Merge remote-tracking branch 'origin/master' into tomato2

5 files changed, 41 insertions, 15 deletions

diff --git a/src/python/doc/nerve_gic_complex_user.rst b/src/python/doc/nerve_gic_complex_user.rst
index 0e67fc78..0b820abf 100644
--- a/src/python/doc/nerve_gic_complex_user.rst
+++ b/src/python/doc/nerve_gic_complex_user.rst
@@ -50,7 +50,7 @@ The cover C comes from the preimages of intervals (10 intervals with gain 0.3)
 covering the height function (coordinate 2),
 which are then refined into their connected components using the triangulation of the .OFF file.
 
-.. testcode::
+.. code-block:: python
 
     import gudhi
     nerve_complex = gudhi.CoverComplex()
@@ -99,9 +99,6 @@ the program output is:
       [-0.171433, 0.367393]
       [-0.909111, 0.745853]
     0 interval(s) in dimension 1:
-
-.. testoutput::
-
     Nerve is of dimension 1 - 41 simplices - 21 vertices.
     [0]
     [1]
diff --git a/src/python/doc/python3-sphinx-build.py b/src/python/doc/python3-sphinx-build.py
deleted file mode 100755
index 84d158cf..00000000
--- a/src/python/doc/python3-sphinx-build.py
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-Emulate sphinx-build for python3
-"""
-
-from sys import exit, argv
-from sphinx import main
-
-if __name__ == '__main__':
-    exit(main(argv))
diff --git a/src/python/doc/rips_complex_ref.rst b/src/python/doc/rips_complex_ref.rst
index 5f3e46c1..2aa6b268 100644
--- a/src/python/doc/rips_complex_ref.rst
+++ b/src/python/doc/rips_complex_ref.rst
@@ -25,3 +25,16 @@ Weighted Rips complex reference manual
    :show-inheritance:
 
    .. automethod:: gudhi.weighted_rips_complex.WeightedRipsComplex.__init__
+
+.. _dtm-rips-complex-reference-manual:
+
+=================================
+DTM Rips complex reference manual
+=================================
+
+.. autoclass:: gudhi.dtm_rips_complex.DTMRipsComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.dtm_rips_complex.DTMRipsComplex.__init__
\ No newline at end of file
diff --git a/src/python/doc/rips_complex_sum.inc b/src/python/doc/rips_complex_sum.inc
index f7580714..9cd8074b 100644
--- a/src/python/doc/rips_complex_sum.inc
+++ b/src/python/doc/rips_complex_sum.inc
@@ -14,6 +14,9 @@
    |                                                                |                                                                        |                                                                      |
    |                                                                | Weighted Rips complex constructs a simplicial complex from a distance  |                                                                      |
    |                                                                | matrix and weights on vertices.                                        |                                                                      |
+   |                                                                |                                                                        |                                                                      |
+   |                                                                | DTM Rips complex builds a simplicial complex from a point set or       |                                                                      |
+   |                                                                | a distance matrix.                                                     |                                                                      |
    +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------+
    | * :doc:`rips_complex_user`                                     | * :doc:`rips_complex_ref`                                                                                                                     |
    +----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------+
diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst
index 819568be..dd2f2cc0 100644
--- a/src/python/doc/rips_complex_user.rst
+++ b/src/python/doc/rips_complex_user.rst
@@ -378,6 +378,7 @@ Example from a point cloud combined with DistanceToMeasure
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Combining with DistanceToMeasure, one can compute the DTM-filtration of a point set, as in `this notebook <https://github.com/GUDHI/TDA-tutorial/blob/master/Tuto-GUDHI-DTM-filtrations.ipynb>`_. 
+Remark that `DTMRipsComplex <rips_complex_user.html#dtm-rips-complex>`_ class provides exactly this function.
 
 .. testcode::
 
@@ -398,3 +399,26 @@ The output is:
 .. testoutput::
 
     [(0, (3.1622776601683795, inf)), (0, (3.1622776601683795, 5.39834563766817)), (0, (3.1622776601683795, 5.39834563766817))]
+
+.. _dtm-rips-complex:
+
+DTM Rips Complex
+----------------
+
+`DTMRipsComplex <rips_complex_ref.html#dtm-rips-complex-reference-manual>`_ builds a simplicial complex from a point set or a full distance matrix (in the form of ndarray), as described in the above example.
+This class constructs a weighted Rips complex giving larger weights to outliers, which reduces their impact on the persistence diagram. See `this notebook <https://github.com/GUDHI/TDA-tutorial/blob/master/Tuto-GUDHI-DTM-filtrations.ipynb>`_ for some experiments.
+
+.. testcode::
+
+    import numpy as np
+    from gudhi.dtm_rips_complex import DTMRipsComplex
+    pts = np.array([[2.0, 2.0], [0.0, 1.0], [3.0, 4.0]])
+    dtm_rips = DTMRipsComplex(points=pts, k=2)
+    st = dtm_rips.create_simplex_tree(max_dimension=2)
+    print(st.persistence())
+
+The output is:
+
+.. testoutput::
+
+    [(0, (3.1622776601683795, inf)), (0, (3.1622776601683795, 5.39834563766817)), (0, (3.1622776601683795, 5.39834563766817))]