multipers 2.2.3__cp310-cp310-win_amd64.whl → 2.3.0__cp310-cp310-win_amd64.whl

multipers/gudhi/truc.h

@@ -1,888 +1,890 @@
-#pragma once
-#include "gudhi/Multi_persistence/Line.h"
-#include "multiparameter_module_approximation/format_python-cpp.h"
-#include <gudhi/One_critical_filtration.h>
-#include <gudhi/Multi_critical_filtration.h>
-#include <algorithm>
-#include <boost/mpl/aux_/na_fwd.hpp>
-#include <cassert>
-#include <cstddef>
-#include <cstdint>
-// #include <gudhi/Simplex_tree/multi_filtrations/Finitely_critical_filtrations.h>
-#include <iostream>
-#include <limits>
-#include <numeric>
-#include <oneapi/tbb/enumerable_thread_specific.h>
-#include <oneapi/tbb/parallel_for.h>
-#include <oneapi/tbb/task_group.h>
-#include <sstream>
-#include <string>
-#include <utility>
-#include <vector>
-#include <type_traits>  //std::invoke_result
-#include "scc_io.h"
-
-namespace Gudhi {
-namespace multiparameter {
-namespace truc_interface {
-using index_type = std::uint32_t;
-
-class PresentationStructure {
- public:
-  PresentationStructure() {}
-
-  /* SimplicialStructure &operator=(const SimplicialStructure &) = default; */
-
-  PresentationStructure(const std::vector<std::vector<index_type>> &generators,
-                        const std::vector<int> &generator_dimensions)
-      : generators(generators), generator_dimensions(generator_dimensions), num_vertices_(0) {
-    for (const auto &stuff : generator_dimensions) {
-      if (stuff == 0) num_vertices_++;
-    }
-    max_dimension_ = generator_dimensions.size() > 0
-                         ? *std::max_element(generator_dimensions.begin(), generator_dimensions.end())
-                         : 0;
-  };
-
-  PresentationStructure(const PresentationStructure &other)
-      : generators(other.generators),
-        generator_dimensions(other.generator_dimensions),
-        num_vertices_(other.num_vertices_),
-        max_dimension_(other.max_dimension_) {}
-
-  /* PresentationStructure &operator=(const PresentationStructure &other) { */
-  /*   generators = other.generators; */
-  /*   generator_dimensions = other.generator_dimensions; */
-  /*   num_vertices_ = other.num_vertices_; */
-  /*   max_dimension_ = other.max_dimension_; */
-  /**/
-  /*   return *this; */
-  /* } */
-
-  const std::vector<unsigned int> &operator[](std::size_t i) const {
-    return generators[i];
-  }  // needs to be iterable (begin, end, size)
-
-  std::vector<unsigned int> &operator[](std::size_t i) {
-    return generators[i];
-  }  // needs to be iterable (begin, end, size)
-
-  inline int dimension(std::size_t i) const { return generator_dimensions[i]; };
-
-  inline friend std::ostream &operator<<(std::ostream &stream, const PresentationStructure &structure) {
-    stream << "Boundary:\n";
-    stream << "{";
-    for (const auto &stuff : structure.generators) {
-      stream << "{";
-      for (auto truc : stuff) stream << truc << ", ";
-
-      if (!stuff.empty()) stream << "\b" << "\b ";
-
-      stream << "},\n";
-    }
-    stream << "}\n";
-    stream << "Degrees: (max " << structure.max_dimension() << ")\n";
-    stream << "{";
-    for (const auto &stuff : structure.generator_dimensions) stream << stuff << ", ";
-    if (structure.size() > 0) {
-      stream << "\b" << "\b";
-    }
-    stream << "}\n";
-    return stream;
-  }
-
-  inline void to_stream(std::ostream &stream, const std::vector<index_type> &order) {
-    for (const auto &i : order) {
-      const auto &stuff = this->operator[](i);
-      stream << i << " : [";
-      for (const auto &truc : stuff) stream << truc << ", ";
-      stream << "]\n";
-    }
-    /* return stream; */
-  }
-
-  inline std::size_t size() const { return generators.size(); };
-
-  unsigned int num_vertices() const { return num_vertices_; };
-
-  unsigned int max_dimension() const { return max_dimension_; }
-
-  int prune_above_dimension(int dim) {
-    int idx = std::lower_bound(generator_dimensions.begin(), generator_dimensions.end(), dim + 1) -
-              generator_dimensions.begin();
-    generators.resize(idx);
-    generator_dimensions.resize(idx);
-    max_dimension_ = generator_dimensions.size() ? generator_dimensions.back() : -1;
-    return idx;
-  }
-
- private:
-  std::vector<std::vector<index_type>> generators;
-  std::vector<int> generator_dimensions;
-  unsigned int num_vertices_;
-  int max_dimension_ = -1;
-};
-
-class SimplicialStructure {
- public:
-  template <typename SimplexTree>
-  void from_simplextree(SimplexTree &st) {
-    auto [filtration, boundary] = Gudhi::multiparameter::mma::simplextree_to_ordered_bf(st);
-    this->boundaries = boundary;
-    this->num_vertices_ = st.num_vertices();
-    this->max_dimension_ = st.dimension();
-  }
-
-  SimplicialStructure() {}
-
-  /* SimplicialStructure &operator=(const SimplicialStructure &) = default; */
-
-  SimplicialStructure(const std::vector<std::vector<index_type>> &boundaries,
-                      unsigned int num_vertices,
-                      unsigned int max_dimension)
-      : boundaries(boundaries), num_vertices_(num_vertices), max_dimension_(max_dimension) {
-
-        };
-
-  const std::vector<unsigned int> &operator[](std::size_t i) const {
-    return boundaries[i];
-  }  // needs to be iterable (begin, end, size)
-
-  std::vector<unsigned int> &operator[](std::size_t i) {
-    return boundaries[i];
-  }  // needs to be iterable (begin, end, size)
-
-  int dimension(std::size_t i) const { return boundaries[i].size() == 0 ? 0 : boundaries[i].size() - 1; };
-
-  inline friend std::ostream &operator<<(std::ostream &stream, const SimplicialStructure &structure) {
-    stream << "{";
-    for (const auto &stuff : structure.boundaries) {
-      stream << "{";
-      for (auto truc : stuff) stream << truc << ", ";
-
-      if (!stuff.empty()) stream << "\b" << "\b ";
-
-      stream << "},\n";
-    }
-    stream << "}\n";
-    return stream;
-  }
-
-  inline void to_stream(std::ostream &stream, const std::vector<index_type> &order) {
-    for (const auto &i : order) {
-      const auto &stuff = this->operator[](i);
-      stream << i << " : [";
-      for (const auto &truc : stuff) stream << truc << ", ";
-      stream << "]\n";
-    }
-    /* return stream; */
-  }
-
-  inline std::size_t size() const { return boundaries.size(); };
-
-  inline unsigned int num_vertices() const { return num_vertices_; }
-
-  inline unsigned int max_dimension() const { return max_dimension_; }
-
-  int prune_above_dimension(int dim) { throw; }
-
- private:
-  std::vector<std::vector<index_type>> boundaries;
-  unsigned int num_vertices_;
-  unsigned int max_dimension_;
-};
-
-template <class PersBackend, class Structure, class MultiFiltration>
-class Truc {
- public:
-  using Filtration_value = MultiFiltration;
-  using value_type = typename MultiFiltration::value_type;
-  using split_barcode =
-      std::vector<std::vector<std::pair<typename MultiFiltration::value_type, typename MultiFiltration::value_type>>>;
-  template <typename value_type = value_type>
-  using flat_barcode = std::vector<std::pair<int, std::pair<value_type, value_type>>>;
-
-  template <typename value_type = value_type>
-  using flat_nodim_barcode = std::vector<std::pair<value_type, value_type>>;
-
-  // CONSTRUCTORS.
-  //  - Need everything of the same size, generator order is a PERMUTATION
-  //
-  Truc(const Structure &structure, const std::vector<MultiFiltration> &generator_filtration_values)
-      : generator_filtration_values(generator_filtration_values),
-        generator_order(structure.size()),
-        structure(structure),
-        filtration_container(structure.size()) {
-    std::iota(generator_order.begin(), generator_order.end(), 0);  // range
-  };
-
-  template <class SimplexTree>
-  Truc(SimplexTree *simplextree) {
-    auto [filtration, boundary] = mma::simplextree_to_ordered_bf(*simplextree);
-    structure = SimplicialStructure(boundary, (*simplextree).num_vertices(), (*simplextree).dimension());
-    generator_filtration_values.resize(filtration.size());
-    for (auto i = 0u; i < filtration.size(); i++)
-      generator_filtration_values[i] = filtration[i];  // there is a copy here. TODO : deal with it.
-    generator_order = std::vector<index_type>(structure.size());
-    std::iota(generator_order.begin(), generator_order.end(), 0);  // range
-    filtration_container.resize(structure.size());
-  }
-
-  Truc(const std::vector<std::vector<index_type>> &generator_maps,
-       const std::vector<int> &generator_dimensions,
-       const std::vector<MultiFiltration> &generator_filtrations)
-      : generator_filtration_values(generator_filtrations),
-        generator_order(generator_filtrations.size(), 0),
-        structure(PresentationStructure(generator_maps, generator_dimensions)),
-        filtration_container(generator_filtrations.size()) {
-    std::iota(generator_order.begin(), generator_order.end(), 0);  // range
-  }
-
-  Truc() {};
-
-  Truc &operator=(const Truc &other) {
-    generator_filtration_values = other.generator_filtration_values;
-    generator_order = other.generator_order;
-    structure = other.structure;
-    persistence = other.persistence;
-    filtration_container = other.filtration_container;
-    persistence._update_permutation_ptr(generator_order);
-    return *this;
-  };
-
-  template <bool ignore_inf>
-  std::vector<std::pair<int, std::vector<index_type>>> get_current_boundary_matrix() {
-    std::vector<index_type> permutation(generator_order.size());
-    std::iota(permutation.begin(), permutation.end(), 0);
-    if constexpr (ignore_inf) {
-      permutation.erase(std::remove_if(permutation.begin(),
-                                       permutation.end(),
-                                       [&](std::size_t val) {
-                                         return filtration_container[val] == MultiFiltration::Generator::T_inf;
-                                       }),
-                        permutation.end());
-      std::sort(permutation.begin(), permutation.end());
-    }
-    std::sort(permutation.begin(), permutation.end(), [&](std::size_t i, std::size_t j) {
-      if (structure.dimension(i) > structure.dimension(j)) return false;
-      if (structure.dimension(i) < structure.dimension(j)) return true;
-      return filtration_container[i] < filtration_container[j];
-    });
-
-    std::vector<std::pair<int, std::vector<index_type>>> matrix(permutation.size());
-
-    std::vector<index_type> permutationInv(generator_order.size());
-    std::size_t newPos = 0;
-    for (std::size_t oldPos : permutation) {
-      permutationInv[oldPos] = newPos;
-      auto &boundary = matrix[newPos].second;
-      boundary.resize(structure[oldPos].size());
-      for (std::size_t j = 0; j < structure[oldPos].size(); ++j) {
-        boundary[j] = permutationInv[structure[oldPos][j]];
-      }
-      std::sort(boundary.begin(), boundary.end());
-      matrix[newPos].first = structure.dimension(oldPos);
-      ++newPos;
-    }
-
-    return matrix;
-  }
-
-  inline std::size_t num_generators() const { return structure.size(); }
-
-  inline std::size_t num_parameters() const {
-    return num_generators() == 0 ? 0 : this->generator_filtration_values[0].num_parameters();
-  }
-
-  inline const Structure &get_structure() const { return structure; }
-
-  template <class SubFiltration, bool original_order = true>
-  inline void push_to_out(const SubFiltration &f,
-                          std::vector<typename MultiFiltration::value_type> &filtration_container,
-                          const std::vector<index_type> &generator_order) const {
-    /* std::vector<NewFilrationType> out(this->num_generators()); */
-
-    // filtration_container.resize(
-    //     this->num_generators()); // for some reasons it is necessary FIXME
-    for (std::size_t i = 0u; i < this->num_generators(); i++) {
-      if constexpr (original_order) {
-        filtration_container[i] = f.compute_forward_intersection(generator_filtration_values[i]);
-      } else {
-        filtration_container[i] = f.compute_forward_intersection(generator_filtration_values[generator_order[i]]);
-      }
-    }
-  }
-
-  template <class SubFiltration, bool original_order = true>
-  inline void push_to(const SubFiltration &f) {
-    this->push_to_out<SubFiltration, original_order>(f, this->filtration_container, this->generator_order);
-  }
-
-  template <class array1d>
-  inline void set_one_filtration(const array1d &truc) {
-    assert(truc.size() == this->num_generators());
-    this->filtration_container = truc;
-  }
-
-  inline const std::vector<typename MultiFiltration::value_type> &get_one_filtration() const {
-    return this->filtration_container;
-  }
-
-  inline PersBackend compute_persistence_out(
-      const std::vector<typename MultiFiltration::value_type> &one_filtration,
-      std::vector<index_type> &out_gen_order, 
-      const bool ignore_inf) const {  // needed ftm as PersBackend only points there
-    constexpr const bool verbose = false;
-    if (one_filtration.size() != this->num_generators()) {
-      throw;
-    }
-    out_gen_order.resize(this->num_generators());
-    std::iota(out_gen_order.begin(),
-              out_gen_order.end(),
-              0);  // we have to reset here, even though we're already doing this
-    std::sort(out_gen_order.begin(), out_gen_order.end(), [&](index_type i, index_type j) {
-      if (structure.dimension(i) > structure.dimension(j)) return false;
-      if (structure.dimension(i) < structure.dimension(j)) return true;
-      return one_filtration[i] < one_filtration[j];
-    });
-    if (!PersBackend::is_vine && ignore_inf) {
-      if constexpr (verbose){
-        std::cout << "Removing infinite simplices" << std::endl;
-      }
-      for (auto &i : out_gen_order)
-        if (one_filtration[i] == MultiFiltration::Generator::T_inf) {
-          // TODO : later
-          // int d = structure.dimension(i);
-          // d = d == 0 ? 1 : 0;
-          // if (degrees.size()>d || degrees[d] || degrees[d-1])
-          //   continue;
-          i = std::numeric_limits<typename std::remove_reference_t<decltype(out_gen_order)>::value_type>::max();
-        }
-    }
-    if constexpr (false) {
-      std::cout << structure << std::endl;
-      std::cout << "[";
-      for (auto i : out_gen_order) {
-        std::cout << i << ", ";
-      }
-      std::cout << "]" << std::endl;
-      std::cout << "[";
-      for (auto i : one_filtration) {
-        std::cout << i << ",";
-      }
-      std::cout << "]" << std::endl;
-    }
-    return PersBackend(structure, out_gen_order);
-  }
-
-  inline const bool has_persistence() { return this->persistence.size(); };
-
-  inline void compute_persistence(const bool ignore_inf = true) {
-    this->persistence = this->compute_persistence_out(
-        // this->filtration_container, this->generator_order, degrees); // TODO
-        // : later
-        this->filtration_container,
-        this->generator_order,
-        ignore_inf);
-  };
-
-  // TODO : static ?
-  inline void vineyard_update(PersBackend &persistence,
-                              const std::vector<typename MultiFiltration::value_type> &one_filtration,
-                              std::vector<index_type> &generator_order) const {
-    constexpr const bool verbose = false;
-    /* static_assert(PersBackend::has_vine_update); */
-    // the first false is to get the generator order
-    // insertion sort
-    auto n = this->num_generators();
-    if constexpr (verbose) {
-      std::cout << "Vine updates : ";
-    }
-    for (std::size_t i = 0; i < n; i++) {
-      auto j = i;
-      while (j > 0 && persistence.get_dimension(j) == persistence.get_dimension(j - 1) &&
-             one_filtration[generator_order[j]] < one_filtration[generator_order[j - 1]]) {
-        if constexpr (verbose) {
-          std::cout << j - 1 << ", ";
-        }
-        persistence.vine_swap(j - 1);
-        std::swap(generator_order[j - 1], generator_order[j]);
-        j--;
-      }
-    }
-    if constexpr (verbose) {
-      std::cout << std::endl;
-    }
-  }
-
-  inline void vineyard_update() {
-    vineyard_update(this->persistence, this->filtration_container, this->generator_order);
-  }
-
-  inline split_barcode get_barcode(
-      PersBackend &persistence,
-      const std::vector<typename MultiFiltration::value_type> &filtration_container) const {
-    auto barcode_indices = persistence.get_barcode();
-    split_barcode out(this->structure.max_dimension() + 1);  // TODO : This doesn't allow for negative dimensions
-    constexpr const bool verbose = false;
-    constexpr const bool debug = false;
-    const auto inf = MultiFiltration::Generator::T_inf;
-    for (const auto &bar : barcode_indices) {
-      if constexpr (verbose) std::cout << "BAR : " << bar.birth << " " << bar.death << "\n";
-      if constexpr (debug) {
-        if (bar.birth >= filtration_container.size() || bar.birth < 0) {
-          std::cout << "Trying to add an incompatible birth... ";
-          std::cout << bar.birth << std::endl;
-          std::cout << "Death is " << bar.death << std::endl;
-          std::cout << "Max size is " << filtration_container.size() << std::endl;
-          continue;
-        }
-        if (bar.dim > static_cast<int>(this->structure.max_dimension())) {
-          std::cout << "Incompatible dimension detected... " << bar.dim << std::endl;
-          std::cout << "While max dim is " << this->structure.max_dimension() << std::endl;
-          continue;
-        }
-      }
-
-      auto birth_filtration = filtration_container[bar.birth];
-      auto death_filtration = inf;
-      if (bar.death != static_cast<typename PersBackend::pos_index>(-1))
-        death_filtration = filtration_container[bar.death];
-
-      if constexpr (verbose) {
-        std::cout << "BAR: " << bar.birth << "(" << birth_filtration << ")"
-                  << " --" << bar.death << "(" << death_filtration << ")"
-                  << " dim " << bar.dim << std::endl;
-      }
-      if (birth_filtration < death_filtration)
-        out[bar.dim].push_back({birth_filtration, death_filtration});
-      else {
-        out[bar.dim].push_back({inf, inf});
-      }
-    }
-    return out;
-  }
-
-  inline split_barcode get_barcode() { return get_barcode(this->persistence, this->filtration_container); }
-
-  template <typename value_type = value_type>
-  static inline flat_nodim_barcode<value_type> get_flat_nodim_barcode(
-      PersBackend &persistence,
-      std::vector<typename MultiFiltration::value_type> &filtration_container) {
-    constexpr const bool verbose = false;
-    const auto &barcode_indices = persistence.get_barcode();
-    auto num_bars = barcode_indices.size();
-    flat_nodim_barcode<value_type> out(num_bars);
-    if (num_bars <= 0) return out;
-    auto idx = 0u;
-    const value_type inf = MultiFiltration::Generator::T_inf;
-    for (const auto &bar : barcode_indices) {
-      value_type birth_filtration = inf;
-      value_type death_filtration = -birth_filtration;
-      if (bar.death == static_cast<typename PersBackend::pos_index>(-1))
-        death_filtration = inf;
-      else
-        death_filtration = static_cast<value_type>(filtration_container[bar.death]);
-      birth_filtration = static_cast<value_type>(filtration_container[bar.birth]);
-      if constexpr (verbose) {
-        std::cout << "PAIRING : " << bar.birth << " / " << bar.death << " dim " << bar.dim << std::endl;
-      }
-      if constexpr (verbose) {
-        std::cout << "PAIRING filtration : " << birth_filtration << " " << death_filtration << " dim " << bar.dim
-                  << std::endl;
-      }
-
-      if (birth_filtration < death_filtration)
-        out[idx] = {birth_filtration, death_filtration};
-      else {
-        out[idx] = {inf, inf};
-      }
-      idx++;
-    }
-    return out;
-  }
-
-  template <typename value_type = value_type>
-  static inline flat_barcode<value_type> get_flat_barcode(
-      PersBackend &persistence,
-      std::vector<typename MultiFiltration::value_type> &filtration_container) {
-    constexpr const bool verbose = false;
-    const auto &barcode_indices = persistence.get_barcode();
-    auto num_bars = barcode_indices.size();
-    flat_barcode<value_type> out(num_bars);
-    if (num_bars <= 0) return out;
-    auto idx = 0u;
-    const value_type inf = MultiFiltration::Generator::T_inf;
-    for (const auto &bar : barcode_indices) {
-      value_type birth_filtration = inf;
-      value_type death_filtration = -birth_filtration;
-      if (bar.death == static_cast<typename PersBackend::pos_index>(-1))
-        death_filtration = inf;
-      else
-        death_filtration = static_cast<value_type>(filtration_container[bar.death]);
-      birth_filtration = static_cast<value_type>(filtration_container[bar.birth]);
-      if constexpr (verbose) {
-        std::cout << "PAIRING : " << bar.birth << " / " << bar.death << " dim " << bar.dim << std::endl;
-      }
-      if constexpr (verbose) {
-        std::cout << "PAIRING filtration : " << birth_filtration << " " << death_filtration << " dim " << bar.dim
-                  << std::endl;
-      }
-
-      if (birth_filtration < death_filtration)
-        out[idx] = {bar.dim, {birth_filtration, death_filtration}};
-      else {
-        out[idx] = {bar.dim, {inf, inf}};
-      }
-      idx++;
-    }
-    return out;
-  }
-
-  template <typename value_type = value_type>
-  inline flat_barcode<value_type> get_flat_barcode() {
-    return get_flat_barcode(this->persistence, this->filtration_container);
-  }
-
-  template <typename value_type = value_type>
-  inline flat_nodim_barcode<value_type> get_flat_nodim_barcode() {
-    return get_flat_nodim_barcode(this->persistence, this->filtration_container);
-  }
-
-  inline friend std::ostream &operator<<(std::ostream &stream, Truc &truc) {
-    stream << "-------------------- Truc \n";
-    stream << "--- Structure \n";
-    stream << truc.structure;
-    /* stream << "-- Dimensions (max " << truc.structure.max_dimension() <<
-     * ")\n"; */
-    /* stream << "{"; */
-    /* for (auto i = 0u; i < truc.num_generators(); i++) */
-    /*   stream << truc.structure.dimension(i) << ", "; */
-    /* stream << "\b" */
-    /*        << "\b"; */
-    /* stream << "}" << std::endl; */
-    stream << "--- Order \n";
-    stream << "{";
-    for (const auto &idx : truc.generator_order) stream << idx << ", ";
-    stream << "}" << std::endl;
-
-    stream << "--- Current slice filtration\n";
-    stream << "{";
-    for (const auto &stuff : truc.filtration_container) stream << stuff << ", ";
-    stream << "\b" << "\b";
-    stream << "}" << std::endl;
-
-    stream << "--- Filtrations \n";
-    for (const auto &i : truc.generator_order) {
-      stream << i << " : ";
-      const auto &stuff = truc.generator_filtration_values[i];
-      stream << stuff << "\n";
-    }
-    stream << "--- PersBackend \n";
-    stream << truc.persistence;
-
-    return stream;
-  }
-
-  inline std::string to_str() {
-    std::stringstream stream;
-    stream << *this;
-    return stream.str();
-  }
-
-  inline std::pair<typename MultiFiltration::Generator, typename MultiFiltration::Generator> get_bounding_box() const {
-    using OC = typename MultiFiltration::Generator;
-    // assert(!generator_filtration_values.empty());
-    OC a = OC::inf();
-    OC b = -1 * a;
-    for (const auto &filtration_value : generator_filtration_values) {
-      if constexpr (MultiFiltration::is_multi_critical) {
-        a.pull_to_greatest_common_lower_bound(factorize_below(filtration_value));
-        b.push_to_least_common_upper_bound(factorize_above(filtration_value));
-      } else {
-        a.pull_to_greatest_common_lower_bound(filtration_value);
-        b.push_to_least_common_upper_bound(filtration_value);
-      }
-    }
-    return {a, b};
-  }
-
-  inline std::vector<typename MultiFiltration::Generator> get_filtration_values() const {
-    if constexpr (MultiFiltration::is_multi_critical) {
-      std::vector<typename MultiFiltration::Generator> out;
-      out.reserve(generator_filtration_values.size());  // at least this, will dooble later
-      for (std::size_t i = 0; i < generator_filtration_values.size(); ++i) {
-        for (const auto &f : generator_filtration_values[i]) {
-          out.push_back(f);
-        }
-      }
-      return out;
-    } else {
-      return generator_filtration_values;  // copy not necessary for Generator
-    }  // (could return const&)
-  }
-
-  inline std::vector<MultiFiltration> &get_filtrations() { return generator_filtration_values; }
-
-  inline const std::vector<MultiFiltration> &get_filtrations() const { return generator_filtration_values; }
-
-  inline const std::vector<int> get_dimensions() const {
-    std::size_t n = this->num_generators();
-    std::vector<int> out(n);
-    for (std::size_t i = 0; i < n; ++i) {
-      out[i] = structure.dimension(i);
-    }
-    return out;
-  }
-
-  inline void prune_above_dimension(int max_dim) {
-    int idx = structure.prune_above_dimension(max_dim);
-    generator_filtration_values.resize(idx);
-    generator_order.resize(idx);
-    filtration_container.resize(idx);
-  }
-
-  inline const std::vector<std::vector<index_type>> get_boundaries() {
-    std::size_t n = this->num_generators();
-    std::vector<std::vector<index_type>> out(n);
-    for (auto i = 0u; i < n; ++i) {
-      out[i] = this->structure[i];
-    }
-    return out;
-  }
-
-  auto coarsen_on_grid(const std::vector<std::vector<typename MultiFiltration::value_type>> grid) {
-    using return_type = decltype(std::declval<MultiFiltration>().template as_type<std::int32_t>());
-    std::vector<return_type> coords(this->num_generators());
-    for (std::size_t gen = 0u; gen < coords.size(); ++gen) {
-      coords[gen] = compute_coordinates_in_grid<int32_t>(generator_filtration_values[gen], grid);
-    }
-    return Truc<PersBackend, Structure, return_type>(structure, coords);
-  }
-
-  inline void coarsen_on_grid_inplace(const std::vector<std::vector<typename MultiFiltration::value_type>> &grid,
-                                      bool coordinate = true) {
-    for (auto gen = 0u; gen < this->num_generators(); ++gen) {
-      generator_filtration_values[gen].project_onto_grid(grid, coordinate);
-    }
-  }
-
-  // dim, num_cycle_of_dim, num_faces_in_cycle, vertices_in_face
-  inline std::vector<std::vector<std::vector<std::vector<index_type>>>> get_representative_cycles(
-      bool update = true,
-      bool detailed = false) {
-    // iterable iterable simplex key
-    auto cycles_key = persistence.get_representative_cycles(update, detailed);
-    auto num_cycles = cycles_key.size();
-    std::vector<std::vector<std::vector<std::vector<index_type>>>> out(structure.max_dimension() + 1);
-    for (auto &cycles_of_dim : out) cycles_of_dim.reserve(num_cycles);
-    for (const auto &cycle : cycles_key) {
-      int cycle_dim = 0;        // for more generality, should be minimal dimension instead
-      if (!cycle[0].empty()) {  // if empty, cycle has no border -> assumes dimension 0 even if it could be min dim
-        cycle_dim = structure.dimension(cycle[0][0]) + 1;  // all faces have the same dim
-      }
-      out[cycle_dim].push_back(cycle);
-    }
-    return out;
-  }
-
-  const std::vector<index_type> &get_current_order() const { return generator_order; }
-
-  const PersBackend &get_persistence() const { return persistence; }
-
-  PersBackend &get_persistence() { return persistence; }
-
-  // TrucThread get_safe_thread() { return TrucThread(*this); }
-
-  class TrucThread {
-   public:
-    using Filtration_value = MultiFiltration;
-    using value_type = typename MultiFiltration::value_type;
-    using ThreadSafe = TrucThread;
-
-    inline TrucThread(const Truc &truc)
-        : truc_ptr(&truc),
-          generator_order(truc.get_current_order()),
-          filtration_container(truc.get_one_filtration()),
-          persistence(truc.get_persistence()) {
-      persistence._update_permutation_ptr(generator_order);
-    };
-
-    inline TrucThread(const TrucThread &truc)
-        : truc_ptr(truc.truc_ptr),
-          generator_order(truc.get_current_order()),
-          filtration_container(truc.get_one_filtration()),
-          persistence(truc.get_persistence()) {
-      persistence._update_permutation_ptr(generator_order);
-    };
-
-    inline TrucThread weak_copy() const { return TrucThread(*truc_ptr); }
-
-    inline const bool has_persistence() { return this->persistence.size(); };
-
-    inline const PersBackend &get_persistence() const { return persistence; }
-
-    inline PersBackend &get_persistence() { return persistence; }
-
-    inline std::pair<MultiFiltration, MultiFiltration> get_bounding_box() const { return truc_ptr->get_bounding_box(); }
-
-    inline const std::vector<index_type> &get_current_order() const { return generator_order; }
-
-    inline const std::vector<MultiFiltration> &get_filtrations() const { return truc_ptr->get_filtrations(); }
-
-    inline const std::vector<int> &get_dimensions() const { return truc_ptr->get_dimensions(); }
-
-    inline const std::vector<std::vector<index_type>> &get_boundaries() const { return truc_ptr->get_boundaries(); }
-
-    inline void coarsen_on_grid_inplace(const std::vector<std::vector<typename MultiFiltration::value_type>> &grid,
-                                        bool coordinate = true) {
-      truc_ptr->coarsen_on_grid_inplace(grid, coordinate);
-    }
-
-    template <typename Subfiltration>
-    inline void push_to(const Subfiltration &f) {
-      truc_ptr->push_to_out(f, this->filtration_container, this->generator_order);
-    }
-
-    inline std::vector<typename PersBackend::cycle_type> get_representative_cycles(bool update = true) {
-      return truc_ptr->get_representative_cycles(update);
-    }
-
-    inline void compute_persistence(const bool ignore_inf=true) {
-      this->persistence =
-          this->truc_ptr->compute_persistence_out(this->filtration_container, this->generator_order, ignore_inf);
-    };
-
-    inline void vineyard_update() {
-      truc_ptr->vineyard_update(this->persistence, this->filtration_container, this->generator_order);
-    }
-
-    template <typename value_type = value_type>
-    inline flat_barcode<value_type> get_flat_barcode() {
-      return truc_ptr->get_flat_barcode(this->persistence, this->filtration_container);
-    }
-
-    template <typename value_type = value_type>
-    inline flat_nodim_barcode<value_type> get_flat_nodim_barcode() {
-      return truc_ptr->get_flat_nodim_barcode(this->persistence, this->filtration_container);
-    }
-
-    inline split_barcode get_barcode() { return truc_ptr->get_barcode(this->persistence, this->filtration_container); }
-
-    inline std::size_t num_generators() const { return this->truc_ptr->structure.size(); }
-
-    inline std::size_t num_parameters() const {
-      return num_generators() == 0 ? 0 : this->get_filtrations()[0].num_parameters();
-    }
-
-    inline const std::vector<typename MultiFiltration::value_type> &get_one_filtration() const {
-      return this->filtration_container;
-    }
-
-    inline std::vector<typename MultiFiltration::value_type> &get_one_filtration() {
-      return this->filtration_container;
-    }
-
-   private:
-    const Truc *truc_ptr;
-    std::vector<index_type> generator_order;                                 // size fixed at construction time,
-    std::vector<typename MultiFiltration::value_type> filtration_container;  // filtration of the current slice
-    PersBackend persistence;  // generated by the structure, and generator_order.
-
-  };  // class TrucThread
-
-  /*
-   * returns barcodes of the f(multipers)
-   *
-   */
-  template <typename Fun, typename Fun_arg>
-  inline std::vector<split_barcode> barcodes(Fun &&f, const std::vector<Fun_arg> &args, const bool ignore_inf = true) {
-    if (args.size() == 0) {
-      return {};
-    }
-    std::vector<split_barcode> out(args.size());
-
-    if constexpr (PersBackend::is_vine) {
-      this->push_to(f(args[0]));
-      this->compute_persistence();
-      out[0] = this->get_barcode();
-      for (auto i = 1u; i < args.size(); ++i) {
-        this->push_to(f(args[i]));
-        this->vineyard_update();
-        out[i] = this->get_barcode();
-      }
-
-    } else {
-      ThreadSafe local_template = this->weak_copy();
-      tbb::enumerable_thread_specific<ThreadSafe> thread_locals(local_template);
-      tbb::parallel_for(static_cast<std::size_t>(0), args.size(), [&](const std::size_t &i) {
-        ThreadSafe &s = thread_locals.local();
-        s.push_to(f(args[i]));
-        s.compute_persistence(ignore_inf);
-        out[i] = s.get_barcode();
-      });
-    }
-    return out;
-  }
-
-  // FOR Python interface, but I'm not fan. Todo: do the lambda function in
-  // cython?
-  inline std::vector<split_barcode> persistence_on_lines(const std::vector<std::vector<value_type>> &basepoints) {
-    return barcodes(
-        [](const std::vector<value_type> &basepoint) { return Gudhi::multi_persistence::Line<value_type>(basepoint); },
-        basepoints);
-  }
-
-  inline std::vector<split_barcode> persistence_on_lines(
-      const std::vector<std::pair<std::vector<value_type>, std::vector<value_type>>> &bp_dirs) {
-    return barcodes(
-        [](const std::pair<std::vector<value_type>, std::vector<value_type>> &bpdir) {
-          return Gudhi::multi_persistence::Line<value_type>(bpdir.first, bpdir.second);
-        },
-        bp_dirs);
-  }
-
-  void build_from_scc_file(const std::string &inFilePath,
-                           bool isRivetCompatible = false,
-                           bool isReversed = false,
-                           int shiftDimensions = 0) {
-    *this = read_scc_file<Truc>(inFilePath, isRivetCompatible, isReversed, shiftDimensions);
-  }
-
-  void write_to_scc_file(const std::string &outFilePath,
-                         int numberOfParameters = -1,
-                         int degree = -1,
-                         bool rivetCompatible = false,
-                         bool IgnoreLastGenerators = false,
-                         bool stripComments = false,
-                         bool reverse = false) {
-    write_scc_file<Truc>(
-        outFilePath, *this, numberOfParameters, degree, rivetCompatible, IgnoreLastGenerators, stripComments, reverse);
-  }
-
- public:
-  using ThreadSafe = TrucThread;  // for outside
-
-  TrucThread weak_copy() const { return TrucThread(*this); }
-
-  // TODO: declare method here instead of scc_io.h
-  // it is just temporary, until Truc is cleaned up
-  // friend void write_scc_file<Truc>(const std::string &outFilePath,
-  //                                  const Truc &slicer,
-  //                                  int numberOfParameters,
-  //                                  int degree,
-  //                                  bool rivetCompatible,
-  //                                  bool IgnoreLastGenerators,
-  //                                  bool stripComments,
-  //                                  bool reverse);
-
- private:
-  std::vector<MultiFiltration> generator_filtration_values;  // defined at construction time. Const
-  std::vector<index_type> generator_order;  // size fixed at construction time, // TODO : CHANGE THAT TO UINT32
-  Structure structure;                      // defined at construction time. Const
-  std::vector<typename MultiFiltration::value_type> filtration_container;  // filtration of the current slice
-  PersBackend persistence;  // generated by the structure, and generator_order.
-
-};  // class Truc
-
-}}}  // namespace Gudhi::multiparameter::interface
+#pragma once
+#include "gudhi/Multi_persistence/Line.h"
+#include "multiparameter_module_approximation/format_python-cpp.h"
+#include <gudhi/One_critical_filtration.h>
+#include <gudhi/Multi_critical_filtration.h>
+#include <algorithm>
+#include <boost/mpl/aux_/na_fwd.hpp>
+#include <cassert>
+#include <cstddef>
+#include <cstdint>
+// #include <gudhi/Simplex_tree/multi_filtrations/Finitely_critical_filtrations.h>
+#include <iostream>
+#include <limits>
+#include <numeric>
+#include <oneapi/tbb/enumerable_thread_specific.h>
+#include <oneapi/tbb/parallel_for.h>
+#include <oneapi/tbb/task_group.h>
+#include <sstream>
+#include <string>
+#include <utility>
+#include <vector>
+#include <type_traits>  //std::invoke_result
+#include "scc_io.h"
+
+namespace Gudhi {
+namespace multiparameter {
+namespace truc_interface {
+using index_type = std::uint32_t;
+
+class PresentationStructure {
+ public:
+  PresentationStructure() {}
+
+  /* SimplicialStructure &operator=(const SimplicialStructure &) = default; */
+
+  PresentationStructure(const std::vector<std::vector<index_type>> &generators,
+                        const std::vector<int> &generator_dimensions)
+      : generators(generators), generator_dimensions(generator_dimensions), num_vertices_(0) {
+    for (const auto &stuff : generator_dimensions) {
+      if (stuff == 0) num_vertices_++;
+    }
+    max_dimension_ = generator_dimensions.size() > 0
+                         ? *std::max_element(generator_dimensions.begin(), generator_dimensions.end())
+                         : 0;
+  };
+
+  PresentationStructure(const PresentationStructure &other)
+      : generators(other.generators),
+        generator_dimensions(other.generator_dimensions),
+        num_vertices_(other.num_vertices_),
+        max_dimension_(other.max_dimension_) {}
+
+  /* PresentationStructure &operator=(const PresentationStructure &other) { */
+  /*   generators = other.generators; */
+  /*   generator_dimensions = other.generator_dimensions; */
+  /*   num_vertices_ = other.num_vertices_; */
+  /*   max_dimension_ = other.max_dimension_; */
+  /**/
+  /*   return *this; */
+  /* } */
+
+  const std::vector<unsigned int> &operator[](std::size_t i) const {
+    return generators[i];
+  }  // needs to be iterable (begin, end, size)
+
+  std::vector<unsigned int> &operator[](std::size_t i) {
+    return generators[i];
+  }  // needs to be iterable (begin, end, size)
+
+  inline int dimension(std::size_t i) const { return generator_dimensions[i]; };
+
+  inline friend std::ostream &operator<<(std::ostream &stream, const PresentationStructure &structure) {
+    stream << "Boundary:\n";
+    stream << "{";
+    for (const auto &stuff : structure.generators) {
+      stream << "{";
+      for (auto truc : stuff) stream << truc << ", ";
+
+      if (!stuff.empty()) stream << "\b" << "\b ";
+
+      stream << "},\n";
+    }
+    stream << "}\n";
+    stream << "Degrees: (max " << structure.max_dimension() << ")\n";
+    stream << "{";
+    for (const auto &stuff : structure.generator_dimensions) stream << stuff << ", ";
+    if (structure.size() > 0) {
+      stream << "\b" << "\b";
+    }
+    stream << "}\n";
+    return stream;
+  }
+
+  inline void to_stream(std::ostream &stream, const std::vector<index_type> &order) {
+    for (const auto &i : order) {
+      const auto &stuff = this->operator[](i);
+      stream << i << " : [";
+      for (const auto &truc : stuff) stream << truc << ", ";
+      stream << "]\n";
+    }
+    /* return stream; */
+  }
+
+  inline std::size_t size() const { return generators.size(); };
+
+  unsigned int num_vertices() const { return num_vertices_; };
+
+  unsigned int max_dimension() const { return max_dimension_; }
+
+  int prune_above_dimension(int dim) {
+    int idx = std::lower_bound(generator_dimensions.begin(), generator_dimensions.end(), dim + 1) -
+              generator_dimensions.begin();
+    generators.resize(idx);
+    generator_dimensions.resize(idx);
+    max_dimension_ = generator_dimensions.size() ? generator_dimensions.back() : -1;
+    return idx;
+  }
+
+ private:
+  std::vector<std::vector<index_type>> generators;
+  std::vector<int> generator_dimensions;
+  unsigned int num_vertices_;
+  int max_dimension_ = -1;
+};
+
+class SimplicialStructure {
+ public:
+  template <typename SimplexTree>
+  void from_simplextree(SimplexTree &st) {
+    auto [filtration, boundary] = Gudhi::multiparameter::mma::simplextree_to_ordered_bf(st);
+    this->boundaries = boundary;
+    this->num_vertices_ = st.num_vertices();
+    this->max_dimension_ = st.dimension();
+  }
+
+  SimplicialStructure() {}
+
+  /* SimplicialStructure &operator=(const SimplicialStructure &) = default; */
+
+  SimplicialStructure(const std::vector<std::vector<index_type>> &boundaries,
+                      unsigned int num_vertices,
+                      unsigned int max_dimension)
+      : boundaries(boundaries), num_vertices_(num_vertices), max_dimension_(max_dimension) {
+
+        };
+
+  const std::vector<unsigned int> &operator[](std::size_t i) const {
+    return boundaries[i];
+  }  // needs to be iterable (begin, end, size)
+
+  std::vector<unsigned int> &operator[](std::size_t i) {
+    return boundaries[i];
+  }  // needs to be iterable (begin, end, size)
+
+  int dimension(std::size_t i) const { return boundaries[i].size() == 0 ? 0 : boundaries[i].size() - 1; };
+
+  inline friend std::ostream &operator<<(std::ostream &stream, const SimplicialStructure &structure) {
+    stream << "{";
+    for (const auto &stuff : structure.boundaries) {
+      stream << "{";
+      for (auto truc : stuff) stream << truc << ", ";
+
+      if (!stuff.empty()) stream << "\b" << "\b ";
+
+      stream << "},\n";
+    }
+    stream << "}\n";
+    return stream;
+  }
+
+  inline void to_stream(std::ostream &stream, const std::vector<index_type> &order) {
+    for (const auto &i : order) {
+      const auto &stuff = this->operator[](i);
+      stream << i << " : [";
+      for (const auto &truc : stuff) stream << truc << ", ";
+      stream << "]\n";
+    }
+    /* return stream; */
+  }
+
+  inline std::size_t size() const { return boundaries.size(); };
+
+  inline unsigned int num_vertices() const { return num_vertices_; }
+
+  inline unsigned int max_dimension() const { return max_dimension_; }
+
+  int prune_above_dimension(int dim) { throw; }
+
+ private:
+  std::vector<std::vector<index_type>> boundaries;
+  unsigned int num_vertices_;
+  unsigned int max_dimension_;
+};
+
+template <class PersBackend, class Structure, class MultiFiltration>
+class Truc {
+ public:
+  using Filtration_value = MultiFiltration;
+  using value_type = typename MultiFiltration::value_type;
+  using split_barcode =
+      std::vector<std::vector<std::pair<typename MultiFiltration::value_type, typename MultiFiltration::value_type>>>;
+  template <typename value_type = value_type>
+  using flat_barcode = std::vector<std::pair<int, std::pair<value_type, value_type>>>;
+
+  template <typename value_type = value_type>
+  using flat_nodim_barcode = std::vector<std::pair<value_type, value_type>>;
+
+  // CONSTRUCTORS.
+  //  - Need everything of the same size, generator order is a PERMUTATION
+  //
+  Truc(const Structure &structure, const std::vector<MultiFiltration> &generator_filtration_values)
+      : generator_filtration_values(generator_filtration_values),
+        generator_order(structure.size()),
+        structure(structure),
+        filtration_container(structure.size()) {
+    std::iota(generator_order.begin(), generator_order.end(), 0);  // range
+  };
+
+  template <class SimplexTree>
+  Truc(SimplexTree *simplextree) {
+    auto [filtration, boundary] = mma::simplextree_to_ordered_bf(*simplextree);
+    structure = SimplicialStructure(boundary, (*simplextree).num_vertices(), (*simplextree).dimension());
+    generator_filtration_values.resize(filtration.size());
+    for (auto i = 0u; i < filtration.size(); i++)
+      generator_filtration_values[i] = filtration[i];  // there is a copy here. TODO : deal with it.
+    generator_order = std::vector<index_type>(structure.size());
+    std::iota(generator_order.begin(), generator_order.end(), 0);  // range
+    filtration_container.resize(structure.size());
+  }
+
+  Truc(const std::vector<std::vector<index_type>> &generator_maps,
+       const std::vector<int> &generator_dimensions,
+       const std::vector<MultiFiltration> &generator_filtrations)
+      : generator_filtration_values(generator_filtrations),
+        generator_order(generator_filtrations.size(), 0),
+        structure(PresentationStructure(generator_maps, generator_dimensions)),
+        filtration_container(generator_filtrations.size()) {
+    std::iota(generator_order.begin(), generator_order.end(), 0);  // range
+  }
+
+  Truc() {};
+
+  Truc &operator=(const Truc &other) {
+    generator_filtration_values = other.generator_filtration_values;
+    generator_order = other.generator_order;
+    structure = other.structure;
+    persistence = other.persistence;
+    filtration_container = other.filtration_container;
+    persistence._update_permutation_ptr(generator_order);
+    return *this;
+  };
+
+  template <bool ignore_inf>
+  std::vector<std::pair<int, std::vector<index_type>>> get_current_boundary_matrix() {
+    std::vector<index_type> permutation(generator_order.size());
+    std::iota(permutation.begin(), permutation.end(), 0);
+    if constexpr (ignore_inf) {
+      permutation.erase(std::remove_if(permutation.begin(),
+                                       permutation.end(),
+                                       [&](std::size_t val) {
+                                         return filtration_container[val] == MultiFiltration::Generator::T_inf;
+                                       }),
+                        permutation.end());
+      std::sort(permutation.begin(), permutation.end());
+    }
+    std::sort(permutation.begin(), permutation.end(), [&](std::size_t i, std::size_t j) {
+      if (structure.dimension(i) > structure.dimension(j)) return false;
+      if (structure.dimension(i) < structure.dimension(j)) return true;
+      return filtration_container[i] < filtration_container[j];
+    });
+
+    std::vector<std::pair<int, std::vector<index_type>>> matrix(permutation.size());
+
+    std::vector<index_type> permutationInv(generator_order.size());
+    std::size_t newPos = 0;
+    for (std::size_t oldPos : permutation) {
+      permutationInv[oldPos] = newPos;
+      auto &boundary = matrix[newPos].second;
+      boundary.resize(structure[oldPos].size());
+      for (std::size_t j = 0; j < structure[oldPos].size(); ++j) {
+        boundary[j] = permutationInv[structure[oldPos][j]];
+      }
+      std::sort(boundary.begin(), boundary.end());
+      matrix[newPos].first = structure.dimension(oldPos);
+      ++newPos;
+    }
+
+    return matrix;
+  }
+
+  inline std::size_t num_generators() const { return structure.size(); }
+
+  inline std::size_t num_parameters() const {
+    return num_generators() == 0 ? 0 : this->generator_filtration_values[0].num_parameters();
+  }
+
+  inline const Structure &get_structure() const { return structure; }
+
+  template <class SubFiltration, bool original_order = true>
+  inline void push_to_out(const SubFiltration &f,
+                          std::vector<typename MultiFiltration::value_type> &filtration_container,
+                          const std::vector<index_type> &generator_order) const {
+    /* std::vector<NewFilrationType> out(this->num_generators()); */
+
+    // filtration_container.resize(
+    //     this->num_generators()); // for some reasons it is necessary FIXME
+    for (std::size_t i = 0u; i < this->num_generators(); i++) {
+      if constexpr (original_order) {
+        filtration_container[i] = f.compute_forward_intersection(generator_filtration_values[i]);
+      } else {
+        filtration_container[i] = f.compute_forward_intersection(generator_filtration_values[generator_order[i]]);
+      }
+    }
+  }
+
+  template <class SubFiltration, bool original_order = true>
+  inline void push_to(const SubFiltration &f) {
+    this->push_to_out<SubFiltration, original_order>(f, this->filtration_container, this->generator_order);
+  }
+
+  template <class array1d>
+  inline void set_one_filtration(const array1d &truc) {
+    assert(truc.size() == this->num_generators());
+    this->filtration_container = truc;
+  }
+
+  inline const std::vector<typename MultiFiltration::value_type> &get_one_filtration() const {
+    return this->filtration_container;
+  }
+
+  inline PersBackend compute_persistence_out(
+      const std::vector<typename MultiFiltration::value_type> &one_filtration,
+      std::vector<index_type> &out_gen_order,
+      const bool ignore_inf) const {  // needed ftm as PersBackend only points there
+    constexpr const bool verbose = false;
+    if (one_filtration.size() != this->num_generators()) {
+      throw;
+    }
+    out_gen_order.resize(this->num_generators());
+    std::iota(out_gen_order.begin(),
+              out_gen_order.end(),
+              0);  // we have to reset here, even though we're already doing this
+    std::sort(out_gen_order.begin(), out_gen_order.end(), [&](index_type i, index_type j) {
+      if (structure.dimension(i) > structure.dimension(j)) return false;
+      if (structure.dimension(i) < structure.dimension(j)) return true;
+      return one_filtration[i] < one_filtration[j];
+    });
+    if (!PersBackend::is_vine && ignore_inf) {
+      if constexpr (verbose) {
+        std::cout << "Removing infinite simplices" << std::endl;
+      }
+      for (auto &i : out_gen_order)
+        if (one_filtration[i] == MultiFiltration::Generator::T_inf) {
+          // TODO : later
+          // int d = structure.dimension(i);
+          // d = d == 0 ? 1 : 0;
+          // if (degrees.size()>d || degrees[d] || degrees[d-1])
+          //   continue;
+          i = std::numeric_limits<typename std::remove_reference_t<decltype(out_gen_order)>::value_type>::max();
+        }
+    }
+    if constexpr (false) {
+      std::cout << structure << std::endl;
+      std::cout << "[";
+      for (auto i : out_gen_order) {
+        std::cout << i << ", ";
+      }
+      std::cout << "]" << std::endl;
+      std::cout << "[";
+      for (auto i : one_filtration) {
+        std::cout << i << ",";
+      }
+      std::cout << "]" << std::endl;
+    }
+    return PersBackend(structure, out_gen_order);
+  }
+
+  inline const bool has_persistence() { return this->persistence.size(); };
+
+  inline void compute_persistence(const bool ignore_inf = true) {
+    this->persistence = this->compute_persistence_out(
+        // this->filtration_container, this->generator_order, degrees); // TODO
+        // : later
+        this->filtration_container,
+        this->generator_order,
+        ignore_inf);
+  };
+
+  // TODO : static ?
+  inline void vineyard_update(PersBackend &persistence,
+                              const std::vector<typename MultiFiltration::value_type> &one_filtration,
+                              std::vector<index_type> &generator_order) const {
+    constexpr const bool verbose = false;
+    /* static_assert(PersBackend::has_vine_update); */
+    // the first false is to get the generator order
+    // insertion sort
+    auto n = this->num_generators();
+    if constexpr (verbose) {
+      std::cout << "Vine updates : ";
+    }
+    for (std::size_t i = 0; i < n; i++) {
+      auto j = i;
+      while (j > 0 && persistence.get_dimension(j) == persistence.get_dimension(j - 1) &&
+             one_filtration[generator_order[j]] < one_filtration[generator_order[j - 1]]) {
+        if constexpr (verbose) {
+          std::cout << j - 1 << ", ";
+        }
+        persistence.vine_swap(j - 1);
+        std::swap(generator_order[j - 1], generator_order[j]);
+        j--;
+      }
+    }
+    if constexpr (verbose) {
+      std::cout << std::endl;
+    }
+  }
+
+  inline void vineyard_update() {
+    vineyard_update(this->persistence, this->filtration_container, this->generator_order);
+  }
+
+  inline split_barcode get_barcode(
+      PersBackend &persistence,
+      const std::vector<typename MultiFiltration::value_type> &filtration_container) const {
+    auto barcode_indices = persistence.get_barcode();
+    split_barcode out(this->structure.max_dimension() + 1);  // TODO : This doesn't allow for negative dimensions
+    constexpr const bool verbose = false;
+    constexpr const bool debug = false;
+    const auto inf = MultiFiltration::Generator::T_inf;
+    for (const auto &bar : barcode_indices) {
+      if constexpr (verbose) std::cout << "BAR : " << bar.birth << " " << bar.death << "\n";
+      if constexpr (debug) {
+        if (bar.birth >= filtration_container.size() || bar.birth < 0) {
+          std::cout << "Trying to add an incompatible birth... ";
+          std::cout << bar.birth << std::endl;
+          std::cout << "Death is " << bar.death << std::endl;
+          std::cout << "Max size is " << filtration_container.size() << std::endl;
+          continue;
+        }
+        if (bar.dim > static_cast<int>(this->structure.max_dimension())) {
+          std::cout << "Incompatible dimension detected... " << bar.dim << std::endl;
+          std::cout << "While max dim is " << this->structure.max_dimension() << std::endl;
+          continue;
+        }
+      }
+
+      auto birth_filtration = filtration_container[bar.birth];
+      auto death_filtration = inf;
+      if (bar.death != static_cast<typename PersBackend::pos_index>(-1))
+        death_filtration = filtration_container[bar.death];
+
+      if constexpr (verbose) {
+        std::cout << "BAR: " << bar.birth << "(" << birth_filtration << ")"
+                  << " --" << bar.death << "(" << death_filtration << ")"
+                  << " dim " << bar.dim << std::endl;
+      }
+      if (birth_filtration < death_filtration)
+        out[bar.dim].push_back({birth_filtration, death_filtration});
+      else {
+        out[bar.dim].push_back({inf, inf});
+      }
+    }
+    return out;
+  }
+
+  inline split_barcode get_barcode() { return get_barcode(this->persistence, this->filtration_container); }
+
+  template <typename value_type = value_type>
+  static inline flat_nodim_barcode<value_type> get_flat_nodim_barcode(
+      PersBackend &persistence,
+      std::vector<typename MultiFiltration::value_type> &filtration_container) {
+    constexpr const bool verbose = false;
+    const auto &barcode_indices = persistence.get_barcode();
+    auto num_bars = barcode_indices.size();
+    flat_nodim_barcode<value_type> out(num_bars);
+    if (num_bars <= 0) return out;
+    auto idx = 0u;
+    const value_type inf = MultiFiltration::Generator::T_inf;
+    for (const auto &bar : barcode_indices) {
+      value_type birth_filtration = inf;
+      value_type death_filtration = -birth_filtration;
+      if (bar.death == static_cast<typename PersBackend::pos_index>(-1))
+        death_filtration = inf;
+      else
+        death_filtration = static_cast<value_type>(filtration_container[bar.death]);
+      birth_filtration = static_cast<value_type>(filtration_container[bar.birth]);
+      if constexpr (verbose) {
+        std::cout << "PAIRING : " << bar.birth << " / " << bar.death << " dim " << bar.dim << std::endl;
+      }
+      if constexpr (verbose) {
+        std::cout << "PAIRING filtration : " << birth_filtration << " " << death_filtration << " dim " << bar.dim
+                  << std::endl;
+      }
+
+      if (birth_filtration < death_filtration)
+        out[idx] = {birth_filtration, death_filtration};
+      else {
+        out[idx] = {inf, inf};
+      }
+      idx++;
+    }
+    return out;
+  }
+
+  template <typename value_type = value_type>
+  static inline flat_barcode<value_type> get_flat_barcode(
+      PersBackend &persistence,
+      std::vector<typename MultiFiltration::value_type> &filtration_container) {
+    constexpr const bool verbose = false;
+    const auto &barcode_indices = persistence.get_barcode();
+    auto num_bars = barcode_indices.size();
+    flat_barcode<value_type> out(num_bars);
+    if (num_bars <= 0) return out;
+    auto idx = 0u;
+    const value_type inf = MultiFiltration::Generator::T_inf;
+    for (const auto &bar : barcode_indices) {
+      value_type birth_filtration = inf;
+      value_type death_filtration = -birth_filtration;
+      if (bar.death == static_cast<typename PersBackend::pos_index>(-1))
+        death_filtration = inf;
+      else
+        death_filtration = static_cast<value_type>(filtration_container[bar.death]);
+      birth_filtration = static_cast<value_type>(filtration_container[bar.birth]);
+      if constexpr (verbose) {
+        std::cout << "PAIRING : " << bar.birth << " / " << bar.death << " dim " << bar.dim << std::endl;
+      }
+      if constexpr (verbose) {
+        std::cout << "PAIRING filtration : " << birth_filtration << " " << death_filtration << " dim " << bar.dim
+                  << std::endl;
+      }
+
+      if (birth_filtration < death_filtration)
+        out[idx] = {bar.dim, {birth_filtration, death_filtration}};
+      else {
+        out[idx] = {bar.dim, {inf, inf}};
+      }
+      idx++;
+    }
+    return out;
+  }
+
+  template <typename value_type = value_type>
+  inline flat_barcode<value_type> get_flat_barcode() {
+    return get_flat_barcode(this->persistence, this->filtration_container);
+  }
+
+  template <typename value_type = value_type>
+  inline flat_nodim_barcode<value_type> get_flat_nodim_barcode() {
+    return get_flat_nodim_barcode(this->persistence, this->filtration_container);
+  }
+
+  inline friend std::ostream &operator<<(std::ostream &stream, Truc &truc) {
+    stream << "-------------------- Truc \n";
+    stream << "--- Structure \n";
+    stream << truc.structure;
+    /* stream << "-- Dimensions (max " << truc.structure.max_dimension() <<
+     * ")\n"; */
+    /* stream << "{"; */
+    /* for (auto i = 0u; i < truc.num_generators(); i++) */
+    /*   stream << truc.structure.dimension(i) << ", "; */
+    /* stream << "\b" */
+    /*        << "\b"; */
+    /* stream << "}" << std::endl; */
+    stream << "--- Order \n";
+    stream << "{";
+    for (const auto &idx : truc.generator_order) stream << idx << ", ";
+    stream << "}" << std::endl;
+
+    stream << "--- Current slice filtration\n";
+    stream << "{";
+    for (const auto &stuff : truc.filtration_container) stream << stuff << ", ";
+    stream << "\b" << "\b";
+    stream << "}" << std::endl;
+
+    stream << "--- Filtrations \n";
+    for (const auto &i : truc.generator_order) {
+      stream << i << " : ";
+      const auto &stuff = truc.generator_filtration_values[i];
+      stream << stuff << "\n";
+    }
+    stream << "--- PersBackend \n";
+    stream << truc.persistence;
+
+    return stream;
+  }
+
+  inline std::string to_str() {
+    std::stringstream stream;
+    stream << *this;
+    return stream.str();
+  }
+
+  inline std::pair<typename MultiFiltration::Generator, typename MultiFiltration::Generator> get_bounding_box() const {
+    using OC = typename MultiFiltration::Generator;
+    // assert(!generator_filtration_values.empty());
+    OC a = OC::inf();
+    OC b = -1 * a;
+    for (const auto &filtration_value : generator_filtration_values) {
+      if constexpr (MultiFiltration::is_multi_critical) {
+        a.pull_to_greatest_common_lower_bound(factorize_below(filtration_value));
+        b.push_to_least_common_upper_bound(factorize_above(filtration_value));
+      } else {
+        a.pull_to_greatest_common_lower_bound(filtration_value);
+        b.push_to_least_common_upper_bound(filtration_value);
+      }
+    }
+    return {a, b};
+  }
+
+  inline std::vector<typename MultiFiltration::Generator> get_filtration_values() const {
+    if constexpr (MultiFiltration::is_multi_critical) {
+      std::vector<typename MultiFiltration::Generator> out;
+      out.reserve(generator_filtration_values.size());  // at least this, will dooble later
+      for (std::size_t i = 0; i < generator_filtration_values.size(); ++i) {
+        for (const auto &f : generator_filtration_values[i]) {
+          out.push_back(f);
+        }
+      }
+      return out;
+    } else {
+      return generator_filtration_values;  // copy not necessary for Generator
+    }  // (could return const&)
+  }
+
+  inline std::vector<MultiFiltration> &get_filtrations() { return generator_filtration_values; }
+
+  inline const std::vector<MultiFiltration> &get_filtrations() const { return generator_filtration_values; }
+
+  inline const std::vector<int> get_dimensions() const {
+    std::size_t n = this->num_generators();
+    std::vector<int> out(n);
+    for (std::size_t i = 0; i < n; ++i) {
+      out[i] = structure.dimension(i);
+    }
+    return out;
+  }
+
+  inline void prune_above_dimension(int max_dim) {
+    int idx = structure.prune_above_dimension(max_dim);
+    generator_filtration_values.resize(idx);
+    generator_order.resize(idx);
+    filtration_container.resize(idx);
+  }
+
+  inline const std::vector<std::vector<index_type>> get_boundaries() {
+    std::size_t n = this->num_generators();
+    std::vector<std::vector<index_type>> out(n);
+    for (auto i = 0u; i < n; ++i) {
+      out[i] = this->structure[i];
+    }
+    return out;
+  }
+
+  auto coarsen_on_grid(const std::vector<std::vector<typename MultiFiltration::value_type>> grid) {
+    using return_type = decltype(std::declval<MultiFiltration>().template as_type<std::int32_t>());
+    std::vector<return_type> coords(this->num_generators());
+    for (std::size_t gen = 0u; gen < coords.size(); ++gen) {
+      coords[gen] = compute_coordinates_in_grid<int32_t>(generator_filtration_values[gen], grid);
+    }
+    return Truc<PersBackend, Structure, return_type>(structure, coords);
+  }
+
+  inline void coarsen_on_grid_inplace(const std::vector<std::vector<typename MultiFiltration::value_type>> &grid,
+                                      bool coordinate = true) {
+    for (auto gen = 0u; gen < this->num_generators(); ++gen) {
+      generator_filtration_values[gen].project_onto_grid(grid, coordinate);
+    }
+  }
+
+  // dim, num_cycle_of_dim, num_faces_in_cycle, vertices_in_face
+  inline std::vector<std::vector<std::vector<std::vector<index_type>>>> get_representative_cycles(
+      bool update = true,
+      bool detailed = false) {
+    // iterable iterable simplex key
+    auto cycles_key = persistence.get_representative_cycles(update, detailed);
+    auto num_cycles = cycles_key.size();
+    std::vector<std::vector<std::vector<std::vector<index_type>>>> out(structure.max_dimension() + 1);
+    for (auto &cycles_of_dim : out) cycles_of_dim.reserve(num_cycles);
+    for (const auto &cycle : cycles_key) {
+      int cycle_dim = 0;        // for more generality, should be minimal dimension instead
+      if (!cycle[0].empty()) {  // if empty, cycle has no border -> assumes dimension 0 even if it could be min dim
+        cycle_dim = structure.dimension(cycle[0][0]) + 1;  // all faces have the same dim
+      }
+      out[cycle_dim].push_back(cycle);
+    }
+    return out;
+  }
+
+  const std::vector<index_type> &get_current_order() const { return generator_order; }
+
+  const PersBackend &get_persistence() const { return persistence; }
+
+  PersBackend &get_persistence() { return persistence; }
+
+  // TrucThread get_safe_thread() { return TrucThread(*this); }
+
+  class TrucThread {
+   public:
+    using Filtration_value = MultiFiltration;
+    using value_type = typename MultiFiltration::value_type;
+    using ThreadSafe = TrucThread;
+
+    inline TrucThread(const Truc &truc)
+        : truc_ptr(&truc),
+          generator_order(truc.get_current_order()),
+          filtration_container(truc.get_one_filtration()),
+          persistence(truc.get_persistence()) {
+      persistence._update_permutation_ptr(generator_order);
+    };
+
+    inline TrucThread(const TrucThread &truc)
+        : truc_ptr(truc.truc_ptr),
+          generator_order(truc.get_current_order()),
+          filtration_container(truc.get_one_filtration()),
+          persistence(truc.get_persistence()) {
+      persistence._update_permutation_ptr(generator_order);
+    };
+
+    inline TrucThread weak_copy() const { return TrucThread(*truc_ptr); }
+
+    inline const bool has_persistence() { return this->persistence.size(); };
+
+    inline const PersBackend &get_persistence() const { return persistence; }
+
+    inline PersBackend &get_persistence() { return persistence; }
+
+    inline std::pair<MultiFiltration, MultiFiltration> get_bounding_box() const { return truc_ptr->get_bounding_box(); }
+
+    inline const std::vector<index_type> &get_current_order() const { return generator_order; }
+
+    inline const std::vector<MultiFiltration> &get_filtrations() const { return truc_ptr->get_filtrations(); }
+
+    inline const std::vector<int> &get_dimensions() const { return truc_ptr->get_dimensions(); }
+
+    inline const std::vector<std::vector<index_type>> &get_boundaries() const { return truc_ptr->get_boundaries(); }
+
+    inline void coarsen_on_grid_inplace(const std::vector<std::vector<typename MultiFiltration::value_type>> &grid,
+                                        bool coordinate = true) {
+      truc_ptr->coarsen_on_grid_inplace(grid, coordinate);
+    }
+
+    template <typename Subfiltration>
+    inline void push_to(const Subfiltration &f) {
+      truc_ptr->push_to_out(f, this->filtration_container, this->generator_order);
+    }
+
+    inline std::vector<typename PersBackend::cycle_type> get_representative_cycles(bool update = true) {
+      return truc_ptr->get_representative_cycles(update);
+    }
+
+    inline void compute_persistence(const bool ignore_inf = true) {
+      this->persistence =
+          this->truc_ptr->compute_persistence_out(this->filtration_container, this->generator_order, ignore_inf);
+    };
+
+    inline void vineyard_update() {
+      truc_ptr->vineyard_update(this->persistence, this->filtration_container, this->generator_order);
+    }
+
+    template <typename value_type = value_type>
+    inline flat_barcode<value_type> get_flat_barcode() {
+      return truc_ptr->get_flat_barcode(this->persistence, this->filtration_container);
+    }
+
+    template <typename value_type = value_type>
+    inline flat_nodim_barcode<value_type> get_flat_nodim_barcode() {
+      return truc_ptr->get_flat_nodim_barcode(this->persistence, this->filtration_container);
+    }
+
+    inline split_barcode get_barcode() { return truc_ptr->get_barcode(this->persistence, this->filtration_container); }
+
+    inline std::size_t num_generators() const { return this->truc_ptr->structure.size(); }
+
+    inline std::size_t num_parameters() const {
+      return num_generators() == 0 ? 0 : this->get_filtrations()[0].num_parameters();
+    }
+
+    inline const std::vector<typename MultiFiltration::value_type> &get_one_filtration() const {
+      return this->filtration_container;
+    }
+
+    inline std::vector<typename MultiFiltration::value_type> &get_one_filtration() {
+      return this->filtration_container;
+    }
+
+   private:
+    const Truc *truc_ptr;
+    std::vector<index_type> generator_order;                                 // size fixed at construction time,
+    std::vector<typename MultiFiltration::value_type> filtration_container;  // filtration of the current slice
+    PersBackend persistence;  // generated by the structure, and generator_order.
+
+  };  // class TrucThread
+
+  /*
+   * returns barcodes of the f(multipers)
+   *
+   */
+  template <typename Fun, typename Fun_arg>
+  inline std::vector<split_barcode> barcodes(Fun &&f, const std::vector<Fun_arg> &args, const bool ignore_inf = true) {
+    if (args.size() == 0) {
+      return {};
+    }
+    std::vector<split_barcode> out(args.size());
+
+    if constexpr (PersBackend::is_vine) {
+      this->push_to(f(args[0]));
+      this->compute_persistence();
+      out[0] = this->get_barcode();
+      for (auto i = 1u; i < args.size(); ++i) {
+        this->push_to(f(args[i]));
+        this->vineyard_update();
+        out[i] = this->get_barcode();
+      }
+
+    } else {
+      ThreadSafe local_template = this->weak_copy();
+      tbb::enumerable_thread_specific<ThreadSafe> thread_locals(local_template);
+      tbb::parallel_for(static_cast<std::size_t>(0), args.size(), [&](const std::size_t &i) {
+        ThreadSafe &s = thread_locals.local();
+        s.push_to(f(args[i]));
+        s.compute_persistence(ignore_inf);
+        out[i] = s.get_barcode();
+      });
+    }
+    return out;
+  }
+
+  // FOR Python interface, but I'm not fan. Todo: do the lambda function in
+  // cython?
+  inline std::vector<split_barcode> persistence_on_lines(const std::vector<std::vector<value_type>> &basepoints) {
+    return barcodes(
+        [](const std::vector<value_type> &basepoint) { return Gudhi::multi_persistence::Line<value_type>(basepoint); },
+        basepoints);
+  }
+
+  inline std::vector<split_barcode> persistence_on_lines(
+      const std::vector<std::pair<std::vector<value_type>, std::vector<value_type>>> &bp_dirs) {
+    return barcodes(
+        [](const std::pair<std::vector<value_type>, std::vector<value_type>> &bpdir) {
+          return Gudhi::multi_persistence::Line<value_type>(bpdir.first, bpdir.second);
+        },
+        bp_dirs);
+  }
+
+  void build_from_scc_file(const std::string &inFilePath,
+                           bool isRivetCompatible = false,
+                           bool isReversed = false,
+                           int shiftDimensions = 0) {
+    *this = read_scc_file<Truc>(inFilePath, isRivetCompatible, isReversed, shiftDimensions);
+  }
+
+  void write_to_scc_file(const std::string &outFilePath,
+                         int numberOfParameters = -1,
+                         int degree = -1,
+                         bool rivetCompatible = false,
+                         bool IgnoreLastGenerators = false,
+                         bool stripComments = false,
+                         bool reverse = false) {
+    write_scc_file<Truc>(
+        outFilePath, *this, numberOfParameters, degree, rivetCompatible, IgnoreLastGenerators, stripComments, reverse);
+  }
+
+ public:
+  using ThreadSafe = TrucThread;  // for outside
+
+  TrucThread weak_copy() const { return TrucThread(*this); }
+
+  // TODO: declare method here instead of scc_io.h
+  // it is just temporary, until Truc is cleaned up
+  // friend void write_scc_file<Truc>(const std::string &outFilePath,
+  //                                  const Truc &slicer,
+  //                                  int numberOfParameters,
+  //                                  int degree,
+  //                                  bool rivetCompatible,
+  //                                  bool IgnoreLastGenerators,
+  //                                  bool stripComments,
+  //                                  bool reverse);
+
+ private:
+  std::vector<MultiFiltration> generator_filtration_values;  // defined at construction time. Const
+  std::vector<index_type> generator_order;  // size fixed at construction time, // TODO : CHANGE THAT TO UINT32
+  Structure structure;                      // defined at construction time. Const
+  std::vector<typename MultiFiltration::value_type> filtration_container;  // filtration of the current slice
+  PersBackend persistence;  // generated by the structure, and generator_order.
+
+};  // class Truc
+
+}  // namespace truc_interface
+}  // namespace multiparameter
+}  // namespace Gudhi