Fix euclidean distance for rips

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1610 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a07dfd4ffe3f17bf242ffb5b57058e99171a8016

11 files changed, 27 insertions, 23 deletions

diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index fa5bafc1..f7048c28 100644
--- a/src/GudhUI/utils/Persistence_compute.h
+++ b/src/GudhUI/utils/Persistence_compute.h
@@ -76,7 +76,7 @@ template<typename SkBlComplex> class Persistence_compute {
     using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
     using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
     
-    Rips_complex rips_complex(points, params.threshold, euclidean_distance<Point_t>);
+    Rips_complex rips_complex(points, params.threshold, euclidean_distance<Filtration_value, Point_t>);
 
     Simplex_tree st;
     if (rips_complex.create_complex(st, params.max_dim)) {
diff --git a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
index 99fcad41..a9eab5dd 100644
--- a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
@@ -33,7 +33,7 @@
 #include <vector>
 
 // Types definition
-using Simplex_tree = Gudhi::Simplex_tree</*Gudhi::Simplex_tree_options_fast_persistence*/>;
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = Simplex_tree::Filtration_value;
 using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
 using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
@@ -84,7 +84,7 @@ int main(int argc, char * argv[]) {
   // Compute the proximity graph of the points
   start = std::chrono::system_clock::now();
   Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
-                                      euclidean_distance<Point>);
+                                      euclidean_distance<Filtration_value, Point>);
   end = std::chrono::system_clock::now();
   elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
   std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n";
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index f4adc7a9..8e5c83a1 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -33,7 +33,7 @@
 #include <vector>
 
 // Types definition
-using Simplex_tree = Gudhi::Simplex_tree</*Gudhi::Simplex_tree_options_fast_persistence*/>;
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = Simplex_tree::Filtration_value;
 using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
 using Multi_field = Gudhi::persistent_cohomology::Multi_field;
@@ -63,7 +63,7 @@ int main(int argc, char * argv[]) {
 
   Points_off_reader off_reader(off_file_points);
   Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
-                                      euclidean_distance<Point>);
+                                      euclidean_distance<Filtration_value, Point>);
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree simplex_tree;
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index 97bab14c..b74d0094 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -34,7 +34,7 @@
 #include <limits>  // infinity
 
 // Types definition
-using Simplex_tree = Gudhi::Simplex_tree</*Gudhi::Simplex_tree_options_fast_persistence*/>;
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = Simplex_tree::Filtration_value;
 using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
 using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
@@ -62,7 +62,7 @@ int main(int argc, char * argv[]) {
 
   Points_off_reader off_reader(off_file_points);
   Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
-                                      euclidean_distance<Point>);
+                                      euclidean_distance<Filtration_value, Point>);
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree simplex_tree;
diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index 991ed4f0..ee6577f4 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -72,7 +72,7 @@ int main(int argc, char * argv[]) {
 
   Points_off_reader off_reader(off_file_points);
   Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
-                                      euclidean_distance<Point>);
+                                      euclidean_distance<Filtration_value, Point>);
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree& st = *new Simplex_tree;
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
index db41b425..2e63d9a6 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
@@ -23,8 +23,9 @@ int main(int argc, char **argv) {
 
   // Type definitions
   using Point = std::vector<double>;
-  using Simplex_tree = Gudhi::Simplex_tree<>;
-  using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>;
+  using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
 
   std::vector<Point> points;
   points.push_back({1.0, 1.0});
@@ -38,10 +39,10 @@ int main(int argc, char **argv) {
   // ----------------------------------------------------------------------------
   // Init of a rips complex from points
   // ----------------------------------------------------------------------------
-  Rips_complex rips_complex_from_file(points, threshold, euclidean_distance<Point>);
+  Rips_complex rips_complex_from_points(points, threshold, euclidean_distance<Filtration_value, Point>);
 
   Simplex_tree simplex;
-  if (rips_complex_from_file.create_complex(simplex, 1)) {
+  if (rips_complex_from_points.create_complex(simplex, 1)) {
     // ----------------------------------------------------------------------------
     // Display information about the one skeleton rips complex
     // ----------------------------------------------------------------------------
diff --git a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
index 82baa68e..60050cea 100644
--- a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
@@ -25,14 +25,15 @@ int main(int argc, char **argv) {
   // Type definitions
   using Point = std::vector<float>;
   using Simplex_tree = Gudhi::Simplex_tree<>;
-  using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
 
   // ----------------------------------------------------------------------------
   // Init of a rips complex from an OFF file
   // ----------------------------------------------------------------------------
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);
   Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold,
-                                      euclidean_distance<Point>);
+                                      euclidean_distance<Filtration_value, Point>);
 
   std::streambuf* streambufffer;
   std::ofstream ouput_file_stream;
diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
index 5f129160..f8be9748 100644
--- a/src/Rips_complex/test/test_rips_complex.cpp
+++ b/src/Rips_complex/test/test_rips_complex.cpp
@@ -40,6 +40,7 @@
 // Type definitions
 using Point = std::vector<double>;
 using Simplex_tree = Gudhi::Simplex_tree<>;
+using Filtration_value = Simplex_tree::Filtration_value;
 using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>;
 
 bool are_almost_the_same(float a, float b) {
@@ -58,7 +59,8 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
       rips_threshold << "==========" << std::endl;
 
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, euclidean_distance<Point>);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold,
+                                      euclidean_distance<Filtration_value, Point>);
 
   const int DIMENSION_1 = 1;
   Simplex_tree st;
@@ -87,10 +89,10 @@ BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
         std::cout << vertex << ",";
         vp.push_back(off_reader.get_point_cloud().at(vertex));
       }
-      std::cout << ") - distance =" << euclidean_distance(vp.at(0), vp.at(1)) <<
+      std::cout << ") - distance =" << euclidean_distance<double>(vp.at(0), vp.at(1)) <<
           " - filtration =" << st.filtration(f_simplex) << std::endl;
       BOOST_CHECK(vp.size() == 2);
-      BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), euclidean_distance(vp.at(0), vp.at(1))));
+      BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), euclidean_distance<double>(vp.at(0), vp.at(1))));
     }
   }
 
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
index df93155b..bcb89e00 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
@@ -77,7 +77,7 @@ namespace witness_complex {
       chosen_landmarks.push_back(curr_max_w);
       unsigned i = 0;
       for (auto& p : points) {
-        double curr_dist = euclidean_distance(p, *(std::begin(points) + chosen_landmarks[current_number_of_landmarks]));
+        double curr_dist = euclidean_distance<double>(p, *(std::begin(points) + chosen_landmarks[current_number_of_landmarks]));
         wit_land_dist[i].push_back(curr_dist);
         knn[i].push_back(current_number_of_landmarks);
         if (curr_dist < dist_to_L[i])
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
index ebf6aad1..b5aab9d5 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
@@ -78,7 +78,7 @@ namespace witness_complex {
       int landmarks_i = 0;
       for (landmarks_it = landmarks.begin(), landmarks_i = 0; landmarks_it != landmarks.end();
            ++landmarks_it, landmarks_i++) {
-        dist_i dist = std::make_pair(euclidean_distance(points[points_i], points[*landmarks_it]), landmarks_i);
+        dist_i dist = std::make_pair(euclidean_distance<double>(points[points_i], points[*landmarks_it]), landmarks_i);
         l_heap.push(dist);
       }
       for (int i = 0; i < dim + 1; i++) {
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index b2726ba8..006df275 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -28,13 +28,13 @@
 /* Compute the Euclidean distance between two Points given
  * by a range of coordinates. The points are assumed to have 
  * the same dimension. */
-template< typename Point >
-double euclidean_distance(const Point &p1,const Point &p2) {
-  double dist = 0.;
+template< typename Filtration_value, typename Point >
+Filtration_value euclidean_distance(const Point &p1,const Point &p2) {
+  Filtration_value dist = 0.;
   auto it1 = p1.begin();
   auto it2 = p2.begin();
   for (; it1 != p1.end(); ++it1, ++it2) {
-    double tmp = *it1 - *it2;
+    Filtration_value tmp = (double)(*it1) - (double)(*it2);
     dist += tmp*tmp;
   }
   return std::sqrt(dist);