Merge pull request #54 from hschreiber/update_from_gudhi

C++ files update

Author: DavidLapous

multipers/gudhi/Persistence_slices_interface.h

@@ -7,7 +7,8 @@
 #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_vineyard.h"
+#include "gudhi/Multi_persistence/Persistence_interface_homology.h"
 #include "gudhi/Multi_persistence/Persistence_interface_cohomology.h"
 #include "gudhi/Dynamic_multi_parameter_filtration.h"
 #include "gudhi/Degree_rips_bifiltration.h"
@@ -39,26 +40,26 @@ enum Filtration_containers_strs : std::uint8_t {
 
 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 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> {
@@ -68,50 +69,61 @@ struct No_vine_multi_persistence_options : Gudhi::persistence_matrix::Default_op
   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 <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 <Gudhi::persistence_matrix::Column_types col = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
+struct Multi_persistence_vineyard_ru_options : Gudhi::vineyard::Default_vineyard_options {
+  static constexpr bool is_RU = true;
+  static const Gudhi::persistence_matrix::Column_types column_type = col;
 };
 
-template <Available_columns col>
-using BackendOptionsWithVine = Multi_persistence_options<col>;
+template <Gudhi::persistence_matrix::Column_types col = Gudhi::persistence_matrix::Column_types::INTRUSIVE_SET>
+struct Multi_persistence_vineyard_chain_options : Gudhi::vineyard::Default_vineyard_options {
+  static constexpr bool is_RU = false;
+  static const Gudhi::persistence_matrix::Column_types column_type = col;
+};
+
+// 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>;
+// 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, class Filtration>
+using MatrixBackendNoVine = Gudhi::multi_persistence::Persistence_interface_homology<BackendOptionsWithoutVine<col>, Filtration>;
 
 template <Available_columns col>
-using MatrixBackendVine = Gudhi::multi_persistence::Persistence_interface_matrix<BackendOptionsWithVine<col>>;
+using MatrixBackendVine = Gudhi::multi_persistence::Persistence_interface_vineyard<Multi_persistence_vineyard_ru_options<col>>;
 
 template <Available_columns col>
-using ClementMatrixBackendVine =
-    Gudhi::multi_persistence::Persistence_interface_matrix<ClementBackendOptionsWithVine<col>>;
+using ClementMatrixBackendVine = Gudhi::multi_persistence::Persistence_interface_vineyard<Multi_persistence_vineyard_chain_options<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 <class Filtration, Available_columns col = Available_columns::INTRUSIVE_SET>
+using SimplicialNoVineMatrixTruc = Gudhi::multi_persistence::Slicer<Filtration_value<>, MatrixBackendNoVine<col, Filtration>>;
 
 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 <class Filtration, Available_columns col = Available_columns::INTRUSIVE_SET>
+using GeneralNoVineTruc = Gudhi::multi_persistence::Slicer<Filtration_value<>, MatrixBackendNoVine<col, Filtration>>;
 
 template <Available_columns col = Available_columns::INTRUSIVE_SET>
 using GeneralVineClementTruc = Gudhi::multi_persistence::Slicer<Filtration_value<>, ClementMatrixBackendVine<col>>;
@@ -128,8 +140,8 @@ using Multi_critical_filtration_value = Gudhi::multi_filtration::Multi_parameter
 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 <bool is_vine, class Filtration, Available_columns col = Available_columns::INTRUSIVE_SET>
+using Matrix_interface = std::conditional_t<is_vine, MatrixBackendVine<col>, MatrixBackendNoVine<col, Filtration>>;
 
 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,
@@ -138,13 +150,12 @@ using filtration_options = std::conditional_t<fil_container == Filtration_contai
                                                                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>>;
+// 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, Filtration, col>>;
 
 enum class BackendsEnum : std::uint8_t { Matrix, Graph, Clement, GudhiCohomology };
 
@@ -154,7 +165,7 @@ 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>;
+  using type = Matrix_interface<is_vine, Filtration, col>;
 };
 
 template <bool is_vine, Available_columns col, typename Filtration>

multipers/gudhi/gudhi/Degree_rips_bifiltration.h

@@ -31,13 +31,16 @@
 #include <vector>
 #include <initializer_list>
 
+#ifdef GUDHI_USE_TBB
+#include <oneapi/tbb/parallel_for.h>
+#endif
+
 #include <gudhi/Debug_utils.h>
 #include <gudhi/simple_mdspan.h>
 #include <gudhi/Multi_filtration/multi_filtration_utils.h>
 #include <gudhi/Simplex_tree/filtration_value_utils.h>
 #include <gudhi/Multi_parameter_filtration.h>
 #include <gudhi/Dynamic_multi_parameter_filtration.h>
-#include <oneapi/tbb/concurrent_vector.h>
 
 namespace Gudhi::multi_filtration {
 
@@ -1708,7 +1711,8 @@ class Degree_rips_bifiltration
 
     GUDHI_CHECK_code(const OneDimArray &indices = grid[1]);
     const OneDimArray &values = grid[0];
-    auto todo = [&](size_type g) {
+
+    auto project_generator = [&](size_type g) {
       GUDHI_CHECK_code(GUDHI_CHECK(static_cast<size_type>(indices[g]) == g, std::invalid_argument("Unvalid grid.")));
 
       auto v = static_cast<typename OneDimArray::value_type>(generators_[g]);
@@ -1718,11 +1722,12 @@ class Degree_rips_bifiltration
       }
       generators_[g] = coordinate ? static_cast<T>(d) : static_cast<T>(values[d]);
     };
+
 #ifdef GUDHI_USE_TBB
-    tbb::parallel_for(size_type{0}, num_generators(), [&](size_type g) { todo(g); });
+    tbb::parallel_for(size_type(0), num_generators(), project_generator);
 #else
     for (size_type g = 0; g < num_generators(); ++g) {
-      todo(g);
+      project_generator(g);
     }
 #endif
   }
@@ -1842,9 +1847,7 @@ class Degree_rips_bifiltration
 
 #ifdef GUDHI_USE_TBB
     std::vector<U> projections(f.num_generators());
-    tbb::parallel_for(size_type{0}, f.num_generators(), [&](size_type g) {
-      projections[g] = project_generator(g);
-    });
+    tbb::parallel_for(size_type{0}, f.num_generators(), [&](size_type g) { projections[g] = project_generator(g); });
     if constexpr (Co) {
       return *std::max_element(projections.begin(), projections.end());
     } else {

multipers/gudhi/gudhi/Dynamic_multi_parameter_filtration.h

@@ -31,10 +31,13 @@
 #include <vector>
 #include <initializer_list>
 
+#ifdef GUDHI_USE_TBB
+#include <oneapi/tbb/parallel_for.h>
+#endif
+
 #include <gudhi/Debug_utils.h>
 #include <gudhi/Multi_filtration/Multi_parameter_generator.h>
 #include <gudhi/Multi_filtration/multi_filtration_utils.h>
-#include <oneapi/tbb/parallel_for.h>
 
 namespace Gudhi::multi_filtration {
 
@@ -1856,9 +1859,8 @@ class Dynamic_multi_parameter_filtration
         std::invalid_argument("The grid should not be smaller than the number of parameters in the filtration value."));
 
 #ifdef GUDHI_USE_TBB
-    tbb::parallel_for(size_type(0), num_generators(), [&](size_type i){
-      generators_[i].project_onto_grid(grid, coordinate);
-    });
+    tbb::parallel_for(
+        size_type(0), num_generators(), [&](size_type i) { generators_[i].project_onto_grid(grid, coordinate); });
 #else
     for (Generator &g : generators_) {
       g.project_onto_grid(grid, coordinate);
@@ -1946,6 +1948,17 @@ class Dynamic_multi_parameter_filtration
   {
     if (f.num_generators() == 1) return compute_linear_projection(f.generators_[0], x);
 
+#ifdef GUDHI_USE_TBB
+    std::vector<U> projections(f.num_generators());
+    tbb::parallel_for(size_type{0}, f.num_generators(), [&](size_type g) {
+      projections[g] = compute_linear_projection(f.generators_[g], x);
+    });
+    if constexpr (Co) {
+      return *std::max_element(projections.begin(), projections.end());
+    } else {
+      return *std::min_element(projections.begin(), projections.end());
+    }
+#else
     if constexpr (Co) {
       U projection = std::numeric_limits<U>::lowest();
       for (const Generator &g : f.generators_) {
@@ -1961,6 +1974,7 @@ class Dynamic_multi_parameter_filtration
       }
       return projection;
     }
+#endif
   }
 
   /**

multipers/gudhi/gudhi/Fields/Multi_field.h

@@ -2,7 +2,7 @@
  *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    Author(s):       Hannah Schreiber, Clément Maria
  *
- *    Copyright (C) 2022-24 Inria
+ *    Copyright (C) 2022 Inria
  *
  *    Modification(s):
  *      - YYYY/MM Author: Description of the modification
@@ -305,7 +305,8 @@ class Multi_field_element
       const Characteristic& productOfCharacteristics) const
   {
     GUDHI_CHECK(productOfCharacteristics >= 0 && productOfCharacteristics <= productOfAllCharacteristics_,
-                "The given product is not the product of a subset of the current Multi-field characteristics.");
+                std::invalid_argument(
+                    "The given product is not the product of a subset of the current Multi-field characteristics."));
 
     Characteristic QR;
     mpz_gcd(QR.get_mpz_t(), element_.get_mpz_t(), productOfCharacteristics.get_mpz_t());  // QR <- gcd(x,QS)
@@ -350,7 +351,8 @@ class Multi_field_element
   static Multi_field_element get_partial_multiplicative_identity(const Characteristic& productOfCharacteristics)
   {
     GUDHI_CHECK(productOfCharacteristics >= 0 && productOfCharacteristics <= productOfAllCharacteristics_,
-                "The given product is not the product of a subset of the current Multi-field characteristics.");
+                std::invalid_argument(
+                    "The given product is not the product of a subset of the current Multi-field characteristics."));
 
     if (productOfCharacteristics == 0 || productOfCharacteristics == productOfAllCharacteristics_) {
       return get_multiplicative_identity();

multipers/gudhi/gudhi/Fields/Multi_field_operators.h

@@ -2,7 +2,7 @@
  *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    Author(s):       Hannah Schreiber, Clément Maria
  *
- *    Copyright (C) 2022-24 Inria
+ *    Copyright (C) 2022 Inria
  *
  *    Modification(s):
  *      - YYYY/MM Author: Description of the modification
@@ -366,7 +366,8 @@ class Multi_field_operators
       const Characteristic& productOfCharacteristics) const
   {
     GUDHI_CHECK(productOfCharacteristics >= 0 && productOfCharacteristics <= productOfAllCharacteristics_,
-                "The given product is not the product of a subset of the current Multi-field characteristics.");
+                std::invalid_argument(
+                    "The given product is not the product of a subset of the current Multi-field characteristics."));
 
     Characteristic QR;
     mpz_gcd(QR.get_mpz_t(), e.get_mpz_t(), productOfCharacteristics.get_mpz_t());  // QR <- gcd(x,QS)
@@ -409,7 +410,8 @@ class Multi_field_operators
   [[nodiscard]] Element get_partial_multiplicative_identity(const Characteristic& productOfCharacteristics) const
   {
     GUDHI_CHECK(productOfCharacteristics >= 0 && productOfCharacteristics <= productOfAllCharacteristics_,
-                "The given product is not the product of a subset of the current Multi-field characteristics.");
+                std::invalid_argument(
+                    "The given product is not the product of a subset of the current Multi-field characteristics."));
 
     if (productOfCharacteristics == nullCharacteristic || productOfCharacteristics == productOfAllCharacteristics_) {
       return get_multiplicative_identity();

multipers/gudhi/gudhi/Fields/Multi_field_shared.h

@@ -2,7 +2,7 @@
  *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    Author(s):       Hannah Schreiber, Clément Maria
  *
- *    Copyright (C) 2022-24 Inria
+ *    Copyright (C) 2022 Inria
  *
  *    Modification(s):
  *      - YYYY/MM Author: Description of the modification
@@ -347,7 +347,8 @@ class Shared_multi_field_element
       const Characteristic& productOfCharacteristics) const
   {
     GUDHI_CHECK(productOfCharacteristics >= 0 && productOfCharacteristics <= productOfAllCharacteristics_,
-                "The given product is not the product of a subset of the current Multi-field characteristics.");
+                std::invalid_argument(
+                    "The given product is not the product of a subset of the current Multi-field characteristics."));
 
     Element QR;
     mpz_gcd(QR.get_mpz_t(), element_.get_mpz_t(), productOfCharacteristics.get_mpz_t());  // QR <- gcd(x,QS)
@@ -390,7 +391,8 @@ class Shared_multi_field_element
   static Shared_multi_field_element get_partial_multiplicative_identity(const Characteristic& productOfCharacteristics)
   {
     GUDHI_CHECK(productOfCharacteristics >= 0 && productOfCharacteristics <= productOfAllCharacteristics_,
-                "The given product is not the product of a subset of the current Multi-field characteristics.");
+                std::invalid_argument(
+                    "The given product is not the product of a subset of the current Multi-field characteristics."));
 
     if (productOfCharacteristics == 0 || productOfCharacteristics == productOfAllCharacteristics_) {
       return get_multiplicative_identity();