bug fixed, parameter name changed

3 files changed, 19 insertions, 15 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index cac4553a..4b87ed9b 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -57,6 +57,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'representations', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${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', ")
 
     add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
     add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
@@ -228,6 +229,7 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/representations" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/")
     file(COPY "gudhi/wasserstein.py" 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")
 
     add_custom_command(
         OUTPUT gudhi.so
diff --git a/src/python/gudhi/weighted_rips_complex.py b/src/python/gudhi/weighted_rips_complex.py
index 7d14ac65..9df2ddf9 100644
--- a/src/python/gudhi/weighted_rips_complex.py
+++ b/src/python/gudhi/weighted_rips_complex.py
@@ -1,6 +1,6 @@
 # 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):       Raphaël Tinarrage and Yuichi Ike
+# Author(s):       Raphaël Tinarrage, Yuichi Ike, Masatoshi Takenouchi
 #
 # Copyright (C) 2020 Inria, Copyright (C) 2020 FUjitsu Laboratories Ltd.
 #
@@ -12,23 +12,26 @@ from gudhi import SimplexTree
 class WeightedRipsComplex:
     """
     class to generate a weighted Rips complex 
-    from a distance matrix and filtration value
+    from a distance matrix and weights on vertices
     """
     def __init__(self, 
-                distance_matrix=None, 
-                filtration_values=None,
+                distance_matrix, 
+                weights=None,
                 max_filtration=float('inf')):
         """
         Parameters:
             distance_matrix: list of list of float,
                 distance matrix (full square or lower triangular)
             filtration_values: list of float,
-                flitration value for each index
+                weight for each vertex
             max_filtration: float,
                 specifies the maximal filtration value to be considered        
         """
         self.distance_matrix = distance_matrix
-        self.filtration_values = filtration_values
+        if weights is not None:
+            self.weights = weights
+        else:
+            self.weights = [0] * len(distance_matrix)
         self.max_filtration = max_filtration
             
     def create_simplex_tree(self, max_dimension):
@@ -38,7 +41,7 @@ class WeightedRipsComplex:
                 graph expansion until this given dimension
         """
         dist = self.distance_matrix
-        F = self.filtration_values
+        F = self.weights
         num_pts = len(dist)
         
         st = SimplexTree()
@@ -47,7 +50,7 @@ class WeightedRipsComplex:
             if F[i] < self.max_filtration:
                 st.insert([i], F[i])
         for i in range(num_pts):
-            for j in range(num_pts):
+            for j in range(i):
                 value = (dist[i][j] + F[i] + F[j]) / 2
                 if value < self.max_filtration:
                     st.insert([i,j], filtration=value)
diff --git a/src/python/test/test_weighted_rips.py b/src/python/test/test_weighted_rips.py
index f0db6798..7896fb78 100644
--- a/src/python/test/test_weighted_rips.py
+++ b/src/python/test/test_weighted_rips.py
@@ -1,6 +1,6 @@
 """ 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
+    Author(s):       Yuichi Ike and Masatoshi Takenouchi
 
     Copyright (C) 2020 Inria
 
@@ -10,18 +10,17 @@
 
 from gudhi.weighted_rips_complex import WeightedRipsComplex
 from gudhi.point_cloud.dtm import DTM
-import numpy
+import numpy as np
 from scipy.spatial.distance import cdist
 import pytest
 
 def test_dtm_rips_complex():
-    pts = numpy.array([[2.0, 2], [0, 1], [3, 4]])
+    pts = np.array([[2.0, 2], [0, 1], [3, 4]])
     dist = cdist(pts,pts)
     dtm = DTM(2, q=2, metric="precomputed")    
     r = dtm.fit_transform(dist)
-    w_rips = WeightedRipsComplex(distance_mattix=dist, filtration_values=r)
+    w_rips = WeightedRipsComplex(distance_mattix=dist, weights=r)
     st = w_rips.create_simplex_tree(max_dimension=2)
-    diag = st.persistence()
-    assert diag == [(0, (1.5811388300841898, float("inf"))), (0, (1.5811388300841898, 2.699172818834085)), (0, (1.5811388300841898, 2.699172818834085))]
+    persistence_intervals0 = st.persistence_intervals_in_dimension(0)
+    assert persistence_intervals0 == pytest.approx(np.array([[1.58113883, 2.69917282],[1.58113883, 2.69917282], [1.58113883, float("inf")]]))
     
-    
\ No newline at end of file