
+
+    assert simplex_tree.__is_defined() == True
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 8
+    assert simplex_tree.num_vertices() == 4