small modif on PWGK

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3612 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c0b8c70acfbf1a7f4b7bddb69a161086fb249c76

3 files changed, 30 insertions, 20 deletions

diff --git a/src/cython/cython/kernels.pyx b/src/cython/cython/kernels.pyx
index 0cb296ec..cb8fc0fd 100644
--- a/src/cython/cython/kernels.pyx
+++ b/src/cython/cython/kernels.pyx
@@ -34,8 +34,8 @@ cdef extern from "Kernels_interface.h" namespace "Gudhi::persistence_diagram":
     vector[vector[double]] sw_matrix     (vector[vector[pair[double, double]]],  vector[vector[pair[double, double]]],  double, int)
     double                 pss           (vector[pair[double, double]],          vector[pair[double, double]],          double, int)
     vector[vector[double]] pss_matrix    (vector[vector[pair[double, double]]],  vector[vector[pair[double, double]]],  double, int)
-    double                 pwg           (vector[pair[double, double]],          vector[pair[double, double]],          double, int, double, double)
-    vector[vector[double]] pwg_matrix    (vector[vector[pair[double, double]]],  vector[vector[pair[double, double]]],  double, int, double, double)
+    double                 pwg           (vector[pair[double, double]],          vector[pair[double, double]],          int, string, double, double, double)
+    vector[vector[double]] pwg_matrix    (vector[vector[pair[double, double]]],  vector[vector[pair[double, double]]],  int, string, double, double, double)
 
 def sliced_wasserstein(diagram_1, diagram_2, sigma = 1, N = 100):
     """
@@ -65,37 +65,39 @@ def sliced_wasserstein_matrix(diagrams_1, diagrams_2, sigma = 1, N = 100):
     """
     return sw_matrix(diagrams_1, diagrams_2, sigma, N)
 
-def persistence_weighted_gaussian(diagram_1, diagram_2, sigma = 1, N = 100, C = 1, p = 1):
+def persistence_weighted_gaussian(diagram_1, diagram_2, N = 100, weight = "arctan", sigma = 1.0, C = 1.0, p = 1.0):
     """
 
     :param diagram_1: The first diagram.
     :type diagram_1: vector[pair[double, double]]
     :param diagram_2: The second diagram.
     :type diagram_2: vector[pair[double, double]]
-    :param sigma: bandwidth of Gaussian
     :param N: number of Fourier features
-    :param C: cost of persistence weight
-    :param p: power of persistence weight
+    :param weight: weight to use for the diagram points
+    :param sigma: bandwidth of Gaussian
+    :param C: cost of arctan persistence weight
+    :param p: power of arctan persistence weight
 
     :returns: the persistence weighted gaussian kernel.
     """
-    return pwg(diagram_1, diagram_2, sigma, N, C, p)
+    return pwg(diagram_1, diagram_2, N, weight, sigma, C, p)
 
-def persistence_weighted_gaussian_matrix(diagrams_1, diagrams_2, sigma = 1, N = 100, C = 1, p = 1):
+def persistence_weighted_gaussian_matrix(diagrams_1, diagrams_2, N = 100, weight = "arctan", sigma = 1.0, C = 1.0, p = 1.0):
     """
 
     :param diagram_1: The first set of diagrams.
     :type diagram_1: vector[vector[pair[double, double]]]
     :param diagram_2: The second set of diagrams.
     :type diagram_2: vector[vector[pair[double, double]]]
-    :param sigma: bandwidth of Gaussian
     :param N: number of Fourier features
-    :param C: cost of persistence weight
-    :param p: power of persistence weight
+    :param weight: weight to use for the diagram points
+    :param sigma: bandwidth of Gaussian
+    :param C: cost of arctan persistence weight
+    :param p: power of arctan persistence weight
 
     :returns: the persistence weighted gaussian kernel matrix.
     """
-    return pwg_matrix(diagrams_1, diagrams_2, sigma, N, C, p)
+    return pwg_matrix(diagrams_1, diagrams_2, N, weight, sigma, C, p)
 
 def persistence_scale_space(diagram_1, diagram_2, sigma = 1, N = 100):
     """
diff --git a/src/cython/cython/vectors.pyx b/src/cython/cython/vectors.pyx
index 42390ae6..af53f739 100644
--- a/src/cython/cython/vectors.pyx
+++ b/src/cython/cython/vectors.pyx
@@ -58,7 +58,10 @@ def persistence_image(diagram, min_x = 0.0, max_x = 1.0, res_x = 10, min_y = 0.0
     :param min_x: Minimum ordinate
     :param max_x: Maximum ordinate
     :param res_x: Number of ordinate pixels 
+    :param weight: Weight to use for the diagram points
     :param sigma: bandwidth of Gaussian
+    :param C: cost of arctan persistence weight
+    :param p: power of arctan persistence weight    
 
     :returns: the persistence image
     """
diff --git a/src/cython/include/Kernels_interface.h b/src/cython/include/Kernels_interface.h
index dd46656f..a07d7820 100644
--- a/src/cython/include/Kernels_interface.h
+++ b/src/cython/include/Kernels_interface.h
@@ -23,6 +23,7 @@
 #ifndef INCLUDE_KERNELS_INTERFACE_H_
 #define INCLUDE_KERNELS_INTERFACE_H_
 
+#include <gudhi/common_persistence_representations.h>
 #include <gudhi/Sliced_Wasserstein.h>
 #include <gudhi/Persistence_weighted_gaussian.h>
 #include <gudhi/Weight_functions.h>
@@ -46,9 +47,13 @@ namespace persistence_diagram {
     return sw1.compute_scalar_product(sw2);
   }
 
-  double pwg(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, double sigma, int N, double C, double p) {
-    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg1(diag1, sigma, N, Gudhi::Persistence_representations::arctan_weight(C,p));
-    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg2(diag2, sigma, N, Gudhi::Persistence_representations::arctan_weight(C,p));
+  double pwg(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, int N, std::string weight, double sigma, double C, double p) {
+    Gudhi::Persistence_representations::Weight weight_fn;
+    if(weight.compare("linear") == 0)  weight_fn = Gudhi::Persistence_representations::linear_weight;
+    if(weight.compare("arctan") == 0)  weight_fn = Gudhi::Persistence_representations::arctan_weight(C,p);
+    if(weight.compare("const")  == 0)  weight_fn = Gudhi::Persistence_representations::const_weight;
+    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg1(diag1, sigma, N, weight_fn);
+    Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg2(diag2, sigma, N, weight_fn);
     return pwg1.compute_scalar_product(pwg2);
   }
 
@@ -87,11 +92,11 @@ namespace persistence_diagram {
     return matrix;
   }
 
-  std::vector<std::vector<double> > pwg_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, double sigma, int N, double C, double p){
+  std::vector<std::vector<double> > pwg_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, int N, std::string weight,  double sigma, double C, double p){
     std::vector<std::vector<double> > matrix; int num_diag_1 = s1.size(); int num_diag_2 = s2.size();
     for(int i = 0; i < num_diag_1; i++){
       std::cout << 100.0*i/num_diag_1 << " %" << std::endl;
-      std::vector<double> ps; for(int j = 0; j < num_diag_2; j++) ps.push_back(pwg(s1[i], s2[j], sigma, N, C, p)); matrix.push_back(ps);
+      std::vector<double> ps; for(int j = 0; j < num_diag_2; j++) ps.push_back(pwg(s1[i], s2[j], N, weight, sigma, C, p)); matrix.push_back(ps);
     }
     return matrix;
   }
@@ -99,13 +104,13 @@ namespace persistence_diagram {
   std::vector<std::vector<double> > pss_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, double sigma, int N){
     std::vector<std::vector<std::pair<double, double> > > ss1, ss2; std::vector<std::vector<double> > matrix; int num_diag_1 = s1.size(); int num_diag_2 = s2.size();
     for(int i = 0; i < num_diag_1; i++){
-      std::vector<std::pair<double, double>> pd1 = s1[i]; int numpts = s1[i].size();    
+      std::vector<std::pair<double, double>> pd1 = s1[i]; int numpts = s1[i].size();
       for(int j = 0; j < numpts; j++)  pd1.emplace_back(s1[i][j].second,s1[i][j].first);
       ss1.push_back(pd1);
     }
-    
+
     for(int i = 0; i < num_diag_2; i++){
-      std::vector<std::pair<double, double>> pd2 = s2[i]; int numpts = s2[i].size();    
+      std::vector<std::pair<double, double>> pd2 = s2[i]; int numpts = s2[i].size();
       for(int j = 0; j < numpts; j++)  pd2.emplace_back(s2[i][j].second,s2[i][j].first);
       ss2.push_back(pd2);
     }