1 files changed, 28 insertions, 44 deletions

diff --git a/matching/include/bifiltration.h b/matching/include/bifiltration.h
index f505ed9..4dd8662 100644
--- a/matching/include/bifiltration.h
+++ b/matching/include/bifiltration.h
@@ -3,19 +3,30 @@
 
 #include <string>
 #include <ostream>
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <cassert>
 
 #include "common_util.h"
 #include "box.h"
 #include "simplex.h"
 #include "dual_point.h"
+#include "phat/boundary_matrix.h"
+#include "phat/compute_persistence_pairs.h"
+
+#include "spdlog/spdlog.h"
+#include "spdlog/fmt/fmt.h"
+#include "spdlog/fmt/ostr.h"
+
+#include "common_util.h"
 
 namespace md {
 
+    template<class Real>
     class Bifiltration {
     public:
-        using Diagram = std::vector<std::pair<Real, Real>>;
-        using Box = md::Box;
-        using SimplexVector = std::vector<Simplex>;
+        using SimplexVector = std::vector<Simplex<Real>>;
 
         Bifiltration() = default;
 
@@ -36,7 +47,7 @@ namespace md {
             init();
         }
 
-        Diagram weighted_slice_diagram(const DualPoint& line, int dim) const;
+        Diagram<Real> weighted_slice_diagram(const DualPoint<Real>& line, int dim) const;
 
         SimplexVector simplices() const { return simplices_; }
 
@@ -48,14 +59,12 @@ namespace md {
         Real minimal_coordinate() const;
 
         // return box that contains positions of all simplices
-        Box bounding_box() const;
+        Box<Real> bounding_box() const;
 
         void sanity_check() const;
 
         int maximal_dim() const { return maximal_dim_; }
 
-        friend std::ostream& operator<<(std::ostream& os, const Bifiltration& bif);
-
         Real max_x() const;
 
         Real max_y() const;
@@ -64,7 +73,7 @@ namespace md {
 
         Real min_y() const;
 
-        void add_simplex(Index _id, Point birth, int _dim, const Column& _bdry);
+        void add_simplex(Index _id, Point<Real> birth, int _dim, const Column& _bdry);
 
         void save(const std::string& filename, BifiltrationFormat format = BifiltrationFormat::rivet); // save to file
 
@@ -72,11 +81,8 @@ namespace md {
 
     private:
         SimplexVector simplices_;
-        // axes names, for rivet bifiltration format only
-        std::string parameter_1_name_ {"axis_1"};
-        std::string parameter_2_name_ {"axis_2"};
 
-        Box bounding_box_;
+        Box<Real> bounding_box_;
         int maximal_dim_ {-1};
 
         void init();
@@ -97,13 +103,15 @@ namespace md {
 
     };
 
-    std::ostream& operator<<(std::ostream& os, const Bifiltration& bif);
+    template<class Real>
+    std::ostream& operator<<(std::ostream& os, const Bifiltration<Real>& bif);
 
+    template<class Real>
     class BifiltrationProxy {
     public:
-        BifiltrationProxy(const Bifiltration& bif, int dim = 0);
+        BifiltrationProxy(const Bifiltration<Real>& bif, int dim = 0);
         // return critical values of simplices that are important for current dimension (dim and dim+1)
-        PointVec positions() const;
+        PointVec<Real> positions() const;
         // set current dimension
         int set_dim(int new_dim);
 
@@ -111,46 +119,22 @@ namespace md {
         int maximal_dim() const;
         void translate(Real a);
         Real minimal_coordinate() const;
-        Box bounding_box() const;
+        Box<Real> bounding_box() const;
         Real max_x() const;
         Real max_y() const;
         Real min_x() const;
         Real min_y() const;
-        Diagram weighted_slice_diagram(const DualPoint& slice) const;
+        Diagram<Real> weighted_slice_diagram(const DualPoint<Real>& slice) const;
 
     private:
         int dim_ { 0 };
-        mutable PointVec cached_positions_;
-        Bifiltration bif_;
+        mutable PointVec<Real> cached_positions_;
+        Bifiltration<Real> bif_;
 
         void cache_positions() const;
     };
 }
 
-
+#include "bifiltration.hpp"
 
 #endif //MATCHING_DISTANCE_BIFILTRATION_H
-
-//// The value type of OutputIterator is Simplex_in_2D_filtration
-//template<typename OutputIterator>
-//void read_input(std::string filename, OutputIterator out)
-//{
-//    std::ifstream ifstr;
-//    ifstr.open(filename.c_str());
-//    long n;
-//    ifstr >> n; // number of simplices is the first number in file
-//
-//    Index k;   // used in loop
-//    for (int i = 0; i < n; i++) {
-//        Simplex_in_2D_filtration next;
-//        next.index = i;
-//        ifstr >> next.dim >> next.pos.x >> next.pos.y;
-//        if (next.dim > 0) {
-//            for (int j = 0; j <= next.dim; j++) {
-//                ifstr >> k;
-//                next.bd.push_back(k);
-//            }
-//        }
-//        *out++ = next;
-//    }
-//}