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| author | Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> | 2020-05-28 21:19:51 +0200 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2020-05-28 21:19:51 +0200 |
| commit | 669960ef3086606165873c8c986a67e9d3d83e9d (patch) | |
| tree | d948ef4b27b964aae8a59478de669fd51659b640 /src/python/doc | |
| parent | 48d9ff9986cb3a6e36f60142784c2a02317dd327 (diff) | |
| parent | a9e1f9bbb4b39bca0d59857f57f5182701532820 (diff) | |
Merge pull request #324 from yuichi-ike/dtm-filtration
DTM Rips complex
Diffstat (limited to 'src/python/doc')
| -rw-r--r-- | src/python/doc/rips_complex_ref.rst | 13 | ||||
| -rw-r--r-- | src/python/doc/rips_complex_sum.inc | 3 | ||||
| -rw-r--r-- | src/python/doc/rips_complex_user.rst | 24 |
3 files changed, 40 insertions, 0 deletions
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))] |