DTM Rips added (straightforward way)

7 files changed, 131 insertions, 1 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index ab08cd6d..96dd3f6f 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -58,6 +58,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'wasserstein', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'point_cloud', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'weighted_rips_complex', ")
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'dtm_rips_complex', ")
 
     add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
     add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
@@ -234,6 +235,7 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/wasserstein" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/point_cloud" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
+    file(COPY "gudhi/dtm_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
 
     add_custom_command(
         OUTPUT gudhi.so
@@ -492,9 +494,15 @@ if(PYTHONINTERP_FOUND)
 
     # Weighted Rips
     if(SCIPY_FOUND)
-      add_gudhi_py_test(test_weighted_rips)
+      add_gudhi_py_test(test_weighted_rips_complex)
     endif()
 
+    # DTM Rips
+    if(SCIPY_FOUND)
+      add_gudhi_py_test(test_dtm_rips_complex)
+    endif()
+
+
     # Set missing or not modules
     set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES")
   else(CYTHON_FOUND)
diff --git a/src/python/doc/rips_complex_ref.rst b/src/python/doc/rips_complex_ref.rst
index 5f3e46c1..f781fd92 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..eb2657df 100644
--- a/src/python/doc/rips_complex_user.rst
+++ b/src/python/doc/rips_complex_user.rst
@@ -398,3 +398,23 @@ The output is:
 .. testoutput::
 
     [(0, (3.1622776601683795, inf)), (0, (3.1622776601683795, 5.39834563766817)), (0, (3.1622776601683795, 5.39834563766817))]
+
+DTM Rips Complex
+----------------
+
+`DtmdRipsComplex <rips_complex_ref.html#dtm-rips-complex-reference-manual>`_ builds a simplicial complex from a point set or a full distence matrix (in the form of ndarray), as described in the above example.
+
+.. testcode::
+
+    import numpy as np
+    from 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))]
diff --git a/src/python/gudhi/dtm_rips_complex.py b/src/python/gudhi/dtm_rips_complex.py
new file mode 100644
index 00000000..6d2f9f31
--- /dev/null
+++ b/src/python/gudhi/dtm_rips_complex.py
@@ -0,0 +1,46 @@
+# This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+# See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+# Author(s):       Yuichi Ike, Raphaël Tinarrage
+#
+# Copyright (C) 2020 Inria, Copyright (C) 2020 FUjitsu Laboratories Ltd.
+#
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
+
+
+from gudhi.weighted_rips_complex import WeightedRipsComplex
+from gudhi.point_cloud.dtm import DistanceToMeasure
+from scipy.spatial.distance import cdist
+
+class DtmRipsComplex(WeightedRipsComplex):
+    """
+    Class to generate a DTM Rips complex from a distance matrix or a point set, 
+    in the way described in :cite:`dtmfiltrations`.
+    Remark that all the filtration values are doubled compared to the definition in the paper 
+    for the consistency with RipsComplex.
+    """
+    def __init__(self, 
+                 points=None, 
+                 distance_matrix=None, 
+                 k=1, 
+                 q=2,
+                 max_filtration=float('inf')):
+        """
+        Args:
+            points (Sequence[Sequence[float]]): list of points.
+            distance_matrix (ndarray): full distance matrix.
+            k (int): number of neighbors for the computation of DTM. Defaults to 1, which is equivalent to the usual Rips complex.
+            q (float): order used to compute the distance to measure. Defaults to 2.
+            max_filtration (float): specifies the maximal filtration value to be considered.      
+        """
+        if distance_matrix is None:
+            if points is None:
+                # Empty Rips construction
+                points=[]
+            distance_matrix = cdist(points,points)
+        self.distance_matrix = distance_matrix
+        dtm = DistanceToMeasure(k, q=q, metric="precomputed")
+        # TODO: address the error when k is too large 
+        self.weights = dtm.fit_transform(distance_matrix)
+        self.max_filtration = max_filtration
+        
diff --git a/src/python/test/test_dtm_rips_complex.py b/src/python/test/test_dtm_rips_complex.py
new file mode 100644
index 00000000..bc6e5a59
--- /dev/null
+++ b/src/python/test/test_dtm_rips_complex.py
@@ -0,0 +1,40 @@
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+    Author(s):       Yuichi Ike
+
+    Copyright (C) 2020 Inria, Copyright (C) 2020 FUjitsu Laboratories Ltd.
+
+    Modification(s):
+      - YYYY/MM Author: Description of the modification
+"""
+
+from gudhi.dtm_rips_complex import DtmRipsComplex
+import numpy as np
+from math import sqrt
+import pytest
+
+def test_dtm_rips_complex():
+    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)
+    st.persistence()
+    persistence_intervals0 = st.persistence_intervals_in_dimension(0)
+    assert persistence_intervals0 == pytest.approx(np.array([[3.16227766, 5.39834564],[3.16227766, 5.39834564], [3.16227766, float("inf")]]))
+    
+def test_compatibility_with_rips():
+    distance_matrix = np.array([[0, 1, 1, sqrt(2)], [1, 0, sqrt(2), 1], [1, sqrt(2), 0, 1], [sqrt(2), 1, 1, 0]])
+    dtm_rips = DtmRipsComplex(distance_matrix=distance_matrix, max_filtration=42)
+    st = dtm_rips.create_simplex_tree(max_dimension=1)
+    assert list(st.get_filtration()) == [
+        ([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], sqrt(2)),
+        ([0, 3], sqrt(2)),
+    ]
+
diff --git a/src/python/test/test_weighted_rips.py b/src/python/test/test_weighted_rips_complex.py
index 7ef48333..7ef48333 100644
--- a/src/python/test/test_weighted_rips.py
+++ b/src/python/test/test_weighted_rips_complex.py