multipers 2.4.0b1__cp312-cp312-macosx_11_0_arm64.whl

multipers/gudhi/Persistence_slices_interface.h

@@ -0,0 +1,213 @@
+#pragma once
+
+#include <array>
+#include <cstdint>
+
+#include "gudhi/Multi_parameter_filtration.h"
+#include "gudhi/multi_simplex_tree_helpers.h"
+#include "gudhi/persistence_matrix_options.h"
+#include "gudhi/Multi_parameter_filtered_complex.h"
+#include "gudhi/Multi_persistence/Persistence_interface_matrix.h"
+#include "gudhi/Multi_persistence/Persistence_interface_cohomology.h"
+#include "gudhi/Dynamic_multi_parameter_filtration.h"
+#include "gudhi/Degree_rips_bifiltration.h"
+#include "gudhi/Slicer.h"
+
+#include "tmp_h0_pers/mma_interface_h0.h"
+
+namespace multipers::tmp_interface {
+
+template <typename Filtration>
+using SimplexTreeMultiOptions = Gudhi::multi_persistence::Simplex_tree_options_multidimensional_filtration<Filtration>;
+
+enum Column_types_strs : std::uint8_t {
+  LIST,
+  SET,
+  HEAP,
+  VECTOR,
+  NAIVE_VECTOR,
+  UNORDERED_SET,
+  INTRUSIVE_LIST,
+  INTRUSIVE_SET
+};
+
+enum Filtration_containers_strs : std::uint8_t {
+  Dynamic_multi_parameter_filtration,
+  Multi_parameter_filtration,
+  Degree_rips_bifiltration
+};
+
+using Available_columns = Gudhi::persistence_matrix::Column_types;
+
+template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
+struct Multi_persistence_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
+  using Index = std::uint32_t;
+  static const bool has_matrix_maximal_dimension_access = false;
+  static const bool has_column_pairings = true;
+  static const bool has_vine_update = true;
+  static const bool can_retrieve_representative_cycles = true;
+};
+
+template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
+struct Multi_persistence_Clement_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
+  using Index = std::uint32_t;
+  static const bool has_matrix_maximal_dimension_access = false;
+  static const bool has_column_pairings = true;
+  static const bool has_vine_update = true;
+  static const bool is_of_boundary_type = false;
+  static const Gudhi::persistence_matrix::Column_indexation_types column_indexation_type =
+      Gudhi::persistence_matrix::Column_indexation_types::POSITION;
+  static const bool can_retrieve_representative_cycles = true;
+};
+
+template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
+struct No_vine_multi_persistence_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
+  using Index = std::uint32_t;
+  static const bool has_matrix_maximal_dimension_access = false;
+  static const bool has_column_pairings = true;
+  static const bool has_vine_update = false;
+};
+
+template <Gudhi::persistence_matrix::Column_types column_type = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET,
+          bool row_access = true>
+struct fix_presentation_options : Gudhi::persistence_matrix::Default_options<column_type, true> {
+  using Index = std::uint32_t;
+  static const bool has_row_access = row_access;
+  static const bool has_map_column_container = false;
+  static const bool has_removable_columns = false;  // WARN : idx will change if map is not true
+};
+
+template <Available_columns col>
+using BackendOptionsWithVine = Multi_persistence_options<col>;
+template <Available_columns col>
+using BackendOptionsWithoutVine = No_vine_multi_persistence_options<col>;
+
+template <Available_columns col>
+using ClementBackendOptionsWithVine = Multi_persistence_Clement_options<col>;
+
+// using SimplicialStructure = Gudhi::multiparameter::truc_interface::SimplicialStructure;
+template <typename Filtration>
+using StructureStuff = Gudhi::multi_persistence::Multi_parameter_filtered_complex<Filtration>;
+
+template <Available_columns col>
+using MatrixBackendNoVine = Gudhi::multi_persistence::Persistence_interface_matrix<BackendOptionsWithoutVine<col>>;
+
+template <Available_columns col>
+using MatrixBackendVine = Gudhi::multi_persistence::Persistence_interface_matrix<BackendOptionsWithVine<col>>;
+
+template <Available_columns col>
+using ClementMatrixBackendVine =
+    Gudhi::multi_persistence::Persistence_interface_matrix<ClementBackendOptionsWithVine<col>>;
+template <typename Filtration>
+using GraphBackendVine = Gudhi::multiparameter::truc_interface::Persistence_backend_h0<StructureStuff<Filtration>>;
+
+template <typename value_type = float>
+using Filtration_value = Gudhi::multi_filtration::Multi_parameter_filtration<value_type, false, true>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using SimplicialNoVineMatrixTruc = Gudhi::multi_persistence::Slicer<Filtration_value<>, MatrixBackendNoVine<col>>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using GeneralVineTruc = Gudhi::multi_persistence::Slicer<Filtration_value<>, MatrixBackendVine<col>>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using GeneralNoVineTruc = Gudhi::multi_persistence::Slicer<Filtration_value<>, MatrixBackendNoVine<col>>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using GeneralVineClementTruc = Gudhi::multi_persistence::Slicer<Filtration_value<>, ClementMatrixBackendVine<col>>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using SimplicialVineMatrixTruc = Gudhi::multi_persistence::Slicer<Filtration_value<>, MatrixBackendVine<col>>;
+using SimplicialVineGraphTruc =
+    Gudhi::multi_persistence::Slicer<Filtration_value<>, GraphBackendVine<Filtration_value<>>>;
+
+// multi-critical
+template <typename value_type = float>
+using Multi_critical_filtration_value = Gudhi::multi_filtration::Multi_parameter_filtration<value_type>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using KCriticalVineTruc = Gudhi::multi_persistence::Slicer<Multi_critical_filtration_value<>, MatrixBackendVine<col>>;
+
+template <bool is_vine, Available_columns col = Available_columns::INTRUSIVE_SET>
+using Matrix_interface = std::conditional_t<is_vine, MatrixBackendVine<col>, MatrixBackendNoVine<col>>;
+
+template <Filtration_containers_strs fil_container,  bool is_k_critical, typename value_type>
+using filtration_options = std::conditional_t<fil_container == Filtration_containers_strs::Dynamic_multi_parameter_filtration,
+                                            Gudhi::multi_filtration::Dynamic_multi_parameter_filtration<value_type, false, !is_k_critical>,
+                                            std::conditional_t<fil_container == Filtration_containers_strs::Multi_parameter_filtration,
+                                                               Gudhi::multi_filtration::Multi_parameter_filtration<value_type, false, !is_k_critical>,
+                                                               Gudhi::multi_filtration::Degree_rips_bifiltration<value_type, false, !is_k_critical>>>;
+
+template <bool is_vine,
+          bool is_k_critical,
+          typename value_type,
+          Available_columns col = Available_columns::INTRUSIVE_SET,
+          Filtration_containers_strs filt_cont = Filtration_containers_strs::Multi_parameter_filtration>
+using MatrixTrucPythonInterface =
+    Gudhi::multi_persistence::Slicer<filtration_options<filt_cont,is_k_critical, value_type>, Matrix_interface<is_vine, col>>;
+
+enum class BackendsEnum : std::uint8_t { Matrix, Graph, Clement, GudhiCohomology };
+
+// Create a template metafunction to simplify the type selection
+template <BackendsEnum backend, bool is_vine, Available_columns col, typename Filtration>
+struct PersBackendOptsImpl;
+
+template <bool is_vine, Available_columns col, typename Filtration>
+struct PersBackendOptsImpl<BackendsEnum::Matrix, is_vine, col, Filtration> {
+  using type = Matrix_interface<is_vine, col>;
+};
+
+template <bool is_vine, Available_columns col, typename Filtration>
+struct PersBackendOptsImpl<BackendsEnum::Clement, is_vine, col, Filtration> {
+  static_assert(is_vine, "Clement is vine");
+  using type = ClementMatrixBackendVine<col>;
+};
+
+template <bool is_vine, Available_columns col, typename Filtration>
+struct PersBackendOptsImpl<BackendsEnum::GudhiCohomology, is_vine, col, Filtration> {
+  static_assert(!is_vine, "Gudhi is not vine");
+  using type = Gudhi::multi_persistence::Persistence_interface_cohomology<Filtration>;
+};
+
+template <bool is_vine, Available_columns col, typename Filtration>
+struct PersBackendOptsImpl<BackendsEnum::Graph, is_vine, col, Filtration> {
+  static_assert(is_vine, "Graph backend requires is_vine to be true");
+  using type = GraphBackendVine<Filtration>;
+};
+
+// Helper alias to extract the type
+template <BackendsEnum backend, bool is_vine, Available_columns col, typename Filtration>
+using PersBackendOpts = typename PersBackendOptsImpl<backend, is_vine, col, Filtration>::type;
+
+template <BackendsEnum backend,
+          bool is_vine,
+          bool is_k_critical,
+          typename value_type,
+          Available_columns col = Available_columns::INTRUSIVE_SET,
+          Filtration_containers_strs filt_cont = Filtration_containers_strs::Multi_parameter_filtration>
+using TrucPythonInterface = Gudhi::multi_persistence::Slicer<
+    filtration_options<filt_cont,is_k_critical, value_type>,
+    PersBackendOpts<backend, is_vine, col, filtration_options<filt_cont,is_k_critical, value_type>>>;
+
+//for python
+template<typename T>
+using One_critical_filtration = Gudhi::multi_filtration::Multi_parameter_filtration<T, false, true>;
+template<typename T>
+using Multi_critical_filtration = Gudhi::multi_filtration::Multi_parameter_filtration<T, false, false>;
+
+template <typename T>
+using Bar = std::array<T, 2>;
+template <class Slicer, typename T = typename Slicer::T>
+using Barcode = typename Slicer::template Flat_barcode<T>;
+template <class Slicer, typename T = typename Slicer::T>
+using Dim_barcode = typename Slicer::template Multi_dimensional_flat_barcode<T>;
+
+template<class Slicer>
+std::string slicer_to_str(Slicer& s)
+{
+  std::stringstream stream;
+  stream << s;
+  return stream.str();
+}
+
+}  // namespace multipers::tmp_interface

multipers/gudhi/Simplex_tree_interface.h

@@ -0,0 +1,274 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2016 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef INCLUDE_SIMPLEX_TREE_INTERFACE_H_
+#define INCLUDE_SIMPLEX_TREE_INTERFACE_H_
+
+#include <cstddef>
+#include <string>
+#include <vector>
+#include <utility>  // std::pair
+#include <tuple>
+
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/Flag_complex_edge_collapser.h>
+
+namespace Gudhi {
+
+/** Model of SimplexTreeOptions.
+ *
+ * Specific to python interfaces of the Simplex_tree */
+struct Simplex_tree_options_for_python {
+  typedef linear_indexing_tag Indexing_tag;
+  typedef int Vertex_handle;
+  typedef double Filtration_value;
+  typedef std::uint32_t Simplex_key;
+  static const bool store_key = true;
+  static const bool store_filtration = true;
+  static const bool contiguous_vertices = false;
+  static const bool link_nodes_by_label = false;
+  static const bool stable_simplex_handles = false;
+};
+
+// CHANGED FROM THE ORIGINAL: added template parameter
+template <class Simplex_tree_options = Simplex_tree_options_for_python>
+class Simplex_tree_interface : public Simplex_tree<Simplex_tree_options>
+{
+ public:
+  using Base = Simplex_tree<Simplex_tree_options>;
+  using Filtration_value = typename Base::Filtration_value;
+  using Vertex_handle = typename Base::Vertex_handle;
+  using Simplex_handle = typename Base::Simplex_handle;
+  using Insertion_result = typename std::pair<Simplex_handle, bool>;
+  using Simplex = std::vector<Vertex_handle>;
+  using Simplex_and_filtration = std::pair<Simplex, Filtration_value>;
+  using Filtered_simplices = std::vector<Simplex_and_filtration>;
+  using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator;
+  using Complex_simplex_iterator = typename Base::Complex_simplex_iterator;
+  using Extended_filtration_data = typename Base::Extended_filtration_data;
+  using Boundary_simplex_iterator = typename Base::Boundary_simplex_iterator;
+  using Siblings = typename Base::Siblings;
+  using Node = typename Base::Node;
+  typedef bool (*blocker_func_t)(Simplex simplex, void* user_data);
+
+  // CHANGED FROM THE ORIGINAL: constructors from simplex tree
+  Simplex_tree_interface() = default;
+  Simplex_tree_interface(const Base& st) : Base(st) {};
+  Simplex_tree_interface(Base&& st) : Base(std::move(st)) {};
+  Simplex_tree_interface& operator=(const Base& st){
+    Base::operator=(st);
+    return *this;
+  }
+  Simplex_tree_interface& operator=(Base&& st){
+    Base::operator=(std::move(st));
+    return *this;
+  }
+
+ public:
+  Extended_filtration_data efd;
+
+  bool find_simplex(const Simplex& simplex) { return (Base::find(simplex) != Base::null_simplex()); }
+
+  void assign_simplex_filtration(const Simplex& simplex, Filtration_value filtration)
+  {
+    Simplex_handle sh = Base::find(simplex);
+    if (sh == Base::null_simplex())
+      throw std::invalid_argument("Cannot assign a filtration to a simplex that is not in the complex");
+    Base::assign_filtration(sh, filtration);
+    Base::clear_filtration();
+  }
+
+  bool insert(const Simplex& simplex, Filtration_value filtration = 0)
+  {
+    Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
+    if (result.first != Base::null_simplex()) Base::clear_filtration();
+    return (result.second);
+  }
+
+  void insert_matrix(double* filtrations, int n, int stride0, int stride1, double max_filtration)
+  {
+    // We could delegate to insert_graph, but wrapping the matrix in a graph interface is too much work,
+    // and this is a bit more efficient.
+    auto& rm = this->root()->members_;
+    for (int i = 0; i < n; ++i) {
+      char* p = reinterpret_cast<char*>(filtrations) + i * stride0;
+      double fv = *reinterpret_cast<double*>(p + i * stride1);
+      if (fv > max_filtration) continue;
+      auto sh = rm.emplace_hint(rm.end(), i, Node(this->root(), fv));
+      Siblings* children = nullptr;
+      // Should we make a first pass to count the number of edges so we can reserve the right space?
+      for (int j = i + 1; j < n; ++j) {
+        double fe = *reinterpret_cast<double*>(p + j * stride1);
+        if (fe > max_filtration) continue;
+        if (!children) {
+          children = new Siblings(this->root(), i);
+          sh->second.assign_children(children);
+        }
+        children->members().emplace_hint(children->members().end(), j, Node(children, fe));
+      }
+    }
+    this->set_dimension(1, false);
+  }
+
+  // Do not interface this function, only used in alpha complex interface for complex creation
+  bool insert_simplex(const Simplex& simplex, Filtration_value filtration = 0)
+  {
+    Insertion_result result = Base::insert_simplex(simplex, filtration);
+    return (result.second);
+  }
+
+  // Do not interface this function, only used in strong witness interface for complex creation
+  bool insert_simplex(const std::vector<std::size_t>& simplex, Filtration_value filtration = 0)
+  {
+    Insertion_result result = Base::insert_simplex(simplex, filtration);
+    return (result.second);
+  }
+
+  Filtration_value simplex_filtration(const Simplex& simplex) { return Base::filtration(Base::find(simplex)); }
+
+  void remove_maximal_simplex(const Simplex& simplex)
+  {
+    Base::remove_maximal_simplex(Base::find(simplex));
+    Base::clear_filtration();
+  }
+
+  Simplex_and_filtration get_simplex_and_filtration(Simplex_handle f_simplex)
+  {
+    Simplex simplex;
+    for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
+      simplex.insert(simplex.begin(), vertex);
+    }
+    return std::make_pair(std::move(simplex), Base::filtration(f_simplex));
+  }
+
+  Filtered_simplices get_star(const Simplex& simplex)
+  {
+    Filtered_simplices star;
+    for (auto f_simplex : Base::star_simplex_range(Base::find(simplex))) {
+      Simplex simplex_star;
+      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
+        simplex_star.insert(simplex_star.begin(), vertex);
+      }
+      star.push_back(std::make_pair(simplex_star, Base::filtration(f_simplex)));
+    }
+    return star;
+  }
+
+  Filtered_simplices get_cofaces(const Simplex& simplex, int dimension)
+  {
+    Filtered_simplices cofaces;
+    for (auto f_simplex : Base::cofaces_simplex_range(Base::find(simplex), dimension)) {
+      Simplex simplex_coface;
+      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
+        simplex_coface.insert(simplex_coface.begin(), vertex);
+      }
+      cofaces.push_back(std::make_pair(simplex_coface, Base::filtration(f_simplex)));
+    }
+    return cofaces;
+  }
+
+  void compute_extended_filtration()
+  {
+    this->efd = this->extend_filtration();
+    return;
+  }
+
+  // CHANGED FROM THE ORIGINAL: Does collapses in a new simplex tree instead of inplace.
+  Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) {
+    using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>;
+    std::vector<Filtered_edge> edges;
+    for (Simplex_handle sh : Base::skeleton_simplex_range(1)) {
+      if (Base::dimension(sh) == 1) {
+        typename Base::Simplex_vertex_range rg = Base::simplex_vertex_range(sh);
+        auto vit = rg.begin();
+        Vertex_handle v = *vit;
+        Vertex_handle w = *++vit;
+        edges.emplace_back(v, w, Base::filtration(sh));
+      }
+    }
+
+    for (int iteration = 0; iteration < nb_collapse_iteration; iteration++) {
+      edges = Gudhi::collapse::flag_complex_collapse_edges(std::move(edges));
+    }
+    Simplex_tree_interface* collapsed_stree_ptr = new Simplex_tree_interface();
+    // Copy the original 0-skeleton
+    for (Simplex_handle sh : Base::skeleton_simplex_range(0)) {
+      collapsed_stree_ptr->insert({*(Base::simplex_vertex_range(sh).begin())}, Base::filtration(sh));
+    }
+    // Insert remaining edges
+    for (auto remaining_edge : edges) {
+      collapsed_stree_ptr->insert({std::get<0>(remaining_edge), std::get<1>(remaining_edge)},
+                                  std::get<2>(remaining_edge));
+    }
+    return collapsed_stree_ptr;
+  }
+
+  void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void* user_data)
+  {
+    Base::expansion_with_blockers(dimension, [&](Simplex_handle sh) {
+      Simplex simplex(Base::simplex_vertex_range(sh).begin(), Base::simplex_vertex_range(sh).end());
+      return user_func(simplex, user_data);
+    });
+  }
+
+  // Iterator over the simplex tree
+  Complex_simplex_iterator get_simplices_iterator_begin()
+  {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::complex_simplex_range().begin();
+  }
+
+  Complex_simplex_iterator get_simplices_iterator_end()
+  {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::complex_simplex_range().end();
+  }
+
+  typename std::vector<Simplex_handle>::const_iterator get_filtration_iterator_begin()
+  {
+    // Base::initialize_filtration(); already performed in filtration_simplex_range
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::filtration_simplex_range().begin();
+  }
+
+  typename std::vector<Simplex_handle>::const_iterator get_filtration_iterator_end()
+  {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::filtration_simplex_range().end();
+  }
+
+  Skeleton_simplex_iterator get_skeleton_iterator_begin(int dimension)
+  {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::skeleton_simplex_range(dimension).begin();
+  }
+
+  Skeleton_simplex_iterator get_skeleton_iterator_end(int dimension)
+  {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::skeleton_simplex_range(dimension).end();
+  }
+
+  std::pair<Boundary_simplex_iterator, Boundary_simplex_iterator> get_boundary_iterators(const Simplex& simplex)
+  {
+    auto bd_sh = Base::find(simplex);
+    if (bd_sh == Base::null_simplex()) throw std::runtime_error("simplex not found - cannot find boundaries");
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    auto boundary_srange = Base::boundary_simplex_range(bd_sh);
+    return std::make_pair(boundary_srange.begin(), boundary_srange.end());
+  }
+};
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_SIMPLEX_TREE_INTERFACE_H_