1 files changed, 140 insertions, 0 deletions
diff --git a/matching/include/bifiltration.h b/matching/include/bifiltration.h
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+++ b/matching/include/bifiltration.h
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+#ifndef MATCHING_DISTANCE_BIFILTRATION_H
+#define MATCHING_DISTANCE_BIFILTRATION_H
+
+#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 SimplexVector = std::vector<Simplex<Real>>;
+
+        Bifiltration() = default;
+
+        Bifiltration(const Bifiltration&) = default;
+
+        Bifiltration(Bifiltration&&) = default;
+
+        Bifiltration& operator=(const Bifiltration& other)& = default;
+
+        Bifiltration& operator=(Bifiltration&& other) = default;
+
+        Bifiltration(const std::string& fname); // read from file
+
+        template<class Iter>
+        Bifiltration(Iter begin, Iter end)
+                : simplices_(begin, end)
+        {
+            init();
+        }
+
+        Diagram<Real> weighted_slice_diagram(const DualPoint<Real>& line, int dim) const;
+
+        SimplexVector simplices() const { return simplices_; }
+
+        // translate all points by vector (a,a)
+        void translate(Real a);
+
+        // return minimal value of x- and y-coordinates
+        // among all simplices
+        Real minimal_coordinate() const;
+
+        // return box that contains positions of all simplices
+        Box<Real> bounding_box() const;
+
+        void sanity_check() const;
+
+        int maximal_dim() const { return maximal_dim_; }
+
+        Real max_x() const;
+
+        Real max_y() const;
+
+        Real min_x() const;
+
+        Real min_y() const;
+
+        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
+
+        void scale(Real lambda);
+
+    private:
+        SimplexVector simplices_;
+
+        Box<Real> bounding_box_;
+        int maximal_dim_ {-1};
+
+        void init();
+
+        void rivet_format_reader(std::ifstream&);
+
+        void phat_like_format_reader(std::ifstream&);
+
+        // in Rene format each simplex knows IDs of its boundary facets
+        // postprocess_phat_like_format fills vector of IDs of boundary facets
+        // in each simplex
+        void postprocess_phat_like_format();
+
+        // in Rivet format each simplex knows its vertices,
+        // postprocess_rivet_format fills vector of IDs of boundary facets
+        // in each simplex
+        void postprocess_rivet_format();
+
+    };
+
+    template<class Real>
+    std::ostream& operator<<(std::ostream& os, const Bifiltration<Real>& bif);
+
+    template<class Real>
+    class BifiltrationProxy {
+    public:
+        BifiltrationProxy(const Bifiltration<Real>& bif, int dim = 0);
+        // return critical values of simplices that are important for current dimension (dim and dim+1)
+        PointVec<Real> positions() const;
+        // set current dimension
+        int set_dim(int new_dim);
+
+        // wrappers of Bifiltration
+        int maximal_dim() const;
+        void translate(Real a);
+        Real minimal_coordinate() const;
+        Box<Real> bounding_box() const;
+        Real max_x() const;
+        Real max_y() const;
+        Real min_x() const;
+        Real min_y() const;
+        Diagram<Real> weighted_slice_diagram(const DualPoint<Real>& slice) const;
+
+    private:
+        int dim_ { 0 };
+        mutable PointVec<Real> cached_positions_;
+        Bifiltration<Real> bif_;
+
+        void cache_positions() const;
+    };
+}
+
+#include "bifiltration.hpp"
+
+#endif //MATCHING_DISTANCE_BIFILTRATION_H