Merge of last modifications on Nerve_GIC branch

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3923 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 785b87581429e8973b9660db0940b9dfb5d37827

2 files changed, 98 insertions, 20 deletions

diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index fea0b861..30f89d65 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -226,7 +226,25 @@ class Cover_complex {
   void set_mask(int nodemask) { mask = nodemask; }
 
  public:
-  /** \brief Reads and stores the input point cloud.
+
+
+  /** \brief Reads and stores the input point cloud from vector stored in memory.
+   *
+   * @param[in] cloud input vector representing the point cloud. Each row is a point and each coordinate is a vector.
+   *
+   */
+  template <class InputRange>
+  void set_point_cloud_from_range(InputRange const & cloud) {
+    n = cloud.size(); data_dimension = cloud[0].size(); point_cloud_name = "matrix";
+    for(int i = 0; i < n; i++){
+      point_cloud.emplace_back(cloud[i].begin(), cloud[i].begin() + data_dimension);
+      boost::add_vertex(one_skeleton_OFF);
+      vertices.push_back(boost::add_vertex(one_skeleton));
+      cover.emplace_back();
+    }
+  }
+
+  /** \brief Reads and stores the input point cloud from .(n)OFF file.
    *
    * @param[in] off_file_name name of the input .OFF or .nOFF file.
    *
@@ -371,6 +389,28 @@ class Cover_complex {
                  distances[index[boost::source(*ei, one_skeleton)]][index[boost::target(*ei, one_skeleton)]]);
   }
 
+ public:
+  /** \brief Reads and stores the distance matrices from vector stored in memory.
+   *
+   * @param[in] distance_matrix input vector representing the distance matrix.
+   *
+   */
+  template <class InputRange>
+  void set_distances_from_range(InputRange const & distance_matrix) {
+    if(point_cloud.size() == 0){
+      n = distance_matrix.size();
+      point_cloud_name = "matrix";
+      data_dimension = 0;
+      for(int i = 0; i < n; i++){
+        point_cloud.emplace_back();
+        boost::add_vertex(one_skeleton_OFF);
+        vertices.push_back(boost::add_vertex(one_skeleton));
+        cover.emplace_back();
+      }
+    }
+    distances = distance_matrix;
+  }
+
  public:  // Pairwise distances.
           /** \private \brief Computes all pairwise distances.
            */
@@ -500,9 +540,17 @@ class Cover_complex {
            *
            */
   void set_function_from_coordinate(int k) {
-    for (int i = 0; i < n; i++) func.push_back(point_cloud[i][k]);
-    functional_cover = true;
-    cover_name = "coordinate " + std::to_string(k);
+    if(point_cloud[0].size() > 0){
+      for (int i = 0; i < n; i++) func.push_back(point_cloud[i][k]);
+      functional_cover = true;
+      cover_name = "coordinate " + std::to_string(k);
+    }
+    else{
+      std::cout << "Only pairwise distances provided---cannot access " << k << "th coordinate; returning null vector instead" << std::endl;
+      for (int i = 0; i < n; i++) func.push_back(0.0);
+      functional_cover = true;
+      cover_name = "null";
+    }
   }
 
  public:  // Set function from vector.
@@ -953,9 +1001,17 @@ class Cover_complex {
            *
            */
   void set_color_from_coordinate(int k = 0) {
-    for (int i = 0; i < n; i++) func_color.push_back(point_cloud[i][k]);
-    color_name = "coordinate ";
-    color_name.append(std::to_string(k));
+    if(point_cloud[0].size() > 0){
+      for (int i = 0; i < n; i++) func_color.push_back(point_cloud[i][k]);
+      color_name = "coordinate ";
+      color_name.append(std::to_string(k));
+    }
+    else{
+      std::cout << "Only pairwise distances provided---cannot access " << k << "th coordinate; returning null vector instead" << std::endl;
+      for (int i = 0; i < n; i++) func.push_back(0.0);
+      functional_cover = true;
+      cover_name = "null";
+    }
   }
 
  public:  // Set color from vector.
@@ -964,7 +1020,7 @@ class Cover_complex {
    * @param[in] color input vector of values.
    *
    */
-  void set_color_from_vector(std::vector<double> color) {
+  void set_color_from_range(std::vector<double> color) {
     for (unsigned int i = 0; i < color.size(); i++) func_color.push_back(color[i]);
   }
 
@@ -1108,7 +1164,7 @@ class Cover_complex {
   /** \brief Computes the extended persistence diagram of the complex.
    *
    */
-  void compute_PD() {
+  Persistence_diagram compute_PD() {
     Simplex_tree st;
 
     // Compute max and min
@@ -1121,15 +1177,18 @@ class Cover_complex {
 
     // Build filtration
     for (auto const& simplex : simplices) {
-      std::vector<int> splx = simplex; splx.push_back(-2);
+      std::vector<int> splx = simplex;
+      splx.push_back(-2);
       st.insert_simplex_and_subfaces(splx, -3);
     }
 
     for (std::map<int, double>::iterator it = cover_std.begin(); it != cover_std.end(); it++) {
       int vertex = it->first; float val = it->second;
       int vert[] = {vertex}; int edge[] = {vertex, -2};
-      st.assign_filtration(st.find(vert), -2 + (val - minf)/(maxf - minf));
-      st.assign_filtration(st.find(edge),  2 - (val - minf)/(maxf - minf));
+      if(st.find(vert) != st.null_simplex()){
+        st.assign_filtration(st.find(vert), -2 + (val - minf)/(maxf - minf));
+        st.assign_filtration(st.find(edge),  2 - (val - minf)/(maxf - minf));
+      }
     }
     st.make_filtration_non_decreasing();
 
@@ -1159,6 +1218,7 @@ class Cover_complex {
         if (verbose) std::cout << "  [" << birth << ", " << death << "]" << std::endl;
       }
     }
+    return PD;
   }
 
  public:
@@ -1184,7 +1244,7 @@ class Cover_complex {
           Cboot.point_cloud.push_back(this->point_cloud[id]); Cboot.cover.emplace_back(); Cboot.func.push_back(this->func[id]);
           boost::add_vertex(Cboot.one_skeleton_OFF); Cboot.vertices.push_back(boost::add_vertex(Cboot.one_skeleton));
         }
-  Cboot.set_color_from_vector(Cboot.func);
+        Cboot.set_color_from_range(Cboot.func);
 
         for (int j = 0; j < n; j++) {
           std::vector<double> dist(n);
@@ -1230,7 +1290,7 @@ class Cover_complex {
     unsigned int N = distribution.size();
     double level = 1;
     for (unsigned int i = 0; i < N; i++)
-      if (distribution[i] > d){ level = i * 1.0 / N; break; }
+      if (distribution[i] >= d){ level = i * 1.0 / N; break; }
     if (verbose)  std::cout << "Confidence level of distance " << d << " is " << level << std::endl;
     return level;
   }
diff --git a/src/cython/cython/nerve_gic.pyx b/src/cython/cython/nerve_gic.pyx
index 30a14d3b..5f01b379 100644
--- a/src/cython/cython/nerve_gic.pyx
+++ b/src/cython/cython/nerve_gic.pyx
@@ -38,14 +38,14 @@ cdef extern from "Nerve_gic_interface.h" namespace "Gudhi":
         double compute_distance_from_confidence_level(double alpha)
         void compute_distribution(int N)
         double compute_p_value()
-        void compute_PD()
+        vector[pair[double, double]] compute_PD()
         void find_simplices()
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree)
         bool read_point_cloud(string off_file_name)
         double set_automatic_resolution()
         void set_color_from_coordinate(int k)
         void set_color_from_file(string color_file_name)
-        void set_color_from_vector(vector[double] color)
+        void set_color_from_range(vector[double] color)
         void set_cover_from_file(string cover_file_name)
         void set_cover_from_function()
         void set_cover_from_Euclidean_Voronoi(int m)
@@ -67,6 +67,8 @@ cdef extern from "Nerve_gic_interface.h" namespace "Gudhi":
         void write_info()
         void plot_DOT()
         void plot_OFF()
+        void set_point_cloud_from_range(vector[vector[double]] cloud)
+        void set_distances_from_range(vector[vector[double]] distance_matrix)
 
 # CoverComplex python interface
 cdef class CoverComplex:
@@ -102,6 +104,22 @@ cdef class CoverComplex:
          """
         return self.thisptr != NULL
 
+    def set_point_cloud_from_range(self, cloud):
+        """ Reads and stores the input point cloud from a vector stored in memory.
+
+        :param cloud: Input vector containing the point cloud.
+        :type cloud: vector[vector[double]]
+        """
+        return self.thisptr.set_point_cloud_from_range(cloud)
+
+    def set_distances_from_range(self, distance_matrix):
+        """ Reads and stores the input distance matrix from a vector stored in memory.
+
+        :param distance_matrix: Input vector containing the distance matrix.
+        :type distance_matrix: vector[vector[double]]
+        """
+        return self.thisptr.set_distances_from_range(distance_matrix)
+
     def compute_confidence_level_from_distance(self, distance):
         """Computes the confidence level of a specific bottleneck distance
         threshold.
@@ -145,7 +163,7 @@ cdef class CoverComplex:
     def compute_PD(self):
         """Computes the extended persistence diagram of the complex.
         """
-        self.thisptr.compute_PD()
+        return self.thisptr.compute_PD()
 
     def create_simplex_tree(self):
         """
@@ -162,7 +180,7 @@ cdef class CoverComplex:
         self.thisptr.find_simplices()
 
     def read_point_cloud(self, off_file):
-        """Reads and stores the input point cloud.
+        """Reads and stores the input point cloud from .(n)OFF file.
 
         :param off_file: Name of the input .OFF or .nOFF file.
         :type off_file: string
@@ -206,14 +224,14 @@ cdef class CoverComplex:
         else:
             print("file " + color_file_name + " not found.")
 
-    def set_color_from_vector(self, color):
+    def set_color_from_range(self, color):
         """Computes the function used to color the nodes of the simplicial
         complex from a vector stored in memory.
 
         :param color: Input vector of values.
         :type color: vector[double]
         """
-        self.thisptr.set_color_from_vector(color)
+        self.thisptr.set_color_from_range(color)
 
     def set_cover_from_file(self, cover_file_name):
         """Creates the cover C from a file containing the cover elements of